HEADER VIRAL PROTEIN/DNA 08-OCT-10 2L4L TITLE STRUCTURAL INSIGHTS INTO THE CTAR DNA RECOGNITION BY THE HIV-1 TITLE 2 NUCLEOCAPSID PROTEIN: ROLE OF SUGAR DEOXYRIBOSES IN THE BINDING TITLE 3 POLARITY OF NC COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 NUCLEOCAPSID PROTEIN NCP7; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*TP*GP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 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 KEYWDS NC(11-55):MINI-CTAR, VIRAL PROTEIN-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.BAZZI,L.ZARGARIAN,F.CHAMINADE,C.BOUDIER,H.DE ROCQUIGNY,B.RENE, AUTHOR 2 Y.MELY,P.FOSSE,O.MAUFFRET REVDAT 2 17-AUG-11 2L4L 1 JRNL VERSN REVDAT 1 08-DEC-10 2L4L 0 JRNL AUTH A.BAZZI,L.ZARGARIAN,F.CHAMINADE,C.BOUDIER,H.DE ROCQUIGNY, JRNL AUTH 2 B.RENE,Y.MELY,P.FOSSE,O.MAUFFRET JRNL TITL STRUCTURAL INSIGHTS INTO THE CTAR DNA RECOGNITION BY THE JRNL TITL 2 HIV-1 NUCLEOCAPSID PROTEIN: ROLE OF SUGAR DEOXYRIBOSES IN JRNL TITL 3 THE BINDING POLARITY OF NC. JRNL REF NUCLEIC ACIDS RES. V. 39 3903 2011 JRNL REFN ISSN 0305-1048 JRNL PMID 21227929 JRNL DOI 10.1093/NAR/GKQ1290 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L4L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-OCT-10. REMARK 100 THE RCSB ID CODE IS RCSB101949. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM HIV-1 NUCLEOCAPSID PROTEIN REMARK 210 NCP7(11-55)-1, 1 MM DNA, 10 % D2O REMARK 210 -3, 90 % H2O-4, 3 MM RZN-5, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR_NIH REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 H CYS A 36 O LYS A 41 1.41 REMARK 500 O CYS A 49 H GLU A 51 1.55 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 HIS A 23 -164.75 -178.39 REMARK 500 1 ALA A 25 -67.10 2.47 REMARK 500 1 ALA A 30 167.06 -43.81 REMARK 500 1 LYS A 41 176.50 -41.11 REMARK 500 1 HIS A 44 -178.20 -174.08 REMARK 500 1 GLN A 45 -156.04 -77.72 REMARK 500 1 THR A 50 63.27 -60.64 REMARK 500 1 GLN A 53 89.47 13.23 REMARK 500 2 HIS A 23 -167.80 -179.75 REMARK 500 2 ALA A 25 -63.43 -3.49 REMARK 500 2 ALA A 30 164.14 -38.64 REMARK 500 2 LYS A 41 174.01 -40.00 REMARK 500 2 HIS A 44 -175.08 -174.18 REMARK 500 2 GLN A 45 -158.90 -82.26 REMARK 500 3 HIS A 23 -165.63 -175.13 REMARK 500 3 ALA A 25 -70.01 -7.89 REMARK 500 3 ALA A 30 162.80 -47.17 REMARK 500 3 LYS A 41 174.91 -40.32 REMARK 500 3 HIS A 44 -179.57 -178.30 REMARK 500 3 THR A 50 68.19 -63.25 REMARK 500 4 HIS A 23 -164.84 -168.08 REMARK 500 4 ALA A 25 -66.15 -5.09 REMARK 500 4 ALA A 30 165.67 -40.42 REMARK 500 4 LYS A 41 161.99 -43.68 REMARK 500 4 HIS A 44 -170.55 -174.22 REMARK 500 4 GLN A 45 -156.52 -87.68 REMARK 500 4 THR A 50 69.06 -56.78 REMARK 500 4 ARG A 52 58.35 120.32 REMARK 500 4 ALA A 54 69.61 -105.99 REMARK 500 5 CYS A 18 -34.15 -150.47 REMARK 500 5 HIS A 23 -165.43 -165.24 REMARK 500 5 ALA A 25 -34.39 -27.28 REMARK 500 5 ALA A 30 165.49 -35.83 REMARK 500 5 GLU A 42 165.09 96.17 REMARK 500 5 HIS A 44 -174.86 -177.86 REMARK 500 5 GLN A 45 -152.24 -70.60 REMARK 500 5 THR A 50 70.23 -55.96 REMARK 500 6 HIS A 23 -167.22 -169.30 REMARK 500 6 ALA A 25 -68.98 -4.95 REMARK 500 6 ALA A 30 165.70 -36.57 REMARK 500 6 LYS A 41 159.64 -38.14 REMARK 500 6 HIS A 44 -176.78 -177.55 REMARK 500 6 GLN A 45 -151.76 -80.40 REMARK 500 7 CYS A 18 -44.73 -132.55 REMARK 500 7 HIS A 23 -165.80 -179.67 REMARK 500 7 ALA A 25 -64.17 -17.16 REMARK 500 7 ALA A 30 164.25 -34.57 REMARK 500 7 LYS A 41 172.62 -43.64 REMARK 500 7 HIS A 44 -168.89 -174.28 REMARK 500 7 GLN A 45 -154.39 -90.66 REMARK 500 REMARK 500 THIS ENTRY HAS 77 RAMACHANDRAN OUTLIERS. 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 1 ZN A 56 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 23 NE2 REMARK 620 2 CYS A 15 SG 108.2 REMARK 620 3 CYS A 18 SG 129.6 104.8 REMARK 620 4 CYS A 28 SG 97.7 126.2 92.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 57 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 36 SG REMARK 620 2 HIS A 44 NE2 103.0 REMARK 620 3 CYS A 49 SG 130.5 109.2 REMARK 620 4 CYS A 39 SG 95.7 115.5 102.9 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 56 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 57 REMARK 999 REMARK 999 SEQUENCE REMARK 999 A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY REMARK 999 EXIST. DBREF 2L4L A 11 55 PDB 2L4L 2L4L 11 55 DBREF 2L4L B 123 126 PDB 2L4L 2L4L 123 126 SEQRES 1 A 45 LYS ASN VAL LYS CYS PHE ASN CYS GLY LYS GLU GLY HIS SEQRES 2 A 45 THR ALA ARG ASN CYS ARG ALA PRO ARG LYS LYS GLY CYS SEQRES 3 A 45 TRP LYS CYS GLY LYS GLU GLY HIS GLN MET LYS ASP CYS SEQRES 4 A 45 THR GLU ARG GLN ALA ASN SEQRES 1 B 4 DC DT DG DG HET ZN A 56 1 HET ZN A 57 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) LINK NE2 HIS A 23 ZN ZN A 56 1555 1555 1.88 LINK SG CYS A 15 ZN ZN A 56 1555 1555 2.02 LINK SG CYS A 36 ZN ZN A 57 1555 1555 2.07 LINK NE2 HIS A 44 ZN ZN A 57 1555 1555 2.07 LINK SG CYS A 49 ZN ZN A 57 1555 1555 2.31 LINK SG CYS A 18 ZN ZN A 56 1555 1555 2.35 LINK SG CYS A 28 ZN ZN A 56 1555 1555 2.38 LINK SG CYS A 39 ZN ZN A 57 1555 1555 2.45 SITE 1 AC1 4 CYS A 15 CYS A 18 HIS A 23 CYS A 28 SITE 1 AC2 4 CYS A 36 CYS A 39 HIS A 44 CYS A 49 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 MODEL 1