HEADER VIRAL PROTEIN 09-JUN-16 5L93 TITLE AN ATOMIC MODEL OF HIV-1 CA-SP1 REVEALS STRUCTURES REGULATING ASSEMBLY TITLE 2 AND MATURATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN P24; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: PR55GAG; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SOURCE 3 SUBTYPE B (ISOLATE NY5); SOURCE 4 ORGANISM_COMMON: HIV-1; SOURCE 5 ORGANISM_TAXID: 11698; SOURCE 6 STRAIN: ISOLATE NY5; SOURCE 7 GENE: GAG; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HIV-1 CAPSID SP1, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR F.K.M.SCHUR,M.OBR,W.J.H.HAGEN,W.WAN,J.J.ARJEN,J.M.KIRKPATRICK, AUTHOR 2 C.SACHSE,H.-G.KRAEUSSLICH,J.A.G.BRIGGS REVDAT 7 11-DEC-19 5L93 1 SCALE REVDAT 6 17-OCT-18 5L93 1 REMARK CRYST1 REVDAT 5 02-AUG-17 5L93 1 REVDAT 4 22-FEB-17 5L93 1 REMARK REVDAT 3 10-AUG-16 5L93 1 JRNL REVDAT 2 27-JUL-16 5L93 1 JRNL REVDAT 1 13-JUL-16 5L93 0 JRNL AUTH F.K.SCHUR,M.OBR,W.J.HAGEN,W.WAN,A.J.JAKOBI,J.M.KIRKPATRICK, JRNL AUTH 2 C.SACHSE,H.G.KRAUSSLICH,J.A.BRIGGS JRNL TITL AN ATOMIC MODEL OF HIV-1 CAPSID-SP1 REVEALS STRUCTURES JRNL TITL 2 REGULATING ASSEMBLY AND MATURATION. JRNL REF SCIENCE V. 353 506 2016 JRNL REFN ESSN 1095-9203 JRNL PMID 27417497 JRNL DOI 10.1126/SCIENCE.AAF9620 REMARK 2 REMARK 2 RESOLUTION. 3.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM, CTFFIND, CTFPHASEFLIP, UCSF REMARK 3 CHIMERA, CCP4 PACKAGE, PHENIX, COOT, REMARK 3 AV3, TOM TOOLBOX, AV3, TOM TOOLBOX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1L6N REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : OTHER 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) : 3.900 REMARK 3 NUMBER OF PARTICLES : 128733 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 5L93 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000325. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SUBTOMOGRAM AVERAGING 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) : 5.00 REMARK 245 SAMPLE SUPPORT DETAILS : AT 20 MA REMARK 245 SAMPLE VITRIFICATION DETAILS : 10NM COLLOIDAL GOLD WAS ADDED REMARK 245 TO THE SAMPLE PRIOR TO PLUNGE REMARK 245 FREEZING. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : VIRUS-LIKE PARTICLES WERE REMARK 245 OBTAINED BY IN VITRO ASSEMBLY OF A TRUNCATED GAG CONSTRUCT REMARK 245 (DELTAMACANCSP2) IN PRESENCE OF THE MATURATION INHIBITOR REMARK 245 BEVIRIMAT 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 K2 QUANTUM (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 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) : 3.40 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 : NANOPROBE 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: OCTADECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTADECAMERIC REMARK 350 SOFTWARE USED: PISA 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 0.500000 -0.866025 0.000000 177.03689 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 -47.43689 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 306.63689 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 82.16311 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 259.20000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 259.20000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -0.500000 