HEADER VIRUS LIKE PARTICLE 28-JAN-23 8FZC TITLE HIV-2 GAG CAPSID FROM IMMATURE VIRUS-LIKE PARTICLES COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPACER PEPTIDE 2; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: SP2,P1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (ISOLATE SOURCE 3 ROD); SOURCE 4 ORGANISM_TAXID: 11720; SOURCE 5 VARIANT: ISOLATE ROD; SOURCE 6 GENE: GAG; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 11 EXPRESSION_SYSTEM_ATCC_NUMBER: CRL-1573; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PN3 KEYWDS RETROVIRUS, LENTIVIRUS, GAG, CAPSID, HIV-2, LATTICE, VIRUS LIKE KEYWDS 2 PARTICLE EXPDTA ELECTRON MICROSCOPY AUTHOR N.TALLEDGE,W.ZHANG,L.M.MANSKY REVDAT 2 14-JUN-23 8FZC 1 JRNL REVDAT 1 07-JUN-23 8FZC 0 JRNL AUTH N.TALLEDGE,H.YANG,K.SHI,R.CORAY,G.YU,W.G.ARNDT,S.MENG, JRNL AUTH 2 G.C.BAXTER,L.M.MENDONCA,D.CASTANO-DIEZ,H.AIHARA,L.M.MANSKY, JRNL AUTH 3 W.ZHANG JRNL TITL HIV-2 IMMATURE PARTICLE MORPHOLOGY PROVIDES INSIGHTS INTO JRNL TITL 2 GAG LATTICE STABILITY AND VIRUS MATURATION. JRNL REF J.MOL.BIOL. V. 435 68143 2023 JRNL REFN ESSN 1089-8638 JRNL PMID 37150290 JRNL DOI 10.1016/J.JMB.2023.168143 REMARK 2 REMARK 2 RESOLUTION. 5.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, SERIALEM, GCTF, PHENIX, RELION, REMARK 3 RELION, RELION, RELION, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2WLV REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : 5.500 REMARK 3 NUMBER OF PARTICLES : 46017 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 8FZC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000271305. 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 REMARK 245 TYPE 2 (ISOLATE ROD) REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 10.00 REMARK 245 SAMPLE SUPPORT DETAILS : LEICA ACE600 GLOW DISCHARGER. REMARK 245 SAMPLE VITRIFICATION DETAILS : LEICA GP2 GRID PLUNGER. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : HIV-2 VLPS GENERATED BY GAG CO REMARK 245 -OVEREXPRESSED WITH HIV-2 ENV IN HEK293T CELLS AND PURIFIED FROM REMARK 245 MEDIA SUPERNATANT REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 2508 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 750.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2250.00 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 : 105000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTADECAMERIC REMARK 350 SOFTWARE USED: UCSF CHIMERA 1.16_B42360. REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 0.500057 0.865993 0.000423 -96.78577 REMARK 350 BIOMT2 2 -0.865993 0.500057 -0.000061 360.62198 REMARK 350 BIOMT3 2 -0.000265 -0.000336 1.000000 0.16275 REMARK 350 BIOMT1 3 -0.499963 0.866047 -0.000011 167.34201 REMARK 350 BIOMT2 3 -0.866047 -0.499963 0.000402 624.49313 REMARK 350 BIOMT3 3 0.000343 0.000210 1.000000 -0.12864 REMARK 350 BIOMT1 4 -1.000000 -0.000043 -0.000057 528.02298 REMARK 350 BIOMT2 4 0.000043 -1.000000 -0.000047 528.00291 REMARK 350 BIOMT3 4 -0.000057 -0.000047 1.000000 0.02536 REMARK 350 BIOMT1 5 -0.500047 -0.865998 