HEADER VIRUS 12-JUN-02 1M0F TITLE STRUCTURAL STUDIES OF BACTERIOPHAGE ALPHA3 ASSEMBLY, CRYO-ELECTRON TITLE 2 MICROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCAFFOLDING PROTEIN D; COMPND 3 CHAIN: 1, 2, 3, 4; COMPND 4 SYNONYM: GPD; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CAPSID PROTEIN F; COMPND 8 CHAIN: F; COMPND 9 SYNONYM: F PROTEIN, GPF; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: MAJOR SPIKE PROTEIN G; COMPND 13 CHAIN: G; COMPND 14 SYNONYM: G PROTEIN, GPG; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: SCAFFOLDING PROTEIN B; COMPND 18 CHAIN: B; COMPND 19 SYNONYM: GPB; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE ALPHA3; SOURCE 3 ORGANISM_TAXID: 10849; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE ALPHA3; SOURCE 8 ORGANISM_TAXID: 10849; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE ALPHA3; SOURCE 13 ORGANISM_TAXID: 10849; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 MOL_ID: 4; SOURCE 17 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE ALPHA3; SOURCE 18 ORGANISM_TAXID: 10849; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BACTERIOPHAGE, CRYO ELECTRON MICROSCOPY, PROCAPSID, MORPHOGENESIS, KEYWDS 2 MICROVIRIDAE, ASSEMBLY, ICOSAHEDRAL VIRUS, VIRUS EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN 1, 2, 3, 4, F, G, B AUTHOR R.A.BERNAL,S.HAFENSTEIN,N.H.OLSON,V.D.BOWMAN,P.R.CHIPMAN,T.S.BAKER, AUTHOR 2 B.A.FANE,M.G.ROSSMANN REVDAT 5 17-APR-24 1M0F 1 REMARK REVDAT 4 14-FEB-24 1M0F 1 REMARK REVDAT 3 18-JUL-18 1M0F 1 REMARK REVDAT 2 24-FEB-09 1M0F 1 VERSN REVDAT 1 25-DEC-02 1M0F 0 JRNL AUTH R.A.BERNAL,S.HAFENSTEIN,N.H.OLSON,V.D.BOWMAN,P.R.CHIPMAN, JRNL AUTH 2 T.S.BAKER,B.A.FANE,M.G.ROSSMANN JRNL TITL STRUCTURAL STUDIES OF BACTERIOPHAGE ALPHA3 ASSEMBLY JRNL REF J.MOL.BIOL. V. 325 11 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12473449 JRNL DOI 10.1016/S0022-2836(02)01201-9 REMARK 2 REMARK 2 RESOLUTION. 16.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EMFIT, ROBEM, EM3DR REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1M06 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : BEST FIT CRITERION USED BY THE REMARK 3 PROGRAM EMFIT IS BASED ON THE REMARK 3 AVERAGE VALUE OF THE DENSITY AT REMARK 3 ALL ATOMIC SITES IN THE FITTED REMARK 3 PROTEIN, THE LACK OF ATOMS IN REMARK 3 NEGATIVE DENSITY, AND THE ABSENCE REMARK 3 OF SYMMETRY RELATED ATOMIC REMARK 3 CLASHES. REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--GENERAL SEARCH FOLLOWED BY A CLIMB REMARK 3 PROCEDURE REFINEMENT PROTOCOL--RIGID MOLECULE FIT USING THE REMARK 3 PROGRAM EMFIT REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 1.840 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 16.00 REMARK 3 NUMBER OF PARTICLES : 2378 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: MAGNIFICATION REMARK 3 CORRECTION WAS DETERMINED USING THE F PENTAMER AS FOUND IN THE REMARK 3 MATURE VIRION OF ALPHA3 AND PHIX174 AND IN THE CLOSED PROCAPSID REMARK 3 AS A CONTROL. SYMMETRY RELATED CONTACTS IN THE CONTROL WERE REMARK 3 FOUND TO BE 6.3% OF ALL ATOMS. THE PIXEL SIZE OF THE REMARK 3 RECONSTRUCTION WAS ADJUSTED SO AS TO OBTAIN THE SAME NUMBER OF REMARK 3 CONTACTS. REMARK 3 REMARK 3 OTHER DETAILS: 2378 PARTICLES WERE INCLUDED IN THE FINAL REMARK 3 RECONSTRUCTION. THE EFFECTIVE RESOLUTION IS 15.0-16.0A. HIGHER REMARK 3 RESOLUTION WAS NOT POSSIBLE BECAUSE OF THE TENDENCY OF PARTICLES REMARK 3 TO ORIENT THEMSELVES NON-RANDOMLY. ONLY CA COORDINATES ARE REMARK 3 PRESENTED IN THE ENTRY. REMARK 4 REMARK 4 1M0F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-02. REMARK 100 THE DEPOSITION ID IS D_1000016442. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : PROCAPSID OF THE BACTERIOPHAGE REMARK 245 ALPHA3 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 8.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : 10 MM TRIS AND 1 MM EDTA REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 16-OCT-98 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 88.00 REMARK 245 MICROSCOPE MODEL : FEI/PHILIPS CM200FEG/ST REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 3200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 1.70 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 38000 REMARK 245 CALIBRATED MAGNIFICATION : 40000 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 ICOSAHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = I). REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: 1, 2, 3, 4, F, G, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.500000 -0.809017 0.309017 0.00000 REMARK 350 BIOMT2 2 0.809017 0.309017 -0.500000 0.00000 REMARK 350 BIOMT3 2 0.309017 0.500000 0.809017 0.00000 REMARK 350 BIOMT1 3 -0.309017 -0.500000 0.809017 0.00000 REMARK 350 BIOMT2 3 0.500000 -0.809017 -0.309017 0.00000 REMARK 350 BIOMT3 3 0.809017 0.309017 0.500000 0.00000 REMARK 350 BIOMT1 4 -0.309017 0.500000 0.809017 0.00000 REMARK 350 BIOMT2 4 -0.500000 -0.809017 0.309017 0.00000 REMARK 350 BIOMT3 4 0.809017 -0.309017 0.500000 0.00000 REMARK 350 BIOMT1 5 0.500000 0.809017 0.309017 0.00000 REMARK 350 BIOMT2 5 -0.809017 0.309017 0.500000 0.00000 REMARK 350 BIOMT3 5 0.309017 -0.500000 0.809017 0.00000 REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 7 -0.500000 0.809017 -0.309017 0.00000 REMARK 350 BIOMT2 7 -0.809017 -0.309017 0.500000 0.00000 REMARK 350 BIOMT3 7 0.309017 0.500000 0.809017 0.00000 REMARK 350 BIOMT1 8 0.309017 0.500000 -0.809017 0.00000 REMARK 350 BIOMT2 8 -0.500000 0.809017 0.309017 0.00000 REMARK 350 BIOMT3 8 0.809017 0.309017 0.500000 0.00000 REMARK 350 BIOMT1 9 0.309017 -0.500000 -0.809017 0.00000 REMARK 350 BIOMT2 9 0.500000 0.809017 -0.309017 0.00000 REMARK 350 BIOMT3 9 0.809017 -0.309017 0.500000 0.00000 REMARK 350 BIOMT1 10 -0.500000 -0.809017 -0.309017 0.00000 REMARK 350 BIOMT2 10 0.809017 -0.309017 -0.500000 0.00000 REMARK 350 BIOMT3 10 0.309017 -0.500000 0.809017 0.00000 REMARK 350 BIOMT1 11 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 11 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 12 0.500000 -0.809017 0.309017 0.00000 REMARK 350 BIOMT2 12 -0.809017 -0.309017 0.500000 0.00000 REMARK 350 BIOMT3 12 -0.309017 -0.500000 -0.809017 0.00000 REMARK 350 BIOMT1 13 -0.309017 -0.500000 0.809017 0.00000 REMARK 350 BIOMT2 13 -0.500000 0.809017 0.309017 0.00000 REMARK 350 BIOMT3 13 -0.809017 -0.309017 -0.500000 0.00000 REMARK 350 BIOMT1 14 -0.309017 0.500000 0.809017 0.00000 REMARK 350 BIOMT2 14 0.500000 0.809017 -0.309017 0.00000 REMARK 350 BIOMT3 14 -0.809017 0.309017 -0.500000 0.00000 REMARK 350 BIOMT1 15 0.500000 0.809017 0.309017 0.00000 REMARK 350 BIOMT2 15 0.809017 -0.309017 -0.500000 0.00000 REMARK 350 BIOMT3 15 -0.309017 0.500000 -0.809017 0.00000 REMARK 350 BIOMT1 16 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 16 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 16 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 17 -0.500000 0.809017 -0.309017 0.00000 REMARK 350 BIOMT2 17 0.809017 0.309017 -0.500000 0.00000 REMARK 350 BIOMT3 17 -0.309017 -0.500000 -0.809017 0.00000 REMARK 350 BIOMT1 18 0.309017 0.500000 -0.809017 0.00000 REMARK 350 BIOMT2 18 0.500000 -0.809017 -0.309017 0.00000 REMARK 350 BIOMT3 18 -0.809017 -0.309017 -0.500000 0.00000 REMARK 350 BIOMT1 19 0.309017 -0.500000 -0.809017 0.00000 REMARK 350 BIOMT2 19 -0.500000 -0.809017 0.309017 0.00000 REMARK 350 BIOMT3 19 -0.809017 0.309017 -0.500000 0.00000 REMARK 350 BIOMT1 20 -0.500000 -0.809017 -0.309017 0.00000 REMARK 350 BIOMT2 20 -0.809017 0.309017 0.500000 0.00000 REMARK 350 BIOMT3 20 -0.309017 0.500000 -0.809017 0.00000 REMARK 350 BIOMT1 21 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 21 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 21 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 22 -0.809017 -0.309017 0.500000 0.00000 REMARK 350 BIOMT2 22 -0.309017 -0.500000 -0.809017 0.00000 REMARK 350 BIOMT3 22 0.500000 -0.809017 0.309017 0.00000 REMARK 350 BIOMT1 23 -0.500000 0.809017 0.309017 0.00000 REMARK 350 BIOMT2 23 -0.809017 -0.309017 -0.500000 0.00000 REMARK 350 BIOMT3 23 -0.309017 -0.500000 0.809017 0.00000 REMARK 350 BIOMT1 24 0.500000 0.809017 -0.309017 0.00000 REMARK 350 BIOMT2 24 -0.809017 0.309017 -0.500000 0.00000 REMARK 350 BIOMT3 24 -0.309017 0.500000 0.809017 0.00000 REMARK 350 BIOMT1 25 0.809017 -0.309017 -0.500000 0.00000 REMARK 350 BIOMT2 25 -0.309017 0.500000 -0.809017 0.00000 REMARK 350 BIOMT3 25 0.500000 0.809017 0.309017 0.00000 REMARK 350 BIOMT1 26 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 26 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 26 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 27 0.809017 0.309017 -0.500000 0.00000 REMARK 350 BIOMT2 27 -0.309017 -0.500000 -0.809017 0.00000 REMARK 350 BIOMT3 27 -0.500000 0.809017 -0.309017 0.00000 REMARK 350 BIOMT1 28 0.500000 -0.809017 -0.309017 0.00000 REMARK 350 BIOMT2 28 -0.809017 -0.309017 -0.500000 0.00000 REMARK 350 BIOMT3 28 0.309017 0.500000 -0.809017 0.00000 REMARK 350 BIOMT1 29 -0.500000 -0.809017 0.309017 0.00000 REMARK 350 BIOMT2 29 -0.809017 0.309017 -0.500000 0.00000 REMARK 350 BIOMT3 29 0.309017 -0.500000 -0.809017 0.00000 REMARK 350 BIOMT1 30 -0.809017 0.309017 0.500000 0.00000 REMARK 350 BIOMT2 30 -0.309017 0.500000 -0.809017 0.00000 REMARK 350 BIOMT3 30 -0.500000 -0.809017 -0.309017 0.00000 REMARK 350 BIOMT1 31 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 31 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 31 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 