HEADER VIRAL PROTEIN/RNA 07-MAY-21 7MRL TITLE STRUCTURE OF HIV-1 MATRIX DOMAIN BOUND TO HUMAN TRNALYS3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 MATRIX DOMAIN; COMPND 3 CHAIN: C, B; COMPND 4 SYNONYM: MATRIX PROTEIN P17,NUCLEOCAPSID PROTEIN P7; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TRNA LYS3; COMPND 8 CHAIN: A; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11676; SOURCE 5 GENE: GAG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS HIV-1, GAG, MATRIX DOMAIN, RNA-PROTEIN INTERACTION, TRNA, TRANSFER KEYWDS 2 RNA, RIBONUCLEOPROTEIN COMPLEX, VIRAL PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.BOU-NADER,J.ZHANG REVDAT 6 25-OCT-23 7MRL 1 REMARK REVDAT 5 07-JUN-23 7MRL 1 REMARK REVDAT 4 22-SEP-21 7MRL 1 JRNL REVDAT 3 25-AUG-21 7MRL 1 JRNL REVDAT 2 18-AUG-21 7MRL 1 REMARK REVDAT 1 11-AUG-21 7MRL 0 JRNL AUTH C.BOU-NADER,F.MUECKSCH,J.B.BROWN,J.M.GORDON,A.YORK,C.PENG, JRNL AUTH 2 R.GHIRLANDO,M.F.SUMMERS,P.D.BIENIASZ,J.ZHANG JRNL TITL HIV-1 MATRIX-TRNA COMPLEX STRUCTURE REVEALS BASIS FOR HOST JRNL TITL 2 CONTROL OF GAG LOCALIZATION. JRNL REF CELL HOST MICROBE V. 29 1421 2021 JRNL REFN ESSN 1934-6069 JRNL PMID 34384537 JRNL DOI 10.1016/J.CHOM.2021.07.006 REMARK 2 REMARK 2 RESOLUTION. 3.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 13657 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2578 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.1100 - 8.2395 0.99 1287 148 0.1623 0.1977 REMARK 3 2 8.2395 - 6.5463 1.00 1283 142 0.1560 0.1810 REMARK 3 3 6.5463 - 5.7207 1.00 1272 142 0.1629 0.1810 REMARK 3 4 5.7207 - 5.1985 1.00 1299 145 0.1575 0.1965 REMARK 3 5 5.1985 - 4.8263 1.00 1306 145 0.1522 0.2222 REMARK 3 6 4.8263 - 4.5421 1.00 1269 142 0.1513 0.1444 REMARK 3 7 4.5421 - 4.3148 1.00 1290 141 0.1624 0.2338 REMARK 3 8 4.3148 - 4.1271 1.00 1274 143 0.1930 0.2566 REMARK 3 9 4.1271 - 3.9683 1.00 1277 140 0.2039 0.2532 REMARK 3 10 3.9683 - 3.8314 1.00 1290 143 0.1937 0.2514 REMARK 3 11 3.8314 - 3.7117 1.00 1301 148 0.2132 0.2249 REMARK 3 12 3.7117 - 3.6057 1.00 1309 145 0.2310 0.3227 REMARK 3 13 3.6057 - 3.5108 1.00 1276 134 0.2652 0.2795 REMARK 3 14 3.5108 - 3.4251 1.00 1267 139 0.2809 0.3185 REMARK 3 15 3.4251 - 3.3473 1.00 1302 149 0.3015 0.3469 REMARK 3 16 3.3473 - 3.2761 1.00 1311 144 0.3161 0.3207 REMARK 3 17 3.2761 - 3.2106 1.00 1249 143 0.3301 0.3618 REMARK 3 18 3.2106 - 3.1500 0.98 1266 145 0.3649 0.3756 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 15.8852 2.4711 180.3268 REMARK 3 T TENSOR REMARK 3 T11: 0.9205 T22: 1.0393 REMARK 3 T33: 1.0138 T12: 0.0799 REMARK 3 T13: -0.0143 T23: -0.0873 REMARK 3 L TENSOR REMARK 3 L11: 0.5838 L22: 1.9321 REMARK 3 L33: 0.3316 L12: 0.6696 REMARK 3 L13: 0.1315 L23: -0.4773 REMARK 3 S TENSOR REMARK 3 S11: -0.1408 S12: -0.0090 S13: -0.0194 REMARK 3 S21: 0.0342 S22: 0.1568 S23: -0.1393 REMARK 3 S31: -0.0450 S32: 0.1909 S33: -0.0119 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN B REMARK 3 SELECTION : (CHAIN C AND RESID 7 THROUGH 107) REMARK 3 ATOM PAIRS NUMBER : 614 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7MRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000252651. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13692 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.150 REMARK 200 RESOLUTION RANGE LOW (A) : 45.114 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 18.