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
(ATOM LINES ARE NOT SHOWN.)
END