32 0.809017 0.309017 -0.500000 0.00000 REMARK 350 BIOMT2 32 0.309017 0.500000 0.809017 0.00000 REMARK 350 BIOMT3 32 0.500000 -0.809017 0.309017 0.00000 REMARK 350 BIOMT1 33 0.500000 -0.809017 -0.309017 0.00000 REMARK 350 BIOMT2 33 0.809017 0.309017 0.500000 0.00000 REMARK 350 BIOMT3 33 -0.309017 -0.500000 0.809017 0.00000 REMARK 350 BIOMT1 34 -0.500000 -0.809017 0.309017 0.00000 REMARK 350 BIOMT2 34 0.809017 -0.309017 0.500000 0.00000 REMARK 350 BIOMT3 34 -0.309017 0.500000 0.809017 0.00000 REMARK 350 BIOMT1 35 -0.809017 0.309017 0.500000 0.00000 REMARK 350 BIOMT2 35 0.309017 -0.500000 0.809017 0.00000 REMARK 350 BIOMT3 35 0.500000 0.809017 0.309017 0.00000 REMARK 350 BIOMT1 36 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 36 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 36 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 37 -0.809017 -0.309017 0.500000 0.00000 REMARK 350 BIOMT2 37 0.309017 0.500000 0.809017 0.00000 REMARK 350 BIOMT3 37 -0.500000 0.809017 -0.309017 0.00000 REMARK 350 BIOMT1 38 -0.500000 0.809017 0.309017 0.00000 REMARK 350 BIOMT2 38 0.809017 0.309017 0.500000 0.00000 REMARK 350 BIOMT3 38 0.309017 0.500000 -0.809017 0.00000 REMARK 350 BIOMT1 39 0.500000 0.809017 -0.309017 0.00000 REMARK 350 BIOMT2 39 0.809017 -0.309017 0.500000 0.00000 REMARK 350 BIOMT3 39 0.309017 -0.500000 -0.809017 0.00000 REMARK 350 BIOMT1 40 0.809017 -0.309017 -0.500000 0.00000 REMARK 350 BIOMT2 40 0.309017 -0.500000 0.809017 0.00000 REMARK 350 BIOMT3 40 -0.500000 -0.809017 -0.309017 0.00000 REMARK 350 BIOMT1 41 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 41 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 41 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT1 42 0.309017 0.500000 0.809017 0.00000 REMARK 350 BIOMT2 42 -0.500000 0.809017 -0.309017 0.00000 REMARK 350 BIOMT3 42 -0.809017 -0.309017 0.500000 0.00000 REMARK 350 BIOMT1 43 0.809017 0.309017 0.500000 0.00000 REMARK 350 BIOMT2 43 0.309017 0.500000 -0.809017 0.00000 REMARK 350 BIOMT3 43 -0.500000 0.809017 0.309017 0.00000 REMARK 350 BIOMT1 44 0.809017 -0.309017 0.500000 0.00000 REMARK 350 BIOMT2 44 0.309017 -0.500000 -0.809017 0.00000 REMARK 350 BIOMT3 44 0.500000 0.809017 -0.309017 0.00000 REMARK 350 BIOMT1 45 0.309017 -0.500000 0.809017 0.00000 REMARK 350 BIOMT2 45 -0.500000 -0.809017 -0.309017 0.00000 REMARK 350 BIOMT3 45 0.809017 -0.309017 -0.500000 0.00000 REMARK 350 BIOMT1 46 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 46 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 46 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 47 0.309017 0.500000 0.809017 0.00000 REMARK 350 BIOMT2 47 0.500000 -0.809017 0.309017 0.00000 REMARK 350 BIOMT3 47 0.809017 0.309017 -0.500000 0.00000 REMARK 350 BIOMT1 48 0.809017 0.309017 0.500000 0.00000 REMARK 350 BIOMT2 48 -0.309017 -0.500000 0.809017 0.00000 REMARK 350 BIOMT3 48 0.500000 -0.809017 -0.309017 0.00000 REMARK 350 BIOMT1 49 0.809017 -0.309017 0.500000 0.00000 REMARK 350 BIOMT2 49 -0.309017 0.500000 0.809017 0.00000 REMARK 350 BIOMT3 49 -0.500000 -0.809017 0.309017 0.00000 REMARK 350 BIOMT1 50 0.309017 -0.500000 0.809017 0.00000 REMARK 350 BIOMT2 50 