0.000666 624.42606 REMARK 350 BIOMT2 5 0.865998 -0.500047 0.000019 167.38525 REMARK 350 BIOMT3 5 0.000316 0.000586 1.000000 -0.22722 REMARK 350 BIOMT1 6 0.500050 -0.865997 0.000250 360.52373 REMARK 350 BIOMT2 6 0.865997 0.500050 0.000455 -96.78174 REMARK 350 BIOMT3 6 -0.000520 -0.000011 1.000000 0.16400 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 LEU A 339 -60.61 -94.86 REMARK 500 ASN A 342 70.53 46.54 REMARK 500 GLN A 353 48.61 -82.57 REMARK 500 LEU B 339 -60.59 -94.85 REMARK 500 ASN B 342 70.50 46.57 REMARK 500 GLN B 353 48.64 -82.61 REMARK 500 LEU C 339 -60.57 -94.90 REMARK 500 ASN C 342 70.52 46.61 REMARK 500 GLN C 353 48.72 -82.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-29606 RELATED DB: EMDB REMARK 900 EMDB-29606 IS THE RECONSTRUCTION FROM THE SUBTOMOGRAM AVERAGING OF REMARK 900 IMMATURE HIV-2 PARTICLES REMARK 900 RELATED ID: EMD-29607 RELATED DB: EMDB REMARK 900 HIV-2 GAG CAPSID FROM IMMATURE VIRUS-LIKE PARTICLES DBREF 8FZC A 150 373 UNP P04590 GAG_HV2RO 150 373 DBREF 8FZC B 150 373 UNP P04590 GAG_HV2RO 150 373 DBREF 8FZC C 150 373 UNP P04590 GAG_HV2RO 150 373 SEQRES 1 A 224 SER PRO ARG THR LEU ASN ALA TRP VAL LYS LEU VAL GLU SEQRES 2 A 224 GLU LYS LYS PHE GLY ALA GLU VAL VAL PRO GLY PHE GLN SEQRES 3 A 224 ALA LEU SER GLU GLY CYS THR PRO TYR ASP ILE ASN GLN SEQRES 4 A 224 MET LEU ASN CYS VAL GLY ASP HIS GLN ALA ALA MET GLN SEQRES 5 A 224 ILE ILE ARG GLU ILE ILE ASN GLU GLU ALA ALA GLU TRP SEQRES 6 A 224 ASP VAL GLN HIS PRO ILE PRO GLY PRO LEU PRO ALA GLY SEQRES 7 A 224 GLN LEU ARG GLU PRO ARG GLY SER ASP ILE ALA GLY THR SEQRES 8 A 224 THR SER THR VAL GLU GLU GLN ILE GLN TRP MET PHE ARG SEQRES 9 A 224 PRO GLN ASN PRO VAL PRO VAL GLY ASN ILE TYR ARG ARG SEQRES 10 A 224 TRP ILE GLN ILE GLY LEU GLN LYS CYS VAL ARG MET TYR SEQRES 11 A 224 ASN PRO THR ASN ILE LEU ASP ILE LYS GLN GLY PRO LYS SEQRES 12 A 224 GLU PRO PHE GLN SER TYR VAL ASP ARG PHE TYR LYS SER SEQRES 13 A 224 LEU ARG ALA GLU GLN THR ASP PRO ALA VAL LYS ASN TRP SEQRES 14 A 224 MET THR GLN THR LEU LEU VAL GLN ASN ALA ASN PRO ASP SEQRES 15 A 224 CYS LYS LEU VAL LEU LYS GLY LEU GLY MET ASN PRO THR SEQRES 16 A 224 LEU GLU GLU MET LEU THR ALA CYS GLN GLY VAL GLY GLY SEQRES 17 A 224 PRO GLY GLN LYS ALA ARG LEU MET ALA GLU ALA LEU LYS SEQRES 18 A 224 GLU VAL ILE SEQRES 1 B 224 SER PRO ARG THR LEU ASN ALA TRP VAL LYS LEU VAL GLU SEQRES 2 B 224 GLU LYS LYS PHE GLY ALA GLU VAL VAL PRO GLY PHE GLN SEQRES 3 B 224 ALA LEU SER GLU GLY CYS THR PRO TYR ASP ILE ASN GLN SEQRES 4 B 224 MET LEU ASN CYS VAL GLY ASP HIS GLN ALA ALA MET GLN SEQRES 5 B 224 ILE ILE ARG GLU ILE ILE ASN GLU GLU ALA ALA GLU TRP SEQRES 6 B 224 ASP VAL GLN HIS PRO ILE PRO GLY PRO LEU PRO ALA GLY SEQRES 7 B 224 GLN LEU ARG GLU PRO ARG GLY SER ASP ILE ALA GLY THR SEQRES 8 B 224 THR SER THR VAL GLU GLU GLN ILE GLN TRP MET PHE ARG SEQRES 9 B 224 PRO GLN ASN PRO VAL PRO VAL GLY ASN ILE TYR ARG ARG SEQRES 10 B 224 TRP ILE GLN ILE GLY LEU GLN LYS CYS VAL ARG MET TYR SEQRES 11 B 224 ASN PRO THR ASN ILE LEU ASP ILE LYS GLN GLY PRO LYS