HEADER VIRAL PROTEIN 23-APR-12 4ARD TITLE STRUCTURE OF THE IMMATURE RETROVIRAL CAPSID AT 8A RESOLUTION BY CRYO- TITLE 2 ELECTRON MICROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN P27; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: M-PMV CA-NTD, RESIDUES 318-433; COMPND 5 SYNONYM: M-PMV DPRO CANC PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MASON-PFIZER MONKEY VIRUS; SOURCE 3 ORGANISM_TAXID: 11855; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIRAL PROTEIN, RETROVIRUS, GAG EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN A, B AUTHOR T.A.M.BHARAT,N.E.DAVEY,P.ULBRICH,J.D.RICHES,A.D.MARCO,M.RUMLOVA, AUTHOR 2 C.SACHSE,T.RUML,J.A.G.BRIGGS REVDAT 5 24-APR-19 4ARD 1 CRYST1 SCALE REVDAT 4 30-AUG-17 4ARD 1 REMARK REVDAT 3 19-APR-17 4ARD 1 REMARK REVDAT 2 01-AUG-12 4ARD 1 JRNL REVDAT 1 30-MAY-12 4ARD 0 JRNL AUTH T.A.M.BHARAT,N.E.DAVEY,P.ULBRICH,J.D.RICHES,A.D.MARCO, JRNL AUTH 2 M.RUMLOVA,C.SACHSE,T.RUML,J.A.G.BRIGGS JRNL TITL STRUCTURE OF THE IMMATURE RETROVIRAL CAPSID AT 8A RESOLUTION JRNL TITL 2 BY CRYO-ELECTRON MICROSCOPY. JRNL REF NATURE V. 487 385 2012 JRNL REFN ISSN 0028-0836 JRNL PMID 22722831 JRNL DOI 10.1038/NATURE11169 REMARK 2 REMARK 2 RESOLUTION. 7.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERA, AV3, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2KGF REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--RIGID BODY REFINEMENT PROTOCOL--NMR REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 1.530 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 7.000 REMARK 3 NUMBER OF PARTICLES : NULL REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: HELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT REMARK 3 AVERAGING SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD- REMARK 3 2090. (DEPOSITION ID: 10768). REMARK 4 REMARK 4 4ARD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1290052175. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : VITREOUS ICE CRYOEM REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : HELICAL ARRAY REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : M-PMV CANC GAG TUBES REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : LIQUID ETHANE REMARK 245 SAMPLE BUFFER : 100MM NACL, 50MM TRIS-HCL, 1UM REMARK 245 ZN REMARK 245 PH : 7.70 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 05-JUL-11 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 0.20 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 47000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 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 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CA GLY A 119 CA GLY B 119 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BAX RELATED DB: PDB REMARK 900 MASON-PFIZER MONKEY VIRUS MATRIX PROTEIN, NMR, AVERAGE STRUCTURE REMARK 900 RELATED ID: 1CL4 RELATED DB: PDB REMARK 900 NUCLEOCAPSID PROTEIN FROM MASON-PFIZER MONKEY VIRUS (MPMV) REMARK 900 RELATED ID: 4ARG RELATED DB: PDB REMARK 900 STRUCTURE OF THE IMMATURE RETROVIRAL CAPSID AT 8A RESOLUTION BY REMARK 900 CRYO-ELECTRON MICROSCOPY REMARK 900 RELATED ID: EMD-2090 RELATED DB: EMDB REMARK 900 STRUCTURE OF THE IMMATURE RETROVIRAL CAPSID AT 8A RESOLUTION BY REMARK 900 CRYO-ELECTRON MICROSCOPY REMARK 900 RELATED ID: EMD-2089 RELATED DB: EMDB DBREF 4ARD A 19 101 UNP P07567 GAG_MPMV 318 433 DBREF 4ARD B 19 101 UNP P07567 GAG_MPMV 318 433 SEQRES 1 A 116 PHE ASP PHE ALA VAL ILE LYS GLU LEU LYS THR ALA ALA SEQRES 2 A 116 SER GLN TYR GLY ALA THR ALA PRO TYR THR LEU ALA ILE SEQRES 3 A 116 VAL GLU SER VAL ALA ASP ASN TRP LEU THR PRO THR ASP SEQRES 4 A 116 TRP ASN THR LEU VAL ARG ALA VAL LEU SER GLY GLY ASP SEQRES 5 A 116 HIS LEU LEU TRP LYS SER GLU PHE PHE GLU ASN CYS ARG SEQRES 6 A 116 ASP THR ALA LYS ARG ASN GLN GLN ALA GLY ASN GLY TRP SEQRES 7 A 116 ASP PHE ASP MET LEU THR GLY SER GLY ASN TYR SER SER SEQRES 8 A 116 THR ASP ALA GLN MET GLN TYR ASP PRO GLY LEU PHE ALA SEQRES 9 A 116 GLN ILE GLN ALA ALA ALA THR LYS ALA TRP ARG LYS SEQRES 1 B 116 PHE ASP PHE ALA VAL ILE LYS GLU LEU LYS THR ALA ALA SEQRES 2 B 116 SER GLN TYR GLY ALA THR ALA PRO TYR THR LEU ALA ILE SEQRES 3 B 116 VAL GLU SER VAL ALA ASP ASN TRP LEU THR PRO THR ASP SEQRES 4 B 116 TRP ASN THR LEU VAL ARG ALA VAL LEU SER GLY GLY ASP SEQRES 5 B 116 HIS LEU LEU TRP LYS SER GLU PHE PHE GLU ASN CYS ARG SEQRES 6 B 116 ASP THR ALA LYS ARG ASN GLN GLN ALA GLY ASN GLY TRP SEQRES 7 B 116 ASP PHE ASP MET LEU THR GLY SER GLY ASN TYR SER SER SEQRES 8 B 116 THR ASP ALA GLN MET GLN TYR ASP PRO GLY LEU PHE ALA SEQRES 9 B 116 GLN ILE GLN ALA ALA ALA THR LYS ALA TRP ARG LYS 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 1.000000 0.000000 0.000000 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