HEADER VIRUS LIKE PARTICLE 02-DEC-23 8RB3 TITLE STRUCTURE OF THE PNMA2 CAPSID COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARANEOPLASTIC ANTIGEN MA2 HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PNMA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENDOGENOUS RETROVIRUS. PNMA2, PNMA, PARANEOPLASTIC SYNDROME, KEYWDS 2 PARANEOPLASTIC ANTIGEN MA2, VLP., VIRUS LIKE PARTICLE EXPDTA ELECTRON MICROSCOPY AUTHOR S.ERLENDSSON,J.XU,J.D.SHEPHERD,J.A.G.BRIGGS REVDAT 2 28-FEB-24 8RB3 1 JRNL REVDAT 1 14-FEB-24 8RB3 0 JRNL AUTH J.XU,S.ERLENDSSON,M.SINGH,G.A.HOLLING,M.REGIER,I.IBIRICU, JRNL AUTH 2 J.EINSTEIN,M.P.HANTAK,G.S.DAY,A.L.PIQUET,T.L.SMITH, JRNL AUTH 3 S.L.CLARDY,A.M.WHITELEY,C.FESCHOTTE,J.A.G.BRIGGS, JRNL AUTH 4 J.D.SHEPHERD JRNL TITL PNMA2 FORMS IMMUNOGENIC NON-ENVELOPED VIRUS-LIKE CAPSIDS JRNL TITL 2 ASSOCIATED WITH PARANEOPLASTIC NEUROLOGICAL SYNDROME. JRNL REF CELL V. 187 831 2024 JRNL REFN ISSN 1097-4172 JRNL PMID 38301645 JRNL DOI 10.1016/J.CELL.2024.01.009 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, CTFFIND, UCSF CHIMERAX, REMARK 3 RELION, RELION, RELION, COOT, PHENIX, REMARK 3 UCSF CHIMERAX, ISOLDE REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 147.000 REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.200 REMARK 3 NUMBER OF PARTICLES : 35420 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8RB3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1292133491. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : STRUCTURE OF THE PNMA2 CAPSID REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : T=1 ICOSAHEDRAL MPNMA2 CAPSID REMARK 245 CONSISTING OF 60 PNMA2 MOLECULES REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 3005 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 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) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 96000 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: 60-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 60-MERIC REMARK 350 SOFTWARE USED: UCSF CHIMERA 1.16_B42360. REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 -0.809017 -0.500000 0.309017 425.98401 REMARK 350 BIOMT2 2 -0.500000 0.309017 -0.809017 425.98401 REMARK 350 BIOMT3 2 0.309017 -0.809017 -0.500000 425.98401 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 425.98401 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 425.98401 REMARK 350 BIOMT1 4 0.809017 -0.500000 -0.309017 212.99200 REMARK 350 BIOMT2 4 -0.500000 -0.309017 -0.809017 557.62031 REMARK 350 BIOMT3 4 0.309017 0.809017 -0.500000 81.35571 REMARK 350 BIOMT1 5 0.500000 0.309017 -0.809017 212.99200 REMARK 350 BIOMT2 5 -0.309017 -0.809017 -0.500000 557.62031 REMARK 350 BIOMT3 5 -0.809017 0.500000 -0.309017 344.62830 REMARK 350 BIOMT1 6 -0.309017 -0.809017 -0.500000 557.62031 REMARK 350 BIOMT2 6 -0.809017 0.500000 -0.309017 344.62830 REMARK 350 BIOMT3 6 0.500000 0.309017 -0.809017 212.99200 REMARK 350 BIOMT1 7 -0.809017 0.500000 -0.309017 344.62830 REMARK 350 BIOMT2 7 0.500000 0.309017 -0.809017 212.99200 REMARK 350 BIOMT3 7 -0.309017 -0.809017 -0.500000 557.62031 REMARK 350 BIOMT1 8 -0.809017 -0.500000 -0.309017 557.62031 REMARK 350 BIOMT2 8 0.500000 -0.309017 -0.809017 344.62830 REMARK 350 BIOMT3 8 0.309017 -0.809017 0.500000 212.99200 REMARK 350 BIOMT1 9 -0.309017 0.809017 -0.500000 212.99200 REMARK 350 BIOMT2 9 -0.809017 -0.500000 -0.309017 557.62031 REMARK 350 BIOMT3 9 -0.500000 0.309017 0.809017 81.35571 REMARK 350 BIOMT1 10 0.500000 -0.309017 -0.809017 344.62830 REMARK 350 BIOMT2 10 -0.309017 0.809017 -0.500000 212.99200 REMARK 350 BIOMT3 10 0.809017 0.500000 