0.866025 0.000000 82.16311 REMARK 350 BIOMT2 5 -0.866025 -0.500000 0.000000 306.63689 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 -47.43689 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 177.03689 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 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 GLU A 167 -55.67 -130.80 REMARK 500 GLN A 195 -71.89 -100.22 REMARK 500 PRO A 222 54.68 -90.29 REMARK 500 PRO A 225 56.70 -68.20 REMARK 500 ARG A 229 -143.37 62.20 REMARK 500 THR A 240 -3.35 69.02 REMARK 500 GLU B 167 -55.99 -130.69 REMARK 500 GLN B 195 -71.95 -100.18 REMARK 500 PRO B 222 54.72 -90.31 REMARK 500 PRO B 225 56.72 -68.19 REMARK 500 ARG B 229 -143.40 62.10 REMARK 500 THR B 240 -3.45 69.00 REMARK 500 GLU C 167 -55.90 -130.84 REMARK 500 GLN C 195 -71.94 -100.20 REMARK 500 PRO C 222 54.69 -90.36 REMARK 500 PRO C 225 56.75 -68.27 REMARK 500 ARG C 229 -143.36 62.08 REMARK 500 THR C 240 -3.50 68.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-4015 RELATED DB: EMDB DBREF 5L93 A 148 371 UNP P12493 GAG_HV1N5 148 371 DBREF 5L93 B 148 371 UNP P12493 GAG_HV1N5 148 371 DBREF 5L93 C 148 371 UNP P12493 GAG_HV1N5 148 371 SEQRES 1 A 224 SER PRO ARG THR LEU ASN ALA TRP VAL LYS VAL VAL GLU SEQRES 2 A 224 GLU LYS ALA PHE SER PRO GLU VAL ILE PRO MET PHE SER SEQRES 3 A 224 ALA LEU SER GLU GLY ALA THR PRO GLN ASP LEU ASN THR SEQRES 4 A 224 MET LEU ASN THR VAL GLY GLY HIS GLN ALA ALA MET GLN SEQRES 5 A 224 MET LEU LYS GLU THR ILE ASN GLU GLU ALA ALA GLU TRP SEQRES 6 A 224 ASP ARG LEU HIS PRO VAL HIS ALA GLY PRO ILE ALA PRO SEQRES 7 A 224 GLY GLN MET ARG GLU PRO ARG GLY SER ASP ILE ALA GLY SEQRES 8 A 224 THR THR SER THR LEU GLN GLU GLN ILE GLY TRP MET THR SEQRES 9 A 224 HIS ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR LYS ARG SEQRES 10 A 224 TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG MET TYR SEQRES 11 A 224 SER PRO THR SER ILE LEU ASP ILE ARG GLN GLY PRO LYS SEQRES 12 A 224 GLU PRO PHE ARG ASP TYR VAL ASP ARG PHE TYR LYS THR SEQRES 13 A 224 LEU ARG ALA GLU GLN ALA SER GLN GLU VAL LYS ASN TRP SEQRES 14 A 224 MET THR GLU THR LEU LEU VAL GLN ASN ALA ASN PRO ASP SEQRES 15 A 224 CYS LYS THR ILE LEU LYS ALA LEU GLY PRO GLY ALA THR SEQRES 16 A 224 LEU GLU GLU MET MET THR ALA CYS GLN GLY VAL GLY GLY SEQRES 17 A 224 PRO GLY HIS LYS ALA ARG VAL LEU ALA GLU ALA MET SER SEQRES 18 A 224 GLN VAL THR SEQRES 1 B 224 SER PRO ARG THR LEU ASN ALA TRP VAL LYS VAL VAL GLU SEQRES 2 B 224 GLU LYS ALA PHE SER PRO GLU VAL ILE PRO MET PHE SER SEQRES 3 B 224 ALA LEU SER GLU GLY ALA THR PRO GLN ASP LEU ASN THR SEQRES 4 B 224 MET LEU ASN THR VAL GLY GLY HIS GLN ALA ALA MET GLN SEQRES 5 B 224 MET LEU LYS GLU THR ILE ASN GLU GLU ALA ALA GLU TRP SEQRES 6 B 224 ASP ARG LEU HIS PRO VAL HIS ALA GLY PRO ILE ALA PRO SEQRES 7 B 224 GLY GLN MET ARG GLU PRO ARG GLY SER ASP ILE ALA GLY SEQRES 8 B 224 THR THR SER THR LEU GLN GLU GLN ILE GLY TRP MET THR SEQRES 9 B 224 HIS ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR LYS ARG SEQRES 10 B 224 TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG MET TYR SEQRES 11 B 224 SER PRO THR SER ILE LEU ASP ILE ARG GLN GLY PRO LYS SEQRES 12 B 224 GLU PRO PHE ARG ASP TYR VAL ASP ARG PHE TYR