HEADER VIRAL PROTEIN 15-JUL-24 9CNV TITLE HIV-2 CA HEXAMER BOUND WITH CPSF6 PEPTIDE; ASSEMBLED VIA LIPOSOME TITLE 2 TEMPLATING COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN P24; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CA; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: HIV-2 CAPSID PROTEIN WITH C-TERMINAL GLY-SER-SER COMPND 7 LINKER TO HEXAHISTIDINE TAG FOLLOWING PROTEOLYTIC PROCESSING OF THE COMPND 8 N-TERMINAL MET.; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY COMPND 11 FACTOR SUBUNIT 6; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 68 KDA COMPND 14 SUBUNIT,CPSF 68 KDA SUBUNIT,CLEAVAGE FACTOR IM COMPLEX 68 KDA COMPND 15 SUBUNIT,CFIM68,PRE-MRNA CLEAVAGE FACTOR IM 68 KDA SUBUNIT,PROTEIN COMPND 16 HPBRII-4/7; COMPND 17 ENGINEERED: YES; COMPND 18 MUTATION: YES; COMPND 19 OTHER_DETAILS: TRUNCATION PEPTIDE OF CPSF6 (313-327) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 2; SOURCE 3 ORGANISM_TAXID: 11709; SOURCE 4 STRAIN: GL-AN; SOURCE 5 GENE: GAG-POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS HIV-2, CAPSID, IP6, CPSF6, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR M.COOK,C.FRENIERE,Y.XIONG REVDAT 1 05-MAR-25 9CNV 0 JRNL AUTH M.COOK,C.FRENIERE,C.WU,F.LOZANO,Y.XIONG JRNL TITL STRUCTURAL INSIGHTS INTO HIV-2 CA LATTICE FORMATION AND JRNL TITL 2 FG-POCKET BINDING REVEALED BY SINGLE-PARTICLE CRYO-EM. JRNL REF CELL REP V. 44 15245 2025 JRNL REFN ESSN 2211-1247 JRNL PMID 39864060 JRNL DOI 10.1016/J.CELREP.2025.115245 REMARK 2 REMARK 2 RESOLUTION. 3.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, COOT, COOT, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : THE HIV-2 CA PENTAMER CHAIN DERIVED FROM REMARK 3 MICELLE-TEMPLATED ICOSAHEDRA DESCRIBED IN THIS PUBLICATION WAS REMARK 3 USED AS AN INITIAL MODEL FOR FITTING. FLEXIBLE FITTING WAS USED REMARK 3 TO MOVE THE CTD INTO ITS PROPER LOCATION. BACKBONE TRACING WAS REMARK 3 USED TO MODEL THE CPSF6 PEPTIDE. 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) : 3.160 REMARK 3 NUMBER OF PARTICLES : 253734 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 9CNV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1000285882. 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-2 CAPSID PROTEIN ASSEMBLED REMARK 245 INTO A LATTICE VIA LIPOSOME REMARK 245 TEMPLATING AND THEN BOUND WITH REMARK 245 CPSF6 PEPTIDE.; HIV-2 CAPSID REMARK 245 PROTEIN; CPSF6 PEPTIDE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 10.70 REMARK 245 SAMPLE SUPPORT DETAILS : 15 MA DISCHARGE CURRENT. REMARK 245 SAMPLE VITRIFICATION DETAILS : GRIDS WERE DUAL-SIDE BLOTTED REMARK 245 WITH BLOT FORCE 0 FOR 5.5 SEC REMARK 245 BEFORE PLUNGE FREEZING IN REMARK 245 LIQUID ETHANE. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : C-TERMINALLY HEXAHISTIDINE REMARK 245 TAGGED HIV-2 CA ASSOCIATED WITH A LIPOSOME DECORATED WITH NINTA REMARK 245 HEADGROUPS WHICH RESULTS IN THE ASSEMBLY OF A LATTICE OF CA. REMARK 245 CPSF6 PEPTIDE WAS THEN INTRODUCED AND ALLOWED TO EQUILIBRATE REMARK 245 BINDING. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 81000 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C1). 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: 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 0.866000 0.000000 -35.18240 REMARK 350 BIOMT2 2 -0.866000 0.500000 0.000000 131.30220 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866000 0.000000 60.93740 REMARK 350 BIOMT2 3 -0.866000 -0.500000 0.000000 227.42230 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 192.23970 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 192.24020 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -0.500000 -0.866000 0.000000 227.42250 REMARK 350 BIOMT2 5 0.866000 -0.500000 0.000000 60.93810 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 