1NCP - Header Asymmetric Unit

HEADER VIRAL PROTEIN 27-NOV-91 1NCP

TITLE STRUCTURAL CHARACTERIZATION OF A 39 RESIDUE SYNTHETIC TITLE 2 PEPTIDE CONTAINING THE TWO ZINC BINDING DOMAINS FROM THE TITLE 3 HIV-1 P7 NUCLEOCAPSID PROTEIN BY CD AND NMR SPECTROSCOPY

COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 P7 NUCLEOCAPSID PROTEIN; COMPND 3 CHAIN: N; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HIV-1 P7 NUCLEOCAPSID PROTEIN; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 6 ORGANISM_TAXID: 11676

KEYWDS NUCLEOCAPSID PROTEIN, VIRAL PROTEIN

EXPDTA SOLUTION NMR

AUTHOR G.M.CLORE,J.G.OMICHINSKI,A.M.GRONENBORN

REVDAT 3 24-FEB-09 1NCP 1 VERSN REVDAT 2 01-APR-03 1NCP 1 JRNL REVDAT 1 31-OCT-93 1NCP 0

JRNL AUTH J.G.OMICHINSKI,G.M.CLORE,K.SAKAGUCHI,E.APPELLA, JRNL AUTH 2 A.M.GRONENBORN JRNL TITL STRUCTURAL CHARACTERIZATION OF A 39-RESIDUE JRNL TITL 2 SYNTHETIC PEPTIDE CONTAINING THE TWO ZINC BINDING JRNL TITL 3 DOMAINS FROM THE HIV-1 P7 NUCLEOCAPSID PROTEIN BY JRNL TITL 4 CD AND NMR SPECTROSCOPY. JRNL REF FEBS LETT. V. 292 25 1991 JRNL REFN ISSN 0014-5793 JRNL PMID 1959614 JRNL DOI 10.1016/0014-5793(91)80825-N

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THIS ENTRY CONTAINS SOLUTION NMR STRUCTURE OF A 39 RESIDUE REMARK 3 SYNTHETIC PEPTIDE CONTAINING THE TWO ZINC BINDING DOMAINS REMARK 3 FROM THE HIV-1 P7 NUCLEOCAPSID PROTEIN. THE TWO DