HEADER VIRUS LIKE PARTICLE 16-FEB-23 8CKY TITLE HIV-1 MATURE CAPSID HEXAMER FROM CA-IP6 CLPS, BOUND TO NUP153 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NUCLEAR PORE COMPLEX PROTEIN NUP153; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: UNP RESIDUES 1407-1423; COMPND 9 SYNONYM: 153 KDA NUCLEOPORIN,NUCLEOPORIN NUP153; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: GAG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS CAPSID, HEXAMER, HIV-1, MATURE, NUP153, VIRUS LIKE PARTICLE EXPDTA ELECTRON MICROSCOPY AUTHOR J.C.V.STACEY,J.A.G.BRIGGS REVDAT 1 26-APR-23 8CKY 0 JRNL AUTH J.C.V.STACEY,A.TAN,J.M.LU,L.C.JAMES,R.A.DICK,J.A.G.BRIGGS JRNL TITL TWO STRUCTURAL SWITCHES IN HIV-1 CAPSID REGULATE CAPSID JRNL TITL 2 CURVATURE AND HOST FACTOR BINDING. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 57120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 37040417 JRNL DOI 10.1073/PNAS.2220557120 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOLO, EPU, CRYOSPARC, UCSF CHIMERA, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, ISOLDE, COOT, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 4XFX REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL 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) : 2.600 REMARK 3 NUMBER OF PARTICLES : 595899 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 8CKY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128314. 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 : HIV-1 MATURE CAPSID REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.50 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.10 REMARK 245 SAMPLE DETAILS : HEXAMER BOUND TO FG REPEAT REMARK 245 CONTAINING NUP153 PEPTIDE. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 4770 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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 : 130000 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: DODECAMERIC 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 350 BIOMT1 2 0.500000 -0.866025 0.000000 243.91750 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 -65.35750 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 422.47750 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 113.20250 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 357.12000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 357.12000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -0.500000 0.866025 0.000000 113.20250 REMARK 350 BIOMT2 5 -0.866025 -0.500000 0.000000 422.47750 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 -65.35750 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 243.91750 REMARK 350 BIOMT3 6 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 MET A 0 REMARK 465 ALA A 88 REMARK 465 GLY A 89 REMARK 465 PRO A 90 REMARK 465 ILE A 91 REMARK 465 ALA A 92 REMARK 465 PRO A 93 REMARK 465 GLY A 94 REMARK 465 GLN A 95 REMARK 465 GLY A 222 REMARK 465 GLY A 223 REMARK 465 PRO A 224 REMARK 465 GLY A 225 REMARK 465 HIS A 226 REMARK 465 LYS A 227 REMARK 465 ALA A 228 REMARK 465 ARG A 229 REMARK 465 VAL A 230 REMARK 465 LEU A 231 REMARK 465 THR B 1407 REMARK 465 ASN B 1408 REMARK 465 ASN B 1409 REMARK 465 SER B 1421 REMARK 465 SER B 1422 REMARK 465 THR B 1423 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 4 CG CD OE1 NE2 REMARK 470 ASN A 5 CG OD1 ND2 REMARK 470 GLN A 7 CG CD OE1 NE2 REMARK 470 GLN A 9 CG CD OE1 NE2 REMARK 470 MET A 10 CG SD CE REMARK 470 GLU A 98 CG CD OE1 OE2 REMARK 470 ASN A 121 CG OD1 ND2 REMARK 470 LYS A 158 CG CD CE NZ REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-16706 RELATED DB: EMDB REMARK 900 HIV-1 MATURE CAPSID HEXAMER FROM CA-IP6 CLPS, BOUND TO NUP153 REMARK 900 PEPTIDE DBREF 8CKY A 1 231 UNP B6DRA0 B6DRA0_9HIV1 133 363 DBREF 8CKY B 1407 1423 UNP P49790 NU153_HUMAN 1407 1423 SEQADV 8CKY MET A 0 UNP B6DRA0 INITIATING METHIONINE SEQRES 1 A 232 MET PRO ILE VAL GLN ASN LEU GLN GLY GLN MET VAL HIS SEQRES 2 A 232 GLN ALA ILE SER PRO ARG THR LEU ASN ALA TRP VAL LYS SEQRES 3 A 232 VAL VAL GLU GLU LYS ALA PHE SER PRO GLU VAL ILE PRO SEQRES 4 A 232 MET PHE SER ALA LEU SER GLU GLY ALA THR PRO GLN ASP SEQRES 5 A 232 LEU ASN THR MET LEU ASN THR VAL GLY GLY HIS GLN ALA SEQRES 6 A 232 ALA MET GLN MET LEU LYS GLU THR ILE ASN GLU GLU ALA SEQRES 7 A 232 ALA GLU TRP ASP ARG LEU HIS PRO VAL HIS ALA GLY PRO SEQRES 8 A 232 ILE ALA PRO GLY GLN MET ARG GLU PRO ARG GLY SER ASP SEQRES 9 A 232 ILE ALA GLY THR THR SER THR LEU GLN GLU GLN ILE GLY SEQRES 10 A 232 TRP MET THR HIS ASN PRO PRO ILE PRO VAL GLY GLU ILE SEQRES 11 A 232 TYR LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL SEQRES 12 A 232 ARG MET TYR SER PRO THR SER ILE LEU ASP ILE ARG GLN SEQRES 13 A 232 GLY PRO LYS GLU PRO PHE ARG ASP TYR VAL ASP ARG PHE SEQRES 14 A 232 TYR LYS THR LEU ARG ALA GLU GLN ALA SER GLN GLU VAL SEQRES 15 A 232 LYS ASN TRP MET THR GLU THR LEU LEU VAL GLN ASN ALA SEQRES 16 A 232 ASN PRO ASP CYS LYS THR ILE LEU LYS ALA LEU GLY PRO SEQRES 17 A 232 GLY ALA THR LEU GLU GLU MET MET THR ALA CYS GLN GLY SEQRES 18 A 232 VAL GLY GLY PRO GLY HIS LYS ALA ARG VAL LEU SEQRES 1 B 17 THR ASN ASN SER PRO SER GLY VAL PHE THR PHE GLY ALA SEQRES 2 B 17 ASN SER SER THR HELIX 1 AA1 SER A 16 ALA A 31 1 16 HELIX 2 AA2 GLU A 35 SER A 44 1 10 HELIX 3 AA3 THR A 48 VAL A 59 1 12 HELIX 4 AA4 HIS A 62 HIS A 84 1 23 HELIX 5 AA5 ARG A 100 ALA A 105 1 6 HELIX 6 AA6 THR A 110 THR A 119 1 10 HELIX 7 AA7 PRO A 125 SER A 146 1 22 HELIX 8 AA8 SER A 149 ILE A 153 5 5 HELIX 9 AA9 PRO A 160 GLN A 176 1 17 HELIX 10 AB1 SER A 178 ASN A 193 1 16 HELIX 11 AB2 ASN A 195 LEU A 205 1 11 HELIX 12 AB3 THR A 210 CYS A 218 1 9 SHEET 1 AA1 2 ILE A 2 GLN A 4 0 SHEET 2 AA1 2 MET A 10 HIS A 12 -1 O VAL A 11 N VAL A 3 CISPEP 1 ASN A 121 PRO A 122 0 -6.28 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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