HEADER VIRAL PROTEIN 10-SEP-25 9Y7J TITLE HIV-1 CA HEXAMER FROM PURIFIED VIRAL CORES BOUND TO LENACAPAVIR, C6 TITLE 2 SYMMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN P24; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: CA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 STRAIN: SG3; SOURCE 5 GENE: GAG-POL; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: 293T; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PROVIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PSG3DELTAENV KEYWDS CAPSID, NATIVE PURIFIED HIV CORES, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR N.F.BARROS DOS SANTOS,B.K.GANSER-PORNILLOS,O.PORNILLOS REVDAT 1 25-FEB-26 9Y7J 0 JRNL AUTH N.F.BARROS DOS SANTOS,B.K.GANSER-PORNILLOS,O.PORNILLOS JRNL TITL HIV-1 CA HEXAMER FROM PURIFIED VIRAL CORES BOUND TO JRNL TITL 2 LENACAPAVIR, C6 SYMMETRY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, PHENIX, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 7URN REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 100.100 REMARK 3 REMARK 3 FITTING PROCEDURE : REAL-SPACE REFINEMENT 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) : 2.830 REMARK 3 NUMBER OF PARTICLES : 106476 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 9Y7J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1000298328. 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 : HUMAN IMMUNODEFICIENCY VIRUS 1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : PROVIRAL PLASMID PSG3DELTAENV REMARK 245 WAS TRANSFECTED INTO 293T CELLS. VIRUS PARTICLES RELEASED INTO REMARK 245 THE CULTURE MEDIA WERE HARVESTED. VIRAL CORES WERE PURIFIED. 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL 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 : NULL 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: 11-MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: L 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 221.54199 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 -59.36200 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 383.72198 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 102.81800 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 324.35999 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 324.35999 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -0.500000 0.866025 0.000000 102.81800 REMARK 350 BIOMT2 5 -0.866025 -0.500000 0.000000 383.72198 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 -59.36200 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 221.54199 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 7 0.500000 -0.866025 0.000000 221.54199 REMARK 350 BIOMT2 7 0.866025 0.500000 0.000000 -59.36200 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 8 -0.500000 -0.866025 0.000000 383.72198 REMARK 350 BIOMT2 8 0.866025 -0.500000 0.000000 102.81800 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 9 -1.000000 0.000000 0.000000 324.35999 REMARK 350 BIOMT2 9 0.000000 -1.000000 0.000000 324.35999 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 10 -0.500000 0.866025 0.000000 102.81800 REMARK 350 BIOMT2 10 -0.866025 -0.500000 0.000000 383.72198 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 11 0.500000 0.866025 0.000000 -59.36200 REMARK 350 BIOMT2 11 -0.866025 0.500000 0.000000 221.54199 REMARK 350 BIOMT3 11 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 GLN L 87 REMARK 465 ALA L 88 REMARK 465 GLY L 89 REMARK 465 PRO L 90 REMARK 465 VAL L 91 REMARK 465 ALA L 92 REMARK 465 PRO L 93 REMARK 465 GLY L 94 REMARK 465 GLN L 95 REMARK 465 GLY L 222 REMARK 465 GLY L 223 REMARK 465 PRO L 224 REMARK 465 GLY L 225 REMARK 465 HIS L 226 REMARK 465 LYS L 227 REMARK 465 ALA L 228 REMARK 465 ARG L 229 REMARK 465 VAL L 230 REMARK 465 LEU L 231 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 ALA L 31 -144.70 55.