HEADER VIRAL PROTEIN 23-APR-12 4ARG TITLE STRUCTURE OF THE IMMATURE RETROVIRAL CAPSID AT 8A RESOLUTION BY CRYO- TITLE 2 ELECTRON MICROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: M-PMV DPRO CANC PROTEIN; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: M-PMV CA-NTD DIMER, RESIDUES 149-277; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: M-PMV DPRO CANC PROTEIN; COMPND 8 CHAIN: B, D; COMPND 9 FRAGMENT: M-PMV CA-NTD DIMER, RESIDUES 283-351; COMPND 10 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; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MASON-PFIZER MONKEY VIRUS; SOURCE 8 ORGANISM_TAXID: 11855; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIRAL PROTEIN, RETROVIRUS EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN A, B, C, D 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 4 08-MAY-24 4ARG 1 REMARK DBREF REVDAT 3 30-AUG-17 4ARG 1 REMARK REVDAT 2 01-AUG-12 4ARG 1 JRNL REVDAT 1 30-MAY-12 4ARG 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 : 1L6N 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- REMARK 3 -NMR,XRAY 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: REAL SPACE HELICAL RECONSTRUCTION WITH 3D REMARK 3 ASYMMETRIC UNIT AVERAGING. SUBMISSION BASED ON EXPERIMENTAL DATA REMARK 3 FROM EMDB EMD-2089. (DEPOSITION ID: 10767). REMARK 4 REMARK 4 4ARG 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_1290052176. 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) : 20.00 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 PRO A 69 REMARK 465 VAL A 70 REMARK 465 HIS A 71 REMARK 465 ALA A 72 REMARK 465 GLY A 73 REMARK 465 PRO A 74 REMARK 465 ILE A 75 REMARK 465 ALA A 76 REMARK 465 PRO A 77 REMARK 465 GLY A 78 REMARK 465 GLN A 79 REMARK 465 MET A 80 REMARK 465 ARG A 81 REMARK 465 GLU A 82 REMARK 465 PRO A 83 REMARK 465 PRO C 69 REMARK 465 VAL C 70 REMARK 465 HIS C 71 REMARK 465 ALA C 72 REMARK 465 GLY C 73 REMARK 465 PRO C 74 REMARK 465 ILE C 75 REMARK 465 ALA C 76 REMARK 465 PRO C 77 REMARK 465 GLY C 78 REMARK 465 GLN C 79 REMARK 465 MET C 80 REMARK 465 ARG C 81 REMARK 465 GLU C 82 REMARK 465 PRO C 83 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 ARG A 84 CA PRO C 107 2.02 REMARK 500 CA PRO A 107 CA ARG C 84 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ARD 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-2089 RELATED DB: EMDB REMARK 900 STRUCTURE OF THE IMMATURE RETROVIRAL CAPSID AT 8A RESOLUTION BY REMARK 900 CRYO-ELECTRON MICROSCOPY REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS ENTRY FITS THE STRUCTURE OF HIV (UNP Q72497) INTO THE ELCTRON REMARK 999 DENSITY MAP OF MPMV (EM 2089). THE CYCLOPHILIN BINDING LOOP OF REMARK 999 HIV-1 (PVHAGPIAPGQMREP) AND THE SEQUENCE OF RESIDUES (SPTSI) IN REMARK 999 THE INTER-DOMAIN LINKER WERE NOT INCLUDED FOR THE FITTING. DBREF 4ARG A 1 129 PDB 4ARG 4ARG 1 129 DBREF 4ARG B 135 203 PDB 4ARG 4ARG 135 203 DBREF 4ARG C 1 129 PDB 4ARG 4ARG 1 129 DBREF 4ARG D 135 203 PDB 4ARG 4ARG 135 203 SEQRES 1 A 129 PRO ARG THR LEU ASN ALA TRP VAL LYS VAL VAL GLU GLU SEQRES 2 A 129 LYS ALA PHE SER PRO GLU VAL ILE PRO MET PHE SER ALA SEQRES 3 A 129 LEU SER GLU GLY ALA THR PRO GLN ASP LEU ASN THR MET SEQRES 4 A 129 LEU ASN THR VAL GLY GLY HIS GLN ALA ALA MET GLN MET SEQRES 5 A 129 LEU LYS GLU THR ILE ASN GLU GLU ALA ALA GLU TRP ASP SEQRES 6 A 129 ARG LEU HIS PRO VAL HIS ALA GLY PRO ILE ALA PRO GLY SEQRES 7 A 129 GLN MET ARG GLU PRO ARG GLY SER ASP ILE ALA GLY THR SEQRES 8 A 129 THR SER THR LEU GLN GLU GLN ILE GLY TRP MET THR HIS SEQRES 9 A 129 ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR LYS ARG TRP SEQRES 10 A 129 ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG MET TYR SEQRES 1 B 69 LEU ASP ILE ARG GLN GLY PRO LYS GLU PRO PHE ARG ASP SEQRES 2 B 69 TYR VAL ASP ARG PHE TYR LYS THR LEU ARG ALA GLU GLN SEQRES 3 B 69 ALA SER GLN GLU VAL LYS ASN ALA ALA THR GLU THR LEU SEQRES 4 B 69 LEU VAL GLN ASN ALA ASN PRO ASP CYS LYS THR ILE LEU SEQRES 5 B 69 LYS ALA LEU GLY PRO GLY ALA THR LEU GLU GLU MET MET SEQRES 6 B 69 THR ALA CYS GLN SEQRES 1 C 129 PRO ARG THR LEU ASN ALA TRP VAL LYS VAL VAL GLU GLU SEQRES 2 C 129 LYS ALA PHE SER PRO GLU VAL ILE PRO MET PHE SER ALA SEQRES 3 C 129 LEU SER GLU GLY ALA THR PRO GLN ASP LEU ASN THR MET SEQRES 4 C 129 LEU ASN THR VAL GLY GLY HIS GLN ALA ALA MET GLN MET SEQRES 5 C 129 LEU LYS GLU THR ILE ASN GLU GLU ALA ALA GLU TRP ASP SEQRES 6 C 129 ARG LEU HIS PRO VAL HIS ALA GLY PRO ILE ALA PRO GLY SEQRES 7 C 129 GLN MET ARG GLU PRO ARG GLY SER ASP ILE ALA GLY THR SEQRES 8 C 129 THR SER THR LEU GLN GLU GLN ILE GLY TRP MET THR HIS SEQRES 9 C 129 ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR LYS ARG TRP SEQRES 10 C 129 ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG MET TYR SEQRES 1 D 69 LEU ASP ILE ARG GLN GLY PRO LYS GLU PRO PHE ARG ASP SEQRES 2 D 69 TYR VAL ASP ARG PHE TYR LYS THR LEU ARG ALA GLU GLN SEQRES 3 D 69 ALA SER GLN GLU VAL LYS ASN ALA ALA THR GLU THR LEU SEQRES 4 D 69 LEU VAL GLN ASN ALA ASN PRO ASP CYS LYS THR ILE LEU SEQRES 5 D 69 LYS ALA LEU GLY PRO GLY ALA THR LEU GLU GLU MET MET SEQRES 6 D 69 THR ALA CYS GLN CRYST1 1.000 1.000 1.000 1.00 1.00 1.00 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