HEADER VIRAL PROTEIN 05-FEB-16 5I1R TITLE QUANTITATIVE CHARACTERIZATION OF CONFIGURATIONAL SPACE SAMPLED BY HIV- TITLE 2 1 NUCLEOCAPSID USING SOLUTION NMR AND X-RAY SCATTERING COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOCAPSID PROTEIN P7; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PR55GAG; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: ZINC ATOMS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HXB2 SOURCE 3 ISOLATE); SOURCE 4 ORGANISM_COMMON: HIV-1; SOURCE 5 ORGANISM_TAXID: 11706; SOURCE 6 STRAIN: ISOLATE HXB2; SOURCE 7 GENE: GAG; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS VIRAL PROTEIN EXPDTA SOLUTION NMR; SOLUTION SCATTERING NUMMDL 21 AUTHOR L.DESHMUKH,C.D.SCHWIETERS,A.GRISHAEV,G.M.CLORE REVDAT 3 14-JUN-23 5I1R 1 COMPND REMARK REVDAT 2 29-JUN-16 5I1R 1 JRNL REVDAT 1 30-MAR-16 5I1R 0 JRNL AUTH L.DESHMUKH,C.D.SCHWIETERS,A.GRISHAEV,G.M.CLORE JRNL TITL QUANTITATIVE CHARACTERIZATION OF CONFIGURATIONAL SPACE JRNL TITL 2 SAMPLED BY HIV-1 NUCLEOCAPSID USING SOLUTION NMR, X-RAY JRNL TITL 3 SCATTERING AND PROTEIN ENGINEERING. JRNL REF CHEMPHYSCHEM V. 17 1548 2016 JRNL REFN ISSN 1439-7641 JRNL PMID 26946052 JRNL DOI 10.1002/CPHC.201600212 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.41 REMARK 3 AUTHORS : C. D. SCHWIETERS, J. J. KUSZEWSKI, N. TJANDRA, G. REMARK 3 M. CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5I1R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218105. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.2 MM [U-13C; U-15N; U-2H] REMARK 210 NUCLEOCAPSID PROTEIN OF HUMAN REMARK 210 IMMUNODEFICIENCY VIRUS 1 (HIV-1), REMARK 210 50 MM SODIUM CHLORIDE, 20 MM REMARK 210 SODIUM PHOSPHATE, 1 MM REMARK 210 DITHIOTHREITOL, 0.1 MM ZINC REMARK 210 CHLORIDE, 93% H2O/7% D2O; 0.2 MM REMARK 210 [U-13C; U-15N; U-2H] REMARK 210 NUCLEOCAPSID PROTEIN OF HUMAN REMARK 210 IMMUNODEFICIENCY VIRUS 1 (HIV-1), REMARK 210 50 MM SODIUM CHLORIDE, 20 MM REMARK 210 SODIUM PHOSPHATE, 1 MM REMARK 210 DITHIOTHREITOL, 0.1 MM ZINC REMARK 210 CHLORIDE, 5 % NEUTRAL BICELLES, REMARK 210 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D HNCACB; 2D ARTSY; 3D REMARK 210 QUNTITAIVE HNCO - NC'; 3D REMARK 210 QUNTITAIVE HNCO - CAC' REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ANALYSIS 2.2.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : ALL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 265 REMARK 265 EXPERIMENTAL DETAILS 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL 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 1 ASN A 382 -70.46 -171.80 REMARK 500 1 ASN A 382 156.31 62.77 REMARK 500 1 ASN A 382 -50.80 -173.99 REMARK 500 1 PHE A 383 -168.37 -57.58 REMARK 500 1 ARG A 384 98.94 -171.48 REMARK 500 1 ASN A 385 117.05 88.41 REMARK 500 1 ASN A 385 71.19 -164.27 REMARK 500 1 GLN A 386 -129.52 61.13 REMARK 500 1 GLN A 386 -116.88 34.89 REMARK 500 1 GLN A 386 -133.41 36.56 REMARK 500 1 ARG A 387 82.92 65.87 REMARK 500 2 ARG A 380 -45.30 -164.72 REMARK 500 2 ASN A 382 102.18 40.54 REMARK 500 2 PHE A 