0.309017 -131.63630 REMARK 350 BIOMT1 11 0.000000 0.000000 -1.000000 425.98401 REMARK 350 BIOMT2 11 -1.000000 0.000000 0.000000 425.98401 REMARK 350 BIOMT3 11 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 12 -0.500000 -0.309017 -0.809017 557.62031 REMARK 350 BIOMT2 12 0.309017 0.809017 -0.500000 81.35571 REMARK 350 BIOMT3 12 0.809017 -0.500000 -0.309017 212.99200 REMARK 350 BIOMT1 13 -0.500000 0.309017 -0.809017 425.98401 REMARK 350 BIOMT2 13 0.309017 -0.809017 -0.500000 425.98401 REMARK 350 BIOMT3 13 -0.809017 -0.500000 0.309017 425.98401 REMARK 350 BIOMT1 14 -0.309017 -0.809017 -0.500000 557.62031 REMARK 350 BIOMT2 14 0.809017 -0.500000 0.309017 81.35571 REMARK 350 BIOMT3 14 -0.500000 -0.309017 0.809017 212.99200 REMARK 350 BIOMT1 15 -0.809017 0.500000 -0.309017 344.62830 REMARK 350 BIOMT2 15 -0.500000 -0.309017 0.809017 212.99200 REMARK 350 BIOMT3 15 0.309017 0.809017 0.500000 -131.63630 REMARK 350 BIOMT1 16 0.500000 0.309017 -0.809017 212.99200 REMARK 350 BIOMT2 16 0.309017 0.809017 0.500000 -131.63630 REMARK 350 BIOMT3 16 0.809017 -0.500000 0.309017 81.35571 REMARK 350 BIOMT1 17 -0.500000 0.309017 -0.809017 425.98401 REMARK 350 BIOMT2 17 -0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT3 17 0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT1 18 0.000000 0.000000 -1.000000 425.98401 REMARK 350 BIOMT2 18 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 18 0.000000 -1.000000 0.000000 425.98401 REMARK 350 BIOMT1 19 -0.500000 -0.309017 -0.809017 557.62031 REMARK 350 BIOMT2 19 -0.309017 -0.809017 0.500000 344.62830 REMARK 350 BIOMT3 19 -0.809017 0.500000 0.309017 212.99200 REMARK 350 BIOMT1 20 0.000000 -1.000000 0.000000 425.98401 REMARK 350 BIOMT2 20 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 20 -1.000000 0.000000 0.000000 425.98401 REMARK 350 BIOMT1 21 -0.809017 0.500000 0.309017 212.99200 REMARK 350 BIOMT2 21 0.500000 0.309017 0.809017 -131.63630 REMARK 350 BIOMT3 21 0.309017 0.809017 -0.500000 81.35571 REMARK 350 BIOMT1 22 0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT2 22 0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT3 22 0.309017 -0.809017 -0.500000 425.98401 REMARK 350 BIOMT1 23 -0.309017 0.809017 -0.500000 212.99200 REMARK 350 BIOMT2 23 0.809017 0.500000 0.309017 -131.63630 REMARK 350 BIOMT3 23 0.500000 -0.309017 -0.809017 344.62830 REMARK 350 BIOMT1 24 0.500000 -0.309017 -0.809017 344.62830 REMARK 350 BIOMT2 24 0.309017 -0.809017 0.500000 212.99200 REMARK 350 BIOMT3 24 -0.809017 -0.500000 -0.309017 557.62031 REMARK 350 BIOMT1 25 -0.809017 -0.500000 -0.309017 557.62031 REMARK 350 BIOMT2 25 -0.500000 0.309017 0.809017 81.35571 REMARK 350 BIOMT3 25 -0.309017 0.809017 -0.500000 212.99200 REMARK 350 BIOMT1 26 -0.309017 -0.809017 0.500000 344.62830 REMARK 350 BIOMT2 26 -0.809017 0.500000 0.309017 212.99200 REMARK 350 BIOMT3 26 -0.500000 -0.309017 -0.809017 557.62031 REMARK 350 BIOMT1 27 -0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT2 27 0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT3 27 -0.500000 0.309017 -0.809017 425.98401 REMARK 350 BIOMT1 28 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 28 0.000000 -1.000000 0.000000 425.98401 REMARK 350 BIOMT3 28 0.000000 0.000000 -1.000000 425.98401 REMARK 350 BIOMT1 29 0.309017 0.809017 -0.500000 81.35571 REMARK 350 BIOMT2 29 0.809017 -0.500000 -0.309017 212.99200 REMARK 350 BIOMT3 29 -0.500000 -0.309017 -0.809017 557.62031 REMARK 350 BIOMT1 30 0.309017 -0.809017 -0.500000 425.98401 REMARK 350 BIOMT2 30 -0.809017 -0.500000 0.309017 425.98401 REMARK 350 BIOMT3 30 -0.500000 0.309017 -0.809017 425.98401 REMARK 350 BIOMT1 31 -1.000000 0.000000 0.000000 425.98401 REMARK 350 BIOMT2 31 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 31 0.000000 0.000000 -1.000000 425.98401 REMARK 350 BIOMT1 32 0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT2 32 -0.500000 0.309017 -0.809017 425.98401 REMARK 350 BIOMT3 32 -0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT1 33 0.000000 -1.000000 0.000000 425.98401 REMARK 350 BIOMT2 33 0.000000 0.000000 -1.000000 425.98401 REMARK 350 BIOMT3 33 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 34 -0.809017 0.500000 0.309017 212.99200 REMARK 350 BIOMT2 34 -0.500000 -0.309017 -0.809017 557.62031 REMARK 350 BIOMT3 34 -0.309017 -0.809017 0.500000 344.62830 REMARK 350 BIOMT1 35 -0.500000 -0.309017 0.809017 212.99200 REMARK 350 BIOMT2 35 -0.309017 -0.809017 -0.500000 557.62031 REMARK 350 BIOMT3 35 0.809017 -0.500000 0.309017 81.35571 REMARK 350 BIOMT1 36 0.309017 0.809017 0.500000 -131.63630 REMARK 350 BIOMT2 36 -0.809017 0.500000 -0.309017 344.62830 REMARK 350 BIOMT3 36 -0.500000 -0.309017 0.809017 212.99200 REMARK 350 BIOMT1 37 0.809017 -0.500000 0.309017 81.35571 REMARK 350 BIOMT2 37 0.500000 0.309017 -0.809017 212.99200 REMARK 350 BIOMT3 37 0.309017 0.809017 0.500000 -131.63630 REMARK 350 BIOMT1 38 0.809017 0.500000 0.309017 -131.63630 REMARK 350 BIOMT2 38 0.500000 -0.309017 -0.809017 344.62830 REMARK 350 BIOMT3 38 -0.309017 0.809017 -0.500000 212.99200 REMARK 350 BIOMT1 39 0.309017 -0.809017 0.500000 212.99200 REMARK 350 BIOMT2 39 -0.809017 -0.500000 -0.309017 557.62031 REMARK 350 BIOMT3 39 0.500000 -0.309017 -0.809017 344.62830 REMARK 350 BIOMT1 40 -0.500000 0.309017 0.809017 81.35571 REMARK 350 BIOMT2 40 -0.309017 0.809017 -0.500000 212.99200 REMARK 350 BIOMT3 40 -0.809017 -0.500000 -0.309017 557.62031 REMARK 350 BIOMT1 41 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 41 -1.000000 0.000000 0.000000 425.98401 REMARK 350 BIOMT3 41 0.000000 -1.000000 0.000000 425.98401 REMARK 350 BIOMT1 42 0.500000 0.309017 0.809017 -131.63630 REMARK 350 BIOMT2 42 0.309017 0.809017 -0.500000 81.35571 REMARK 350 BIOMT3 42 -0.809017 0.500000 0.309017 212.99200 REMARK 350 BIOMT1 43 0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT2 43 0.309017 -0.809017 -0.500000 425.98401 REMARK 350 BIOMT3 43 0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT1 44 0.309017 0.809017 0.500000 -131.63630 REMARK 350 BIOMT2 44 0.809017 -0.500000 0.309017 81.35571 REMARK 350 BIOMT3 44 0.500000 0.309017 -0.809017 212.99200 REMARK 350 BIOMT1 45 0.809017 -0.500000 0.309017 81.35571 REMARK 350 BIOMT2 45 -0.500000 -0.309017 0.809017 212.99200 REMARK 350 BIOMT3 45 -0.309017 -0.809017 -0.500000 557.62031 REMARK 350 BIOMT1 46 -0.500000 -0.309017 0.809017 212.99200 REMARK 350 BIOMT2 46 0.309017 0.809017 0.500000 -131.63630 REMARK 350 BIOMT3 46 -0.809017 0.500000 -0.309017 344.62830 REMARK 350 BIOMT1 47 0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT2 47 -0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT3 47 -0.809017 -0.500000 0.309017 425.98401 REMARK 350 BIOMT1 48 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 48 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 48 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 49 0.500000 0.309017 0.809017 -131.63630 REMARK 350 BIOMT2 49 -0.309017 -0.809017 0.500000 344.62830 REMARK 350 BIOMT3 49 0.809017 -0.500000 -0.309017 212.99200 REMARK 350 BIOMT1 50 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 50 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 50 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 51 0.809017 -0.500000 -0.309017 212.99200 REMARK 350 BIOMT2 