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.230 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRIES 1HIW & 1FIR REMARK 200 REMARK 200 REMARK: CUBIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, 20% PEG500 MME, 10% REMARK 280 PEG20000, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 48.35850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.42300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 73.01050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 48.35850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.42300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 73.01050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 48.35850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.42300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.01050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 48.35850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 54.42300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 73.01050 REMARK 290 REMARK 290 REMARK: NULL 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, A, B 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 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 C 2 REMARK 465 ALA C 3 REMARK 465 ARG C 4 REMARK 465 ALA C 5 REMARK 465 SER C 6 REMARK 465 ASN C 109 REMARK 465 GLY B 2 REMARK 465 ALA B 3 REMARK 465 ARG B 4 REMARK 465 ALA B 5 REMARK 465 SER B 6 REMARK 465 GLN B 108 REMARK 465 ASN B 109 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 GLN C 90 1.48 -69.81 REMARK 500 SER B 67 -9.72 -57.30 REMARK 500 REMARK 500 REMARK: NULL DBREF 7MRL C 2 109 UNP C1JB69 C1JB69_9HIV1 2 109 DBREF 7MRL A 1 75 PDB 7MRL 7MRL 1 75 DBREF 7MRL B 2 109 UNP C1JB69 C1JB69_9HIV1 2 109 SEQRES 1 C 108 GLY ALA ARG ALA SER VAL LEU SER GLY GLY GLU LEU ASP SEQRES 2 C 108 LYS TRP GLU LYS ILE ARG LEU ARG PRO GLY GLY LYS LYS SEQRES 3 C 108 GLN TYR LYS LEU LYS HIS ILE VAL TRP ALA SER ARG GLU SEQRES 4 C 108 LEU GLU ARG PHE ALA VAL ASN PRO GLY LEU LEU GLU THR SEQRES 5 C 108 SER GLU GLY CYS ARG GLN ILE LEU GLY GLN LEU GLN PRO SEQRES 6 C 108 SER LEU GLN THR GLY SER GLU GLU LEU ARG SER LEU TYR SEQRES 7 C 108 ASN THR ILE ALA VAL LEU TYR CYS VAL HIS GLN ARG ILE SEQRES 8 C 108 ASP VAL LYS ASP THR LYS GLU ALA LEU ASP LYS ILE GLU SEQRES 9 C 108 GLU GLU GLN ASN SEQRES 1 A 75 A C C C G G A U A G C U C SEQRES 2 A 75 A G U C G G U A G A G C A SEQRES 3 A 75 U C A G A C A G G A A A C SEQRES 4 A 75 U G U C U G A G G G U C C SEQRES 5 A 75 A G G G U U C A A G U C C SEQRES 6 A 75 C U G U U C G G G U SEQRES 1 B 108 GLY ALA ARG ALA SER VAL LEU SER GLY GLY GLU LEU ASP SEQRES 2 B 108 LYS TRP GLU LYS ILE ARG LEU ARG PRO GLY GLY LYS LYS SEQRES 3 B 108 GLN TYR LYS LEU LYS HIS ILE VAL TRP ALA SER ARG GLU SEQRES 4 B 108 LEU GLU ARG PHE ALA VAL ASN PRO GLY LEU LEU GLU THR SEQRES 5 B 108 SER GLU GLY CYS ARG GLN ILE LEU GLY GLN LEU GLN PRO SEQRES 6 B 108 SER LEU GLN THR GLY SER GLU GLU LEU ARG SER LEU TYR SEQRES 7 B 108 ASN THR ILE ALA VAL LEU TYR CYS VAL HIS GLN ARG ILE SEQRES 8 B 108 ASP VAL LYS ASP THR LYS GLU ALA LEU ASP LYS ILE GLU SEQRES 9 B 108 GLU GLU GLN ASN HET MG A 101 1 HETNAM MG MAGNESIUM ION FORMUL 4 MG MG 2+ HELIX 1 AA1 SER C 9 GLU C 17 1 9 HELIX 2 AA2 LYS C 30 PHE C 44 1 15 HELIX 3 AA3 ASN C 47 GLU C 52 5 6 HELIX 4 AA4 THR C 53 GLY C 71 1 19 HELIX 5 AA5 SER C 72 GLN C 90 1 19 HELIX 6 AA6 ASP C 96 GLN C 108 1 13 HELIX 7 AA7 SER B 9 GLU B 17 1 9 HELIX 8 AA8 LYS B 30 PHE B 44 1 15 HELIX 9 AA9 ASN B 47 GLU B 52 5 6 HELIX 10 AB1 THR B 53 GLN B 65 1 13 HELIX 11 AB2 PRO B 66 GLN B 69 5 4 HELIX 12 AB3 SER B 72 GLN B 90 1 19 HELIX 13 AB4 ASP B 96 GLU B 107 1 12 LINK OP2 U A 12 MG MG A 101 1555 1555 2.44 CRYST1 96.717 108.846 146.021 90.00 90.00 90.00 I 2 2 2 16 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 0.010339 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006848 0.00000