SEQRES 12 B 224 GLU PRO PHE GLN SER TYR VAL ASP ARG PHE TYR LYS SER SEQRES 13 B 224 LEU ARG ALA GLU GLN THR ASP PRO ALA VAL LYS ASN TRP SEQRES 14 B 224 MET THR GLN THR LEU LEU VAL GLN ASN ALA ASN PRO ASP SEQRES 15 B 224 CYS LYS LEU VAL LEU LYS GLY LEU GLY MET ASN PRO THR SEQRES 16 B 224 LEU GLU GLU MET LEU THR ALA CYS GLN GLY VAL GLY GLY SEQRES 17 B 224 PRO GLY GLN LYS ALA ARG LEU MET ALA GLU ALA LEU LYS SEQRES 18 B 224 GLU VAL ILE SEQRES 1 C 224 SER PRO ARG THR LEU ASN ALA TRP VAL LYS LEU VAL GLU SEQRES 2 C 224 GLU LYS LYS PHE GLY ALA GLU VAL VAL PRO GLY PHE GLN SEQRES 3 C 224 ALA LEU SER GLU GLY CYS THR PRO TYR ASP ILE ASN GLN SEQRES 4 C 224 MET LEU ASN CYS VAL GLY ASP HIS GLN ALA ALA MET GLN SEQRES 5 C 224 ILE ILE ARG GLU ILE ILE ASN GLU GLU ALA ALA GLU TRP SEQRES 6 C 224 ASP VAL GLN HIS PRO ILE PRO GLY PRO LEU PRO ALA GLY SEQRES 7 C 224 GLN LEU ARG GLU PRO ARG GLY SER ASP ILE ALA GLY THR SEQRES 8 C 224 THR SER THR VAL GLU GLU GLN ILE GLN TRP MET PHE ARG SEQRES 9 C 224 PRO GLN ASN PRO VAL PRO VAL GLY ASN ILE TYR ARG ARG SEQRES 10 C 224 TRP ILE GLN ILE GLY LEU GLN LYS CYS VAL ARG MET TYR SEQRES 11 C 224 ASN PRO THR ASN ILE LEU ASP ILE LYS GLN GLY PRO LYS SEQRES 12 C 224 GLU PRO PHE GLN SER TYR VAL ASP ARG PHE TYR LYS SER SEQRES 13 C 224 LEU ARG ALA GLU GLN THR ASP PRO ALA VAL LYS ASN TRP SEQRES 14 C 224 MET THR GLN THR LEU LEU VAL GLN ASN ALA ASN PRO ASP SEQRES 15 C 224 CYS LYS LEU VAL LEU LYS GLY LEU GLY MET ASN PRO THR SEQRES 16 C 224 LEU GLU GLU MET LEU THR ALA CYS GLN GLY VAL GLY GLY SEQRES 17 C 224 PRO GLY GLN LYS ALA ARG LEU MET ALA GLU ALA LEU LYS SEQRES 18 C 224 GLU VAL ILE HELIX 1 AA1 SER A 150 LYS A 164 1 15 HELIX 2 AA2 GLU A 169 SER A 178 1 10 HELIX 3 AA3 THR A 182 GLY A 194 1 13 HELIX 4 AA4 HIS A 196 HIS A 218 1 23 HELIX 5 AA5 ARG A 233 ALA A 238 1 6 HELIX 6 AA6 THR A 243 ARG A 253 1 11 HELIX 7 AA7 PRO A 259 TYR A 279 1 21 HELIX 8 AA8 PRO A 294 GLU A 309 1 16 HELIX 9 AA9 ASP A 312 ASN A 327 1 16 HELIX 10 AB1 ASN A 329 GLY A 338 1 10 HELIX 11 AB2 THR A 344 GLN A 353 1 10 HELIX 12 AB3 GLY A 357 ILE A 373 1 17 HELIX 13 AB4 PRO B 151 LYS B 164 1 14 HELIX 14 AB5 GLU B 169 SER B 178 1 10 HELIX 15 AB6 THR B 182 GLY B 194 1 13 HELIX 16 AB7 HIS B 196 HIS B 218 1 23 HELIX 17 AB8 ARG B 233 ALA B 238 1 6 HELIX 18 AB9 THR B 243 ARG B 253 1 11 HELIX 19 AC1 PRO B 259 TYR B 279 1 21 HELIX 20 AC2 PRO B 294 GLU B 309 1 16 HELIX 21 AC3 ASP B 312 ASN B 327 1 16 HELIX 22 AC4 ASN B 329 GLY B 338 1 10 HELIX 23 AC5 THR B 344 GLN B 353 1 10 HELIX 24 AC6 GLY B 357 ILE B 373 1 17 HELIX 25 AC7 PRO C 151 LYS C 164 1 14 HELIX 26 AC8 GLU C 169 SER C 178 1 10 HELIX 27 AC9 THR C 182 GLY C 194 1 13 HELIX 28 AD1 HIS C 196 HIS C 218 1 23 HELIX 29 AD2 ARG C 233 ALA C 238 1 6 HELIX 30 AD3 THR C 243 ARG C 253 1 11 HELIX 31 AD4 PRO C 259 TYR C 279 1 21 HELIX 32 AD5 PRO C 294 GLU C 309 1 16 HELIX 33 AD6 ASP C 312 ASN C 327 1 16 HELIX 34 AD7 ASN C 329 GLY C 338 1 10 HELIX 35 AD8 THR C 344 GLN C 353 1 10 HELIX 36 AD9 GLY C 357 ILE C 373 1 17 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