51 0.500000 0.309017 0.809017 -131.63630 REMARK 350 BIOMT3 51 -0.309017 -0.809017 0.500000 344.62830 REMARK 350 BIOMT1 52 -0.809017 -0.500000 0.309017 425.98401 REMARK 350 BIOMT2 52 0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT3 52 -0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT1 53 0.309017 -0.809017 0.500000 212.99200 REMARK 350 BIOMT2 53 0.809017 0.500000 0.309017 -131.63630 REMARK 350 BIOMT3 53 -0.500000 0.309017 0.809017 81.35571 REMARK 350 BIOMT1 54 -0.500000 0.309017 0.809017 81.35571 REMARK 350 BIOMT2 54 0.309017 -0.809017 0.500000 212.99200 REMARK 350 BIOMT3 54 0.809017 0.500000 0.309017 -131.63630 REMARK 350 BIOMT1 55 0.809017 0.500000 0.309017 -131.63630 REMARK 350 BIOMT2 55 -0.500000 0.309017 0.809017 81.35571 REMARK 350 BIOMT3 55 0.309017 -0.809017 0.500000 212.99200 REMARK 350 BIOMT1 56 0.309017 0.809017 -0.500000 81.35571 REMARK 350 BIOMT2 56 -0.809017 0.500000 0.309017 212.99200 REMARK 350 BIOMT3 56 0.500000 0.309017 0.809017 -131.63630 REMARK 350 BIOMT1 57 0.309017 -0.809017 -0.500000 425.98401 REMARK 350 BIOMT2 57 0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT3 57 0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT1 58 -1.000000 0.000000 0.000000 425.98401 REMARK 350 BIOMT2 58 0.000000 -1.000000 0.000000 425.98401 REMARK 350 BIOMT3 58 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 59 -0.309017 -0.809017 0.500000 344.62830 REMARK 350 BIOMT2 59 0.809017 -0.500000 -0.309017 212.99200 REMARK 350 BIOMT3 59 0.500000 0.309017 0.809017 -131.63630 REMARK 350 BIOMT1 60 -0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT2 60 -0.809017 -0.500000 0.309017 425.98401 REMARK 350 BIOMT3 60 0.500000 -0.309017 0.809017 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 121 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 138 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 155 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 5 -178.93 -67.10 REMARK 500 ASN A 69 87.95 -154.07 REMARK 500 ASN A 147 46.33 -85.75 REMARK 500 ASN A 150 -159.81 55.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 92 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-19024 RELATED DB: EMDB REMARK 900 STRUCTURE OF THE PNMA2 CAPSID DBREF 8RB3 A 1 180 UNP Q8BHK0 PNMA2_MOUSE 157 336 SEQRES 1 A 180 LEU LEU PRO VAL LYS TYR CYS LYS MET ARG ILE PHE SER SEQRES 2 A 180 GLY SER THR ALA ALA ALA PRO GLU GLU GLU PRO PHE GLU SEQRES 3 A 180 VAL TRP LEU GLU GLN ALA THR GLU ILE ALA LYS GLU TRP SEQRES 4 A 180 PRO ILE PRO GLU ALA GLU LYS LYS ARG TRP VAL ALA GLU SEQRES 5 A 180 SER LEU ARG GLY PRO ALA LEU ASP LEU MET HIS ILE VAL SEQRES 6 A 180 GLN ALA ASP ASN PRO SER ILE SER VAL GLY GLU CYS LEU SEQRES 7 A 180 GLU ALA PHE LYS GLN VAL PHE GLY SER THR GLU SER ARG SEQRES 8 A 180 ARG THR SER GLN VAL LYS TYR LEU ARG THR TYR GLN GLN SEQRES 9 A 180 GLU GLY GLU LYS ILE SER ALA TYR VAL LEU ARG LEU GLU SEQRES 10 A 180 THR LEU LEU ARG ARG ALA VAL GLU LYS ARG ALA ILE PRO SEQRES 11 A 180 ARG ASN ILE ALA ASP GLN VAL ARG LEU GLU GLN VAL MET SEQRES 12 A 180 ALA GLY ALA ASN LEU GLY ASN VAL LEU TRP CYS ARG LEU SEQRES 13 A 180 GLN GLU LEU LYS ASP GLN GLY PRO LEU PRO THR PHE LEU SEQRES 14 A 180 GLN LEU MET LYS VAL ILE ARG GLU GLU GLU GLU HELIX 1 AA1 PRO A 24 GLU A 38 1 15 HELIX 2 AA2 PRO A 42 SER A 53 1 12 HELIX 3 AA3 GLY A 56 ASN A 69 1 14 HELIX 4 AA4 SER A 73 GLY A 86 1 14 HELIX 5 AA5 SER A 90 ARG A 100 1 11 HELIX 6 AA6 LYS A 108 LYS A 126 1 19 HELIX 7 AA7 PRO A 130 ASN A 132 5 3 HELIX 8 AA8 ILE A 133 ALA A 146 1 14 HELIX 9 AA9 GLY A 149 GLN A 162 1 14 HELIX 10 AB1 THR A 167 GLU A 180 1 14 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