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-71816 RELATED DB: EMDB REMARK 900 UNBOUND CA HEXAMER REMARK 900 RELATED ID: EMD-71817 RELATED DB: EMDB REMARK 900 UNBOUND CA HEXAMER REMARK 900 RELATED ID: 9PRY RELATED DB: PDB REMARK 900 UNBOUND CA HEXAMER REMARK 900 RELATED ID: 9PRZ RELATED DB: PDB REMARK 900 UNBOUND CA HEXAMER REMARK 900 RELATED ID: EMD-72657 RELATED DB: EMDB REMARK 900 HIV-1 CA HEXAMER FROM PURIFIED VIRAL CORES BOUND TO LENACAPAVIR, C6 REMARK 900 SYMMETRY DBREF 9Y7J L 1 231 UNP Q73368 POL_HV1B9 133 363 SEQADV 9Y7J ARG L 154 UNP Q73368 LYS 286 CONFLICT SEQADV 9Y7J SER L 160 UNP Q73368 PRO 292 CONFLICT SEQRES 1 L 231 PRO ILE VAL GLN ASN ILE GLN GLY GLN MET VAL HIS GLN SEQRES 2 L 231 ALA ILE SER PRO ARG THR LEU ASN ALA TRP VAL LYS VAL SEQRES 3 L 231 VAL GLU GLU LYS ALA PHE SER PRO GLU VAL ILE PRO MET SEQRES 4 L 231 PHE SER ALA LEU SER GLU GLY ALA THR PRO GLN ASP LEU SEQRES 5 L 231 ASN THR MET LEU ASN THR VAL GLY GLY HIS GLN ALA ALA SEQRES 6 L 231 MET GLN MET LEU LYS GLU THR ILE ASN GLU GLU ALA ALA SEQRES 7 L 231 GLU TRP ASP ARG LEU HIS PRO VAL GLN ALA GLY PRO VAL SEQRES 8 L 231 ALA PRO GLY GLN MET ARG GLU PRO ARG GLY SER ASP ILE SEQRES 9 L 231 ALA GLY THR THR SER THR LEU GLN GLU GLN ILE GLY TRP SEQRES 10 L 231 MET THR ASN ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR SEQRES 11 L 231 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG SEQRES 12 L 231 MET TYR SER PRO SER SER ILE LEU ASP ILE ARG GLN GLY SEQRES 13 L 231 PRO LYS GLU SER PHE ARG ASP TYR VAL ASP ARG PHE TYR SEQRES 14 L 231 LYS THR LEU ARG ALA GLU GLN ALA SER GLN GLU VAL LYS SEQRES 15 L 231 ASN TRP MET THR GLU THR LEU LEU VAL GLN ASN ALA ASN SEQRES 16 L 231 PRO ASP CYS LYS THR ILE LEU LYS ALA LEU GLY PRO GLY SEQRES 17 L 231 ALA THR LEU GLU GLU MET MET THR ALA CYS GLN GLY VAL SEQRES 18 L 231 GLY GLY PRO GLY HIS LYS ALA ARG VAL LEU HET QNG L 300 64 HETNAM QNG LENACAPAVIR HETSYN QNG SUNLENCA; GS-CA1; GS-6207 FORMUL 2 QNG C39 H32 CL F10 N7 O5 S2 HELIX 1 AA1 SER L 16 LYS L 30 1 15 HELIX 2 AA2 GLU L 35 SER L 44 1 10 HELIX 3 AA3 THR L 48 THR L 58 1 11 HELIX 4 AA4 HIS L 62 HIS L 84 1 23 HELIX 5 AA5 ARG L 100 ALA L 105 1 6 HELIX 6 AA6 THR L 110 ASN L 120 1 11 HELIX 7 AA7 PRO L 125 TYR L 145 1 21 HELIX 8 AA8 SER L 149 ILE L 153 5 5 HELIX 9 AA9 SER L 160 GLU L 175 1 16 HELIX 10 AB1 SER L 178 ASN L 193 1 16 HELIX 11 AB2 ASN L 195 GLY L 206 1 12 HELIX 12 AB3 THR L 210 ALA L 217 1 8 SHEET 1 AA1 2 ILE L 2 GLN L 4 0 SHEET 2 AA1 2 MET L 10 HIS L 12 -1 O VAL L 11 N VAL L 3 CISPEP 1 ASN L 121 PRO L 122 0 -1.09 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 CONECT 1664 1668 1678 1719 CONECT 1665 1666 1695 1713 CONECT 1666 1665 1667 CONECT 1667 1666 1675 CONECT 1668 1664 1675 1713 CONECT 1669 1670 1674 1675 CONECT 1670 1669 1671 1714 CONECT 1671 1670 1672 1676 CONECT 1672 1671 1673 1727 CONECT 1673 1672 1674 CONECT 1674 1669 1673 CONECT 1675 1667 1668 1669 CONECT 1676 1671 1715 1716 CONECT 1677 1702 1714 CONECT 1678 1664 1679 CONECT 1679 1678 1680 1684 CONECT 1680 1679 1681 CONECT 1681 1680 1682 1704 CONECT 1682 1681 1683 CONECT 1683 1682 1684 1703 CONECT 1684 1679 1683 CONECT 1685 1686 1719 1720 CONECT 1686 1685 1717 CONECT 1687 1688 1689 1690 CONECT 1688 1687 1692 1717 CONECT 1689 1687 1694 1718 CONECT 1690 1687 1691 1693 CONECT 1691 1690 1692 1693 CONECT 1692 1688 1691 1705 1706 CONECT 1693 1690 1691 CONECT 1694 1689 1707 1708 1712 CONECT 1695 1665 1696 CONECT 1696 1695 1697 CONECT 1697 1696 1699 1700 1726 CONECT 1698 1725 CONECT 1699 1697 CONECT 1700 1697 CONECT 1701 1726 CONECT 1702 1677 1709 1710 1711 CONECT 1703 1683 CONECT 1704 1681 CONECT 1705 1692 CONECT 1706 1692 CONECT 1707 1694 CONECT 1708 1694 CONECT 1709 1702 CONECT 1710 1702 CONECT 1711 1702 CONECT 1712 1694 CONECT 1713 1665 1668 CONECT 1714 1670 1677 1715 CONECT 1715 1676 1714 CONECT 1716 1676 1725 CONECT 1717 1686 1688 1718 CONECT 1718 1689 1717 CONECT 1719 1664 1685 CONECT 1720 1685 CONECT 1721 1725 CONECT 1722 1725 CONECT 1723 1726 CONECT 1724 1726 CONECT 1725 1698 1716 1721 1722 CONECT 1726 1697 1701 1723 1724 CONECT 1727 1672 MASTER 183 0 1 12 2 0 0 6 1726 1 64 18 END