383 77.00 52.02 REMARK 500 2 ASN A 385 -154.00 49.44 REMARK 500 2 ASN A 385 -4.95 -165.30 REMARK 500 2 GLN A 386 -166.56 -68.45 REMARK 500 2 GLN A 386 152.12 57.47 REMARK 500 2 ARG A 387 140.60 65.57 REMARK 500 2 ARG A 387 42.63 92.43 REMARK 500 2 LYS A 388 175.05 -50.00 REMARK 500 3 PHE A 383 173.12 124.91 REMARK 500 3 GLN A 386 -161.11 -112.34 REMARK 500 3 ARG A 387 -4.78 -55.26 REMARK 500 3 LYS A 388 167.02 -48.08 REMARK 500 3 ARG A 429 75.04 -68.85 REMARK 500 4 ASN A 382 -124.23 -129.21 REMARK 500 4 PHE A 383 115.36 50.87 REMARK 500 4 PHE A 383 177.05 86.33 REMARK 500 4 PHE A 383 155.41 59.67 REMARK 500 4 PHE A 383 155.35 84.29 REMARK 500 4 ASN A 385 -141.24 73.84 REMARK 500 4 ASN A 385 -159.37 52.96 REMARK 500 4 ASN A 385 163.24 66.74 REMARK 500 4 ASN A 385 98.75 38.04 REMARK 500 4 ARG A 387 -47.71 -160.39 REMARK 500 4 ARG A 387 37.44 -92.80 REMARK 500 4 ARG A 387 -65.07 -173.52 REMARK 500 4 THR A 427 97.00 -69.76 REMARK 500 4 THR A 427 27.21 -64.26 REMARK 500 4 ARG A 429 171.29 -57.85 REMARK 500 4 ARG A 429 109.92 -18.53 REMARK 500 5 ARG A 380 -136.70 -152.23 REMARK 500 5 ASN A 382 33.22 -164.28 REMARK 500 5 ASN A 382 -152.21 -143.82 REMARK 500 5 ASN A 382 -80.45 -99.73 REMARK 500 5 PHE A 383 167.24 49.20 REMARK 500 5 ARG A 384 90.82 -50.43 REMARK 500 5 ASN A 385 100.73 79.30 REMARK 500 5 ASN A 385 -140.26 -140.58 REMARK 500 REMARK 500 THIS ENTRY HAS 316 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 8 ARG A 429 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 392 SG REMARK 620 2 CYS A 395 SG 112.0 REMARK 620 3 HIS A 400 NE2 98.6 101.6 REMARK 620 4 CYS A 405 SG 117.8 120.0 101.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 413 SG REMARK 620 2 CYS A 416 SG 109.2 REMARK 620 3 HIS A 421 NE2 100.4 105.1 REMARK 620 4 CYS A 426 SG 117.6 116.1 106.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 902 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30008 RELATED DB: BMRB DBREF 5I1R A 378 432 UNP P04591 GAG_HV1H2 378 432 SEQRES 1 A 55 MET GLN ARG GLY ASN PHE ARG ASN GLN ARG LYS ILE VAL SEQRES 2 A 55 LYS CYS PHE ASN CYS GLY LYS GLU GLY HIS THR ALA ARG SEQRES 3 A 55 ASN CYS ARG ALA PRO ARG LYS LYS GLY CYS TRP LYS CYS SEQRES 4 A 55 GLY LYS GLU GLY HIS GLN MET LYS ASP CYS THR GLU ARG SEQRES 5 A 55 GLN ALA ASN HET ZN A 901 1 HET ZN A 902 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) LINK SG CYS A 392 ZN ZN A 901 1555 1555 2.38 LINK SG CYS A 395 ZN ZN A 901 1555 1555 2.39 LINK NE2 HIS A 400 ZN ZN A 901 1555 1555 2.27 LINK SG CYS A 405 ZN ZN A 901 1555 1555 2.40 LINK SG CYS A 413 ZN ZN A 902 1555 1555 2.38 LINK SG CYS A 416 ZN ZN A 902 1555 1555 2.37 LINK NE2 HIS A 421 ZN ZN A 902 1555 1555 2.29 LINK SG CYS A 426 ZN ZN A 902 1555 1555 2.40 SITE 1 AC1 4 CYS A 392 CYS A 395 HIS A 400 CYS A 405 SITE 1 AC2 4 CYS A 413 CYS A 416 HIS A 421 CYS A 426 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 0.001000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.001000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001000 0.00000 MODEL 1