0.500000 0.809017 0.309017 0.00000 REMARK 350 BIOMT3 50 -0.809017 0.309017 0.500000 0.00000 REMARK 350 BIOMT1 51 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 51 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 51 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 52 -0.309017 -0.500000 -0.809017 0.00000 REMARK 350 BIOMT2 52 -0.500000 0.809017 -0.309017 0.00000 REMARK 350 BIOMT3 52 0.809017 0.309017 -0.500000 0.00000 REMARK 350 BIOMT1 53 -0.809017 -0.309017 -0.500000 0.00000 REMARK 350 BIOMT2 53 0.309017 0.500000 -0.809017 0.00000 REMARK 350 BIOMT3 53 0.500000 -0.809017 -0.309017 0.00000 REMARK 350 BIOMT1 54 -0.809017 0.309017 -0.500000 0.00000 REMARK 350 BIOMT2 54 0.309017 -0.500000 -0.809017 0.00000 REMARK 350 BIOMT3 54 -0.500000 -0.809017 0.309017 0.00000 REMARK 350 BIOMT1 55 -0.309017 0.500000 -0.809017 0.00000 REMARK 350 BIOMT2 55 -0.500000 -0.809017 -0.309017 0.00000 REMARK 350 BIOMT3 55 -0.809017 0.309017 0.500000 0.00000 REMARK 350 BIOMT1 56 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 56 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 56 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT1 57 -0.309017 -0.500000 -0.809017 0.00000 REMARK 350 BIOMT2 57 0.500000 -0.809017 0.309017 0.00000 REMARK 350 BIOMT3 57 -0.809017 -0.309017 0.500000 0.00000 REMARK 350 BIOMT1 58 -0.809017 -0.309017 -0.500000 0.00000 REMARK 350 BIOMT2 58 -0.309017 -0.500000 0.809017 0.00000 REMARK 350 BIOMT3 58 -0.500000 0.809017 0.309017 0.00000 REMARK 350 BIOMT1 59 -0.809017 0.309017 -0.500000 0.00000 REMARK 350 BIOMT2 59 -0.309017 0.500000 0.809017 0.00000 REMARK 350 BIOMT3 59 0.500000 0.809017 -0.309017 0.00000 REMARK 350 BIOMT1 60 -0.309017 0.500000 -0.809017 0.00000 REMARK 350 BIOMT2 60 0.500000 0.809017 0.309017 0.00000 REMARK 350 BIOMT3 60 0.809017 -0.309017 -0.500000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET 1 1 REMARK 465 SER 1 2 REMARK 465 GLN 1 3 REMARK 465 VAL 1 4 REMARK 465 THR 1 5 REMARK 465 GLU 1 149 REMARK 465 GLY 1 150 REMARK 465 VAL 1 151 REMARK 465 MET 1 152 REMARK 465 MET 2 1 REMARK 465 SER 2 2 REMARK 465 GLN 2 3 REMARK 465 VAL 2 4 REMARK 465 THR 2 5 REMARK 465 ASN 2 141 REMARK 465 VAL 2 142 REMARK 465 ARG 2 143 REMARK 465 GLN 2 144 REMARK 465 LYS 2 145 REMARK 465 LEU 2 146 REMARK 465 ARG 2 147 REMARK 465 ALA 2 148 REMARK 465 GLU 2 149 REMARK 465 GLY 2 150 REMARK 465 VAL 2 151 REMARK 465 MET 2 152 REMARK 465 MET 3 1 REMARK 465 SER 3 2 REMARK 465 GLN 3 3 REMARK 465 VAL 3 4 REMARK 465 LYS 3 145 REMARK 465 LEU 3 146 REMARK 465 ARG 3 147 REMARK 465 ALA 3 148 REMARK 465 GLU 3 149 REMARK 465 GLY 3 150 REMARK 465 VAL 3 151 REMARK 465 MET 3 152 REMARK 465 MET 4 1 REMARK 465 SER 4 2 REMARK 465 GLN 4 3 REMARK 465 VAL 4 4 REMARK 465 THR 4 5 REMARK 465 GLU 4 6 REMARK 465 MET F 1 REMARK 465 SER F 2 REMARK 465 ASN F 3 REMARK 465 VAL F 4 REMARK 465 GLN F 5 REMARK 465 THR F 6 REMARK 465 SER F 7 REMARK 465 ALA F 8 REMARK 465 GLU F 9 REMARK 465 SER F 171 REMARK 465 ALA F 172 REMARK 465 PRO F 173 REMARK 465 LEU F 174 REMARK 465 PRO F 175 REMARK 465 PRO F 176 REMARK 465 GLU F 177 REMARK 465 THR F 178 REMARK 465 LYS F 179 REMARK 465 LEU F 180 REMARK 465 ALA F 181 REMARK 465 GLU