0.500000 -0.866000 0.000000 131.30290 REMARK 350 BIOMT2 6 0.866000 0.500000 0.000000 -35.18220 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 GLY A 222 REMARK 465 GLY A 223 REMARK 465 PRO A 224 REMARK 465 GLY A 225 REMARK 465 GLN A 226 REMARK 465 LYS A 227 REMARK 465 ALA A 228 REMARK 465 ARG A 229 REMARK 465 LEU A 230 REMARK 465 MET A 231 REMARK 465 GLY A 232 REMARK 465 SER A 233 REMARK 465 SER A 234 REMARK 465 HIS A 235 REMARK 465 HIS A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 HIS A 239 REMARK 465 HIS A 240 REMARK 465 PRO B 13 REMARK 465 LEU B 14 REMARK 465 GLY B 15 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 ASP A 61 -169.02 -124.25 REMARK 500 ALA A 92 -133.77 54.99 REMARK 500 ARG A 99 -167.28 -124.80 REMARK 500 THR A 188 -60.80 -140.58 REMARK 500 ALA A 194 -166.00 -121.51 REMARK 500 ASN A 208 54.04 37.25 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 18 0.08 SIDE CHAIN REMARK 500 ARG A 70 0.15 SIDE CHAIN REMARK 500 ARG A 131 0.13 SIDE CHAIN REMARK 500 ARG A 143 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-45761 RELATED DB: EMDB REMARK 900 HIV-2 CA HEXAMER BOUND WITH CPSF6 PEPTIDE; ASSEMBLED VIA LIPOSOME REMARK 900 TEMPLATING DBREF 9CNV A 1 231 UNP P18042 POL_HV2G1 136 366 DBREF 9CNV B 1 15 UNP Q16630 CPSF6_HUMAN 313 327 SEQADV 9CNV GLY A 232 UNP P18042 EXPRESSION TAG SEQADV 9CNV SER A 233 UNP P18042 EXPRESSION TAG SEQADV 9CNV SER A 234 UNP P18042 EXPRESSION TAG SEQADV 9CNV HIS A 235 UNP P18042 EXPRESSION TAG SEQADV 9CNV HIS A 236 UNP P18042 EXPRESSION TAG SEQADV 9CNV HIS A 237 UNP P18042 EXPRESSION TAG SEQADV 9CNV HIS A 238 UNP P18042 EXPRESSION TAG SEQADV 9CNV HIS A 239 UNP P18042 EXPRESSION TAG SEQADV 9CNV HIS A 240 UNP P18042 EXPRESSION TAG SEQRES 1 A 240 PRO VAL GLN GLN THR GLY GLY GLY ASN TYR ILE HIS VAL SEQRES 2 A 240 PRO LEU SER PRO ARG THR LEU ASN ALA TRP VAL LYS LEU SEQRES 3 A 240 VAL GLU ASP LYS LYS PHE GLY ALA GLU VAL VAL PRO GLY SEQRES 4 A 240 PHE GLN ALA LEU SER GLU GLY CYS THR PRO TYR ASP ILE SEQRES 5 A 240 ASN GLN MET LEU ASN CYS VAL GLY ASP HIS GLN ALA ALA SEQRES 6 A 240 MET GLN ILE ILE ARG GLU ILE ILE ASN ASP GLU ALA ALA SEQRES 7 A 240 ASP TRP ASP ALA GLN HIS PRO ILE PRO GLY PRO LEU PRO SEQRES 8 A 240 ALA GLY GLN LEU ARG ASP PRO ARG GLY SER ASP ILE ALA SEQRES 9 A 240 GLY THR THR SER THR VAL GLU GLU GLN ILE GLN TRP MET SEQRES 10 A 240 TYR ARG PRO GLN ASN PRO VAL PRO VAL GLY ASN ILE TYR SEQRES 11 A 240 ARG ARG TRP ILE GLN ILE GLY LEU GLN LYS CYS VAL ARG SEQRES 12 A 240 MET TYR ASN PRO THR ASN ILE LEU ASP VAL LYS GLN GLY SEQRES 13 A 240 PRO LYS GLU PRO PHE GLN SER TYR VAL ASP ARG PHE TYR SEQRES 14 A 240 LYS SER LEU ARG ALA GLU GLN THR ASP PRO ALA VAL LYS SEQRES 15 A 240 ASN TRP MET THR GLN THR LEU LEU ILE GLN ASN ALA ASN SEQRES 16 A 240 PRO ASP CYS LYS LEU VAL LEU LYS GLY LEU GLY MET ASN SEQRES 17 A 240 PRO THR LEU GLU GLU MET LEU THR ALA CYS GLN GLY VAL SEQRES 18 A 240 GLY GLY PRO GLY GLN LYS ALA ARG LEU MET GLY SER SER SEQRES 19 A 240 HIS HIS HIS HIS HIS HIS SEQRES 1 B 15 PRO VAL LEU PHE PRO GLY GLN PRO PHE GLY GLN PRO PRO SEQRES 2 B 15 LEU GLY HET IHP A 301 36 HET IHP A 302 36 HETNAM IHP INOSITOL HEXAKISPHOSPHATE HETSYN IHP MYO-INOSITOL HEXAKISPHOSPHATE; INOSITOL 1,2,3,4,5,6- HETSYN 2 IHP HEXAKISPHOSPHATE FORMUL 3 IHP 2(C6 H18 O24 P6) HELIX 1 AA1 SER A 16 LYS A 30 1 15 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 99 GLY A 105 1 7 HELIX 6 AA6 THR A 109 TYR A 118 1 10 HELIX 7 AA7 PRO A 125 ASN A 146 1 22 HELIX 8 AA8 PRO A 160 GLU A 175 1 16 HELIX 9 AA9 ASP A 178 THR A 186 1 9 HELIX 10 AB1 THR A 188 ASN A 193 1 6 HELIX 11 AB2 ASP A 197 GLY A 204 1 8 HELIX 12 AB3 THR A 210 CYS A 218 1 9 SHEET 1 AA1 2 VAL A 2 GLN A 4 0 SHEET 2 AA1 2 TYR A 10 HIS A 12 -1 O ILE A 11 N GLN A 3 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