HEADER VIRAL PROTEIN 18-DEC-24 9MKQ TITLE MVV CA PENTAMER ASSEMBLED VIA LIPOSOME TEMPLATING COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN P25; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: MVV CA WITH C-TERMINAL HIS TAG WITH GSS LINKER. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VISNA-MAEDI VIRUS; SOURCE 3 ORGANISM_TAXID: 2169971; SOURCE 4 GENE: GAG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MVV, CAPSID, PENTAMER, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR F.ARIZAGA,C.FRENIERE,Y.XIONG REVDAT 1 08-OCT-25 9MKQ 0 JRNL AUTH F.ARIZAGA JR.,C.FRENIERE,J.S.REY,M.COOK,C.WU,J.R.PERILLA, JRNL AUTH 2 Y.XIONG JRNL TITL EXPLORING THE STRUCTURAL DIVERGENCE OF HIV AND SRLV JRNL TITL 2 LENTIVIRAL CAPSIDS. JRNL REF J.AM.CHEM.SOC. V. 147 32883 2025 JRNL REFN ESSN 1520-5126 JRNL PMID 40878534 JRNL DOI 10.1021/JACS.5C09436 REMARK 2 REMARK 2 RESOLUTION. 3.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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 : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL 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) : 3.250 REMARK 3 NUMBER OF PARTICLES : 239010 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 9MKQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1000290397. 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 : VISNA-MAEDI VIRUS 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 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2800.00 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 : 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 = C5). 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 0.309017 -0.951057 0.000000 226.27319 REMARK 350 BIOMT2 2 0.951057 0.309017 0.000000 -35.83806 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.809017 -0.587785 0.000000 330.27947 REMARK 350 BIOMT2 3 0.587785 -0.809017 0.000000 168.28597 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.809017 0.587785 0.000000 168.28570 REMARK 350 BIOMT2 4 -0.587785 -0.809017 0.000000 330.27961 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.309017 0.951057 0.000000 -35.83824 REMARK 350 BIOMT2 5 -0.951057 0.309017 0.000000 226.27316 REMARK 350 BIOMT3 5 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 216 REMARK 465 SER A 217 REMARK 465 GLU A 218 REMARK 465 GLY A 219 REMARK 465 PHE A 220 REMARK 465 GLY A 221 REMARK 465 SER A 222 REMARK 465 SER A 223 REMARK 465 HIS A 224 REMARK 465 HIS A 225 REMARK 465 HIS A 226 REMARK 465 HIS A 227 REMARK 465 HIS A 228 REMARK 465 HIS A 229 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 SER A 34 135.58 -34.80 REMARK 500 ARG A 199 6.69 -62.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-48334 RELATED DB: EMDB REMARK 900 MVV CA PENTAMER ASSEMBLED VIA LIPOSOME TEMPLATING DBREF 9MKQ A 1 220 UNP P03352 GAG_VILV 144 363 SEQADV 9MKQ GLY A 221 UNP P03352 EXPRESSION TAG SEQADV 9MKQ SER A 222 UNP P03352 EXPRESSION TAG SEQADV 9MKQ SER A 223 UNP P03352 EXPRESSION TAG SEQADV 9MKQ HIS A 224 UNP P03352 EXPRESSION TAG SEQADV 9MKQ HIS A 225 UNP P03352 EXPRESSION TAG SEQADV 9MKQ HIS A 226 UNP P03352 EXPRESSION TAG SEQADV 9MKQ HIS A 227 UNP P03352 EXPRESSION TAG SEQADV 9MKQ HIS A 228 UNP P03352 EXPRESSION TAG SEQADV 9MKQ HIS A 229 UNP P03352 EXPRESSION TAG SEQRES 1 A 229 PRO ILE VAL ASN LEU GLN ALA GLY GLY ARG SER TRP LYS SEQRES 2 A 229 ALA VAL GLU SER VAL VAL PHE GLN GLN LEU GLN THR VAL SEQRES 3 A 229 ALA MET GLN HIS GLY LEU VAL SER GLU ASP PHE GLU ARG SEQRES 4 A 229 GLN LEU ALA TYR TYR ALA THR THR TRP THR SER LYS ASP SEQRES 5 A 229 ILE LEU GLU VAL LEU ALA MET MET PRO GLY ASN ARG ALA SEQRES 6 A 229 GLN LYS GLU LEU ILE GLN GLY LYS LEU ASN GLU GLU ALA SEQRES 7 A 229 GLU ARG TRP VAL ARG GLN ASN PRO PRO GLY PRO ASN VAL SEQRES 8 A 229 LEU THR VAL ASP GLN ILE MET GLY VAL GLY GLN THR ASN SEQRES 9 A 229 GLN GLN ALA SER GLN ALA ASN MET ASP GLN ALA ARG GLN SEQRES 10 A 229 ILE CYS LEU GLN TRP VAL ILE THR ALA LEU ARG SER VAL SEQRES 11 A 229 ARG HIS MET SER HIS ARG PRO GLY ASN PRO MET LEU VAL SEQRES 12 A 229 LYS GLN LYS ASN THR GLU SER TYR GLU ASP PHE ILE ALA SEQRES 13 A 229 ARG LEU LEU GLU ALA ILE ASP ALA GLU PRO VAL THR ASP SEQRES 14 A 229 PRO ILE LYS THR TYR LEU LYS VAL THR LEU SER TYR THR SEQRES 15 A 229 ASN ALA SER THR ASP CYS GLN LYS GLN MET ASP ARG THR SEQRES 16 A 229 LEU GLY THR ARG VAL GLN GLN ALA THR VAL GLU GLU LYS SEQRES 17 A 229 MET GLN ALA CYS ARG ASP VAL GLY SER GLU GLY PHE GLY SEQRES 18 A 229 SER SER HIS HIS HIS HIS HIS HIS HELIX 1 AA1 GLU A 16 GLY A 31 1 16 HELIX 2 AA2 SER A 34 THR A 46 1 13 HELIX 3 AA3 THR A 49 MET A 60 1 12 HELIX 4 AA4 ASN A 63 ASN A 85 1 23 HELIX 5 AA5 THR A 93 GLY A 99 1 7 HELIX 6 AA6 THR A 103 GLN A 109 1 7 HELIX 7 AA7 MET A 112 HIS A 135 1 24 HELIX 8 AA8 SER A 150 GLU A 165 1 16 HELIX 9 AA9 THR A 168 ALA A 184 1 17 HELIX 10 AB1 SER A 185 LEU A 196 1 12 HELIX 11 AB2 GLY A 197 GLN A 202 5 6 HELIX 12 AB3 THR A 204 ASP A 214 1 11 SHEET 1 AA1 2 ILE A 2 ASN A 4 0 SHEET 2 AA1 2 ARG A 10 TRP A 12 -1 O SER A 11 N VAL A 3 SSBOND 1 CYS A 188 CYS A 212 1555 1555 2.06 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 TER 1702 VAL A 215 CONECT 1485 1675 CONECT 1675 1485 MASTER 152 0 0 12 2 0 0 6 1701 1 2 18 END