F 182 REMARK 465 GLU F 183 REMARK 465 MET F 184 REMARK 465 GLY F 185 REMARK 465 ILE F 186 REMARK 465 GLU F 187 REMARK 465 SER F 188 REMARK 465 ASN F 189 REMARK 465 SER F 190 REMARK 465 ILE F 191 REMARK 465 ASP F 192 REMARK 465 ILE F 193 REMARK 465 MET F 194 REMARK 465 GLY F 195 REMARK 465 LEU F 196 REMARK 465 GLN F 197 REMARK 465 ALA F 198 REMARK 465 ALA F 199 REMARK 465 TYR F 200 REMARK 465 ALA F 201 REMARK 465 GLN F 202 REMARK 465 LEU F 203 REMARK 465 HIS F 204 REMARK 465 THR F 205 REMARK 465 GLU F 206 REMARK 465 GLN F 207 REMARK 465 GLU F 208 REMARK 465 ARG F 209 REMARK 465 THR F 210 REMARK 465 TYR F 211 REMARK 465 PHE F 212 REMARK 465 MET F 213 REMARK 465 GLN F 214 REMARK 465 ARG F 215 REMARK 465 TYR F 216 REMARK 465 ARG F 217 REMARK 465 ASP F 218 REMARK 465 VAL F 219 REMARK 465 ILE F 220 REMARK 465 SER F 221 REMARK 465 SER F 222 REMARK 465 PHE F 223 REMARK 465 GLY F 224 REMARK 465 GLY F 225 REMARK 465 SER F 226 REMARK 465 THR F 227 REMARK 465 SER F 228 REMARK 465 TYR F 229 REMARK 465 ASP F 230 REMARK 465 ALA F 231 REMARK 465 ASP F 232 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CD3 RELATED DB: PDB REMARK 900 PROCAPSID OF THE BACTERIOPHAGE PHIX174 REMARK 900 RELATED ID: 1GFF RELATED DB: PDB REMARK 900 STRUCTURE OF THE DEGRADED PROCAPSID PARTICLE OF BACTERIOPHAGE G4 REMARK 900 RELATED ID: 1PHX RELATED DB: PDB REMARK 900 DNA PACKAGING INTERMEDIATES OF THE BACTERIOPHAGE PHIX174 REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE 160 OF THE F PROTEIN IS AN ARG ACCORDING REMARK 999 TO THE REPORTED SEQUENCE BUT NO DENSITY IS SEEN REMARK 999 FOR THE SIDE CHAIN IN THE CRYSTAL STRUCTURE FOR REMARK 999 THIS RESIDUE. AFTER A STRUCTURAL SEQUENCE REMARK 999 ALIGNMENT WITH HOMOLOGOUS BACTERIOPHAGES PHIX174 REMARK 999 AND G4, RESIDUE 160 WAS FOUND TO BE A GLYCINE REMARK 999 IN THE OTHER PHAGES. CONSEQUENTLY, THE AUTHORS REMARK 999 STATE RESIDUE 160 SHOULD BE A GLYCINE. REMARK 999 CHAINS 1,2,3,4 ARE SCAFFOLDING PROTEIN D AND REMARK 999 CHAIN B IS SCAFFOLDING PROTEIN B, ALL FROM REMARK 999 BACTERIOPHAGE ALPHA3. THE PROTEIN SEQUENCES WERE REMARK 999 TAKEN FROM 1CD3 PHIX174 COORDINATES AND FITTED REMARK 999 INTO THE CRYO-EM STRUCTURE. THE SEQUENCE REMARK 999 DATABASE REFERENCE FOR THE PHIX174 SCAFFOLDING REMARK 999 PROTEINS D AND B ARE P03637 AND P07929 RESPECTIVELY. DBREF 1M0F F 1 431 UNP P08767 VGF_BPAL3 1 431 DBREF 1M0F G 1 187 UNP P31281 VGG_BPAL3 1 187 DBREF 1M0F 1 1 152 PDB 1M0F 1M0F 1 152 DBREF 1M0F 2 1 152 PDB 1M0F 1M0F 1 152 DBREF 1M0F 3 1 152 PDB 1M0F 1M0F 1 152 DBREF 1M0F 4 1 152 PDB 1M0F 1M0F 1 152 DBREF 1M0F B 1 120 PDB 1M0F 1M0F 1 120 SEQADV 1M0F GLY F 160 UNP P08767 ARG 160 SEE REMARK 999 SEQRES 1 1 152 MET SER GLN VAL THR GLU GLN SER VAL ARG PHE GLN THR SEQRES 2 1 152 ALA LEU ALA SER ILE LYS LEU ILE GLN ALA SER ALA VAL SEQRES 3 1 152 LEU ASP LEU THR GLU ASP ASP PHE ASP PHE LEU THR SER SEQRES 4 1 152 ASN LYS VAL TRP ILE ALA THR ASP ARG SER ARG ALA ARG SEQRES 5 1 152 ARG CYS VAL GLU ALA CYS VAL TYR GLY THR LEU ASP PHE SEQRES 6 1 152 VAL GLY TYR PRO ARG PHE PRO ALA PRO VAL GLU PHE ILE SEQRES 7 1 152 ALA ALA VAL ILE ALA TYR TYR VAL HIS PRO VAL ASN ILE SEQRES 8 1 152 GLN THR ALA CYS LEU