LYS THR SEQRES 13 B 224 LEU ARG ALA GLU GLN ALA SER GLN GLU VAL LYS ASN TRP SEQRES 14 B 224 MET THR GLU THR LEU LEU VAL GLN ASN ALA ASN PRO ASP SEQRES 15 B 224 CYS LYS THR ILE LEU LYS ALA LEU GLY PRO GLY ALA THR SEQRES 16 B 224 LEU GLU GLU MET MET THR ALA CYS GLN GLY VAL GLY GLY SEQRES 17 B 224 PRO GLY HIS LYS ALA ARG VAL LEU ALA GLU ALA MET SER SEQRES 18 B 224 GLN VAL THR SEQRES 1 C 224 SER PRO ARG THR LEU ASN ALA TRP VAL LYS VAL VAL GLU SEQRES 2 C 224 GLU LYS ALA PHE SER PRO GLU VAL ILE PRO MET PHE SER SEQRES 3 C 224 ALA LEU SER GLU GLY ALA THR PRO GLN ASP LEU ASN THR SEQRES 4 C 224 MET LEU ASN THR VAL GLY GLY HIS GLN ALA ALA MET GLN SEQRES 5 C 224 MET LEU LYS GLU THR ILE ASN GLU GLU ALA ALA GLU TRP SEQRES 6 C 224 ASP ARG LEU HIS PRO VAL HIS ALA GLY PRO ILE ALA PRO SEQRES 7 C 224 GLY GLN MET ARG GLU PRO ARG GLY SER ASP ILE ALA GLY SEQRES 8 C 224 THR THR SER THR LEU GLN GLU GLN ILE GLY TRP MET THR SEQRES 9 C 224 HIS ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR LYS ARG SEQRES 10 C 224 TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG MET TYR SEQRES 11 C 224 SER PRO THR SER ILE LEU ASP ILE ARG GLN GLY PRO LYS SEQRES 12 C 224 GLU PRO PHE ARG ASP TYR VAL ASP ARG PHE TYR LYS THR SEQRES 13 C 224 LEU ARG ALA GLU GLN ALA SER GLN GLU VAL LYS ASN TRP SEQRES 14 C 224 MET THR GLU THR LEU LEU VAL GLN ASN ALA ASN PRO ASP SEQRES 15 C 224 CYS LYS THR ILE LEU LYS ALA LEU GLY PRO GLY ALA THR SEQRES 16 C 224 LEU GLU GLU MET MET THR ALA CYS GLN GLY VAL GLY GLY SEQRES 17 C 224 PRO GLY HIS LYS ALA ARG VAL LEU ALA GLU ALA MET SER SEQRES 18 C 224 GLN VAL THR HELIX 1 AA1 SER A 148 GLU A 161 1 14 HELIX 2 AA2 GLU A 167 GLU A 177 1 11 HELIX 3 AA3 THR A 180 THR A 190 1 11 HELIX 4 AA4 GLN A 195 HIS A 216 1 22 HELIX 5 AA5 ARG A 232 ALA A 237 1 6 HELIX 6 AA6 THR A 242 HIS A 252 1 11 HELIX 7 AA7 PRO A 257 TYR A 277 1 21 HELIX 8 AA8 PRO A 292 GLU A 307 1 16 HELIX 9 AA9 SER A 310 ASN A 325 1 16 HELIX 10 AB1 ASN A 327 ALA A 336 1 10 HELIX 11 AB2 THR A 342 GLY A 352 1 11 HELIX 12 AB3 GLY A 355 THR A 371 1 17 HELIX 13 AB4 PRO B 149 GLU B 161 1 13 HELIX 14 AB5 GLU B 167 GLU B 177 1 11 HELIX 15 AB6 THR B 180 THR B 190 1 11 HELIX 16 AB7 GLN B 195 HIS B 216 1 22 HELIX 17 AB8 ARG B 232 ALA B 237 1 6 HELIX 18 AB9 THR B 242 HIS B 252 1 11 HELIX 19 AC1 PRO B 257 TYR B 277 1 21 HELIX 20 AC2 PRO B 292 GLU B 307 1 16 HELIX 21 AC3 SER B 310 ASN B 325 1 16 HELIX 22 AC4 ASN B 327 ALA B 336 1 10 HELIX 23 AC5 THR B 342 GLY B 352 1 11 HELIX 24 AC6 GLY B 355 THR B 371 1 17 HELIX 25 AC7 PRO C 149 GLU C 161 1 13 HELIX 26 AC8 GLU C 167 GLU C 177 1 11 HELIX 27 AC9 THR C 180 THR C 190 1 11 HELIX 28 AD1 GLN C 195 HIS C 216 1 22 HELIX 29 AD2 ARG C 232 ALA C 237 1 6 HELIX 30 AD3 THR C 242 HIS C 252 1 11 HELIX 31 AD4 PRO C 257 TYR C 277 1 21 HELIX 32 AD5 PRO C 292 GLU C 307 1 16 HELIX 33 AD6 SER C 310 ASN C 325 1 16 HELIX 34 AD7 ASN C 327 ALA C 336 1 10 HELIX 35 AD8 THR C 342 GLY C 352 1 11 HELIX 36 AD9 GLY C 355 THR C 371 1 17 CISPEP 1 GLY A 221 PRO A 222 0 -4.59 CISPEP 2 ASN A 253 PRO A 254 0 -0.33 CISPEP 3 GLY B 221 PRO B 222 0 -4.61 CISPEP 4 ASN B 253 PRO B 254 0 -0.33 CISPEP 5 GLY C 221 PRO C 222 0 -4.52 CISPEP 6 ASN C 253 PRO C 254 0 -0.44 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