HEADER VIRUS LIKE PARTICLE 06-FEB-24 8VXV TITLE HIV-1 R18L CA HEXAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN P24; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CA; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: GAG-POL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CAPSID, VIRUS LIKE PARTICLE EXPDTA ELECTRON MICROSCOPY AUTHOR R.T.SCHIRRA,O.PORNILLOS,B.K.GANSER-PORNILLOS REVDAT 1 31-DEC-25 8VXV 0 JRNL AUTH R.T.SCHIRRA,N.F.B.DOS SANTOS,B.K.GANSER-PORNILLOS, JRNL AUTH 2 O.PORNILLOS JRNL TITL ARG18 SUBSTITUTIONS REVEAL THE CAPACITY OF THE HIV-1 CAPSID JRNL TITL 2 PROTEIN FOR NON-FULLERENE ASSEMBLY. JRNL REF VIRUSES V. 16 2024 JRNL REFN ESSN 1999-4915 JRNL PMID 39066201 JRNL DOI 10.3390/V16071038 REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 8CKV REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 249.000 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) : 3.700 REMARK 3 NUMBER OF PARTICLES : 737346 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 8VXV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281395. 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 CA R18L HEXAMER FROM REMARK 245 CAPSID-LIKE PARTICLES ASSEMBLED REMARK 245 IN 1 M NACL 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 : NULL 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C6). 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 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 144.31239 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 -38.66838 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 249.95638 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 66.97562 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 211.28799 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 211.28800 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -0.500000 0.866025 0.000000 66.97560 REMARK 350 BIOMT2 5 -0.866025 -0.500000 0.000000 249.95638 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 -38.66839 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 144.31238 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 VAL A 3 REMARK 465 GLN A 4 REMARK 465 ASN A 5 REMARK 465 LEU A 6 REMARK 465 GLN A 7 REMARK 465 GLY A 8 REMARK 465 GLN A 9 REMARK 465 MET A 10 REMARK 465 VAL A 11 REMARK 465 PRO A 85 REMARK 465 VAL A 86 REMARK 465 HIS A 87 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 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 GLU A 45 CG CD OE1 OE2 REMARK 470 ASP A 81 CG OD1 OD2 REMARK 470 MET A 96 CG SD CE REMARK 470 GLU A 98 CG CD OE1 OE2 REMARK 470 GLN A 112 CG CD OE1 NE2 REMARK 470 GLU A 113 CG CD OE1 OE2 REMARK 470 ASN A 121 CG OD1 ND2 REMARK 470 SER A 146 OG REMARK 470 ASP A 152 CG OD1 OD2 REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 ASP A 166 CG OD1 OD2 REMARK 470 GLN A 176 CG CD OE1 NE2 REMARK 470 GLU A 180 CG CD OE1 OE2 REMARK 470 LYS A 182 CG CD CE NZ REMARK 470 LYS A 199 CG CD CE NZ REMARK 470 LYS A 203 CG CD CE NZ 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 A 31 -131.93 55.79 REMARK 500 PRO A 34 -6.72 -58.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-43641 RELATED DB: EMDB REMARK 900 HIV-1 R18L CA HEXAMER REMARK 900 RELATED ID: 8VXW RELATED DB: PDB REMARK 900 HIV-1 R18L CA PENTAMER DBREF 8VXV A 1 231 UNP P12497 POL_HV1N5 133 363 SEQADV 8VXV LEU A 18 UNP P12497 ARG 150 CONFLICT SEQRES 1 A 231 PRO ILE VAL GLN ASN LEU GLN GLY GLN MET VAL HIS GLN SEQRES 2 A 231 ALA ILE SER PRO LEU THR LEU ASN ALA TRP VAL LYS VAL SEQRES 3 A 231 VAL GLU GLU LYS ALA PHE SER PRO GLU VAL ILE PRO MET SEQRES 4 A 231 PHE SER ALA LEU SER GLU GLY ALA THR PRO GLN ASP LEU SEQRES 5 A 231 ASN THR MET LEU ASN THR VAL GLY GLY HIS GLN ALA ALA SEQRES 6 A 231 MET GLN MET LEU LYS GLU THR ILE ASN GLU GLU ALA ALA SEQRES 7 A 231 GLU TRP ASP ARG LEU HIS PRO VAL HIS ALA GLY PRO ILE SEQRES 8 A 231 ALA PRO GLY GLN MET ARG GLU PRO ARG GLY SER ASP ILE SEQRES 9 A 231 ALA GLY THR THR SER THR LEU GLN GLU GLN ILE GLY TRP SEQRES 10 A 231 MET THR HIS ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR SEQRES 11 A 231 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG SEQRES 12 A 231 MET TYR SER PRO THR SER ILE LEU ASP ILE ARG GLN GLY SEQRES 13 A 231 PRO LYS GLU PRO PHE ARG ASP TYR VAL ASP ARG PHE TYR SEQRES 14 A 231 LYS THR LEU ARG ALA GLU GLN ALA SER GLN GLU VAL LYS SEQRES 15 A 231 ASN TRP MET THR GLU THR LEU LEU VAL GLN ASN ALA ASN SEQRES 16 A 231 PRO ASP CYS LYS THR ILE LEU LYS ALA LEU GLY PRO GLY SEQRES 17 A 231 ALA THR LEU GLU GLU MET MET THR ALA CYS GLN GLY VAL SEQRES 18 A 231 GLY GLY PRO GLY HIS LYS ALA ARG VAL LEU 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 THR A 58 1 11 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 HIS A 120 1 11 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 GLU A 175 1 16 HELIX 10 AB1 SER A 178 ASN A 193 1 16 HELIX 11 AB2 ASN A 195 GLY A 206 1 12 HELIX 12 AB3 THR A 210 CYS A 218 1 9 CISPEP 1 ASN A 121 PRO A 122 0 0.21 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 TER 1525 VAL A 221 MASTER 195 0 0 12 0 0 0 6 1524 1 0 18 END