ILE MET GLU GLY ALA GLU PHE THR SEQRES 9 1 152 GLU ASN ILE ILE ASN GLY VAL GLU ARG PRO VAL LYS ALA SEQRES 10 1 152 ALA GLU LEU PHE ALA PHE THR LEU ARG VAL ARG ALA GLY SEQRES 11 1 152 ASN THR ASP VAL LEU THR ASP ALA GLU GLU ASN VAL ARG SEQRES 12 1 152 GLN LYS LEU ARG ALA GLU GLY VAL MET SEQRES 1 2 152 MET SER GLN VAL THR GLU GLN SER VAL ARG PHE GLN THR SEQRES 2 2 152 ALA LEU ALA SER ILE LYS LEU ILE GLN ALA SER ALA VAL SEQRES 3 2 152 LEU ASP LEU THR GLU ASP ASP PHE ASP PHE LEU THR SER SEQRES 4 2 152 ASN LYS VAL TRP ILE ALA THR ASP ARG SER ARG ALA ARG SEQRES 5 2 152 ARG CYS VAL GLU ALA CYS VAL TYR GLY THR LEU ASP PHE SEQRES 6 2 152 VAL GLY TYR PRO ARG PHE PRO ALA PRO VAL GLU PHE ILE SEQRES 7 2 152 ALA ALA VAL ILE ALA TYR TYR VAL HIS PRO VAL ASN ILE SEQRES 8 2 152 GLN THR ALA CYS LEU ILE MET GLU GLY ALA GLU PHE THR SEQRES 9 2 152 GLU ASN ILE ILE ASN GLY VAL GLU ARG PRO VAL LYS ALA SEQRES 10 2 152 ALA GLU LEU PHE ALA PHE THR LEU ARG VAL ARG ALA GLY SEQRES 11 2 152 ASN THR ASP VAL LEU THR ASP ALA GLU GLU ASN VAL ARG SEQRES 12 2 152 GLN LYS LEU ARG ALA GLU GLY VAL MET SEQRES 1 3 152 MET SER GLN VAL THR GLU GLN SER VAL ARG PHE GLN THR SEQRES 2 3 152 ALA LEU ALA SER ILE LYS LEU ILE GLN ALA SER ALA VAL SEQRES 3 3 152 LEU ASP LEU THR GLU ASP ASP PHE ASP PHE LEU THR SER SEQRES 4 3 152 ASN LYS VAL TRP ILE ALA THR ASP ARG SER ARG ALA ARG SEQRES 5 3 152 ARG CYS VAL GLU ALA CYS VAL TYR GLY THR LEU ASP PHE SEQRES 6 3 152 VAL GLY TYR PRO ARG PHE PRO ALA PRO VAL GLU PHE ILE SEQRES 7 3 152 ALA ALA VAL ILE ALA TYR TYR VAL HIS PRO VAL ASN ILE SEQRES 8 3 152 GLN THR ALA CYS LEU ILE MET GLU GLY ALA GLU PHE THR SEQRES 9 3 152 GLU ASN ILE ILE ASN GLY VAL GLU ARG PRO VAL LYS ALA SEQRES 10 3 152 ALA GLU LEU PHE ALA PHE THR LEU ARG VAL ARG ALA GLY SEQRES 11 3 152 ASN THR ASP VAL LEU THR ASP ALA GLU GLU ASN VAL ARG SEQRES 12 3 152 GLN LYS LEU ARG ALA GLU GLY VAL MET SEQRES 1 4 152 MET SER GLN VAL THR GLU GLN SER VAL ARG PHE GLN THR SEQRES 2 4 152 ALA LEU ALA SER ILE LYS LEU ILE GLN ALA SER ALA VAL SEQRES 3 4 152 LEU ASP LEU THR GLU ASP ASP PHE ASP PHE LEU THR SER SEQRES 4 4 152 ASN LYS VAL TRP ILE ALA THR ASP ARG SER ARG ALA ARG SEQRES 5 4 152 ARG CYS VAL GLU ALA CYS VAL TYR GLY THR LEU ASP PHE SEQRES 6 4 152 VAL GLY TYR PRO ARG PHE PRO ALA PRO VAL GLU PHE ILE SEQRES 7 4 152 ALA ALA VAL ILE ALA TYR TYR VAL HIS PRO VAL ASN ILE SEQRES 8 4 152 GLN THR ALA CYS LEU ILE MET GLU GLY ALA GLU PHE THR SEQRES 9 4 152 GLU ASN ILE ILE ASN GLY VAL GLU ARG PRO VAL LYS ALA SEQRES 10 4 152 ALA GLU LEU PHE ALA PHE THR LEU ARG VAL ARG ALA GLY SEQRES 11 4 152 ASN THR ASP VAL LEU THR ASP ALA GLU GLU ASN VAL ARG SEQRES 12 4 152 GLN LYS LEU ARG ALA GLU GLY VAL MET SEQRES 1 F 431 MET SER ASN VAL GLN THR SER ALA GLU ARG GLU ILE VAL SEQRES 2 F 431 ASP LEU SER HIS LEU ALA PHE ASP CYS GLY MET LEU GLY SEQRES 3 F 431 ARG LEU LYS THR VAL SER TRP THR PRO VAL ILE ALA GLY SEQRES 4 F 431 ASP SER PHE GLU LEU ASP ALA VAL GLY ALA LEU ARG LEU SEQRES 5 F 431 SER PRO LEU ARG ARG GLY LEU ALA ILE ASP SER LYS VAL SEQRES 6 F 431 ASP PHE PHE THR PHE TYR ILE PRO HIS ARG HIS VAL TYR SEQRES 7 F 431 GLY ASP GLN TRP ILE GLN PHE MET ARG ASP GLY VAL ASN SEQRES 8 F 431 ALA GLN PRO LEU PRO SER VAL THR CYS ASN ARG TYR PRO SEQRES 9 F 431 ASP HIS ALA GLY TYR VAL GLY THR ILE VAL PRO ALA ASN SEQRES 10 F 431 ASN ARG ILE PRO LYS PHE LEU HIS GLN SER TYR LEU ASN SEQRES 11 F 431 ILE TYR ASN ASN TYR PHE ARG ALA PRO TRP MET PRO GLU SEQRES 12 F 431 ARG THR GLU ALA ASN PRO SER ASN LEU ASN GLU ASP ASP SEQRES 13 F 431 ALA ARG TYR GLY PHE ARG CYS CYS HIS LEU LYS ASN ILE SEQRES 14 F 431 TRP SER ALA PRO LEU PRO PRO GLU THR LYS LEU ALA GLU SEQRES 15 F 431 GLU MET GLY ILE GLU SER ASN SER ILE ASP ILE MET GLY SEQRES 16 F 431 LEU GLN ALA ALA TYR ALA GLN LEU HIS THR GLU GLN GLU SEQRES 17 F 431 ARG THR TYR PHE MET GLN ARG TYR ARG ASP VAL ILE SER SEQRES 18 F 431 SER PHE GLY GLY SER THR SER TYR ASP ALA ASP ASN ARG SEQRES 19 F 431 PRO LEU LEU VAL MET HIS THR ASP PHE TRP ALA SER GLY SEQRES 20 F 431 TYR ASP VAL ASP GLY THR ASP GLN SER SER LEU GLY GLN SEQRES 21 F 431 PHE SER GLY ARG VAL GLN GLN THR PHE LYS HIS SER VAL SEQRES 22 F 431 PRO ARG PHE PHE VAL PRO GLU HIS GLY VAL MET MET THR SEQRES 23 F 431 LEU ALA LEU ILE ARG PHE PRO PRO ILE SER PRO LEU GLU SEQRES 24 F 431 HIS HIS TYR LEU ALA GLY LYS SER GLN LEU THR TYR THR SEQRES 25 F 431 ASP LEU ALA GLY ASP PRO ALA LEU ILE GLY ASN LEU PRO SEQRES 26 F 431 PRO ARG GLU ILE SER TYR ARG ASP LEU PHE ARG ASP GLY SEQRES 27 F 431 ARG SER GLY ILE LYS ILE LYS VAL ALA GLU SER ILE TRP SEQRES 28 F 431 TYR ARG THR HIS PRO ASP TYR VAL ASN PHE LYS TYR HIS SEQRES 29 F 431 ASP LEU HIS GLY PHE PRO PHE LEU ASP ASP ALA PRO GLY SEQRES 30 F 431 THR SER THR GLY ASP ASN LEU GLN GLU ALA ILE LEU VAL SEQRES 31 F 431 ARG HIS GLN ASP TYR ASP ALA CYS PHE GLN SER GLN GLN SEQRES 32 F 431 LEU LEU GLN TRP ASN LYS GLN ALA ARG TYR ASN VAL SER SEQRES 33 F 431 VAL TYR ARG HIS MET PRO THR VAL ARG ASP SER ILE MET SEQRES 34 F 431 THR SER SEQRES 1 G 187 MET TYR GLN ASN PHE VAL THR LYS HIS ASP THR ALA ILE SEQRES 2 G 187 GLN THR SER ARG PHE SER VAL THR GLY ASN VAL ILE PRO SEQRES 3 G 187 ALA ALA PRO THR GLY ASN ILE PRO VAL ILE ASN GLY GLY SEQRES 4 G 187 SER ILE THR ALA GLU ARG ALA VAL VAL ASN LEU TYR ALA SEQRES 5 G 187 ASN MET ASN VAL SER THR SER SER ASP GLY SER PHE ILE SEQRES 6 G 187 VAL ALA MET LYS VAL ASP THR SER PRO THR ASP PRO ASN SEQRES 7 G 187 CYS VAL ILE SER ALA GLY VAL ASN LEU SER PHE ALA GLY SEQRES 8 G 187 THR SER TYR PRO ILE VAL GLY ILE VAL ARG PHE GLU SER SEQRES 9 G 187 ALA SER GLU GLN PRO THR SER ILE ALA GLY SER GLU VAL SEQRES 10 G 187 GLU HIS TYR PRO ILE GLU MET SER VAL GLY SER GLY GLY SEQRES 11 G 187 VAL CYS SER ALA ARG ASP CYS ALA THR VAL ASP ILE HIS SEQRES 12 G 187 PRO ARG THR SER GLY ASN ASN VAL PHE VAL GLY VAL ILE SEQRES 13 G 187 CYS SER SER ALA LYS TRP THR SER GLY ARG VAL ILE GLY SEQRES 14 G 187 THR ILE ALA THR THR GLN VAL ILE HIS GLU TYR GLN VAL SEQRES 15 G 187 LEU GLN PRO LEU LYS SEQRES 1 B 68 MET GLU GLN LEU THR LYS ASN GLN ARG LYS LYS ARG ASP SEQRES 2 B 68 GLU ILE GLU ALA GLY LYS SER TYR CYS SER ARG ARG PHE SEQRES 3 B 68 GLY GLY ALA THR CYS ASP ASP LYS SER ALA GLN ILE TYR SEQRES 4 B 68 ALA ARG PHE ASP LYS ASN ASP TRP ARG ILE GLN PRO ALA SEQRES 5 B 68 GLU PHE TYR ARG PHE HIS ASP ALA GLU VAL ASN THR PHE SEQRES 6 B 68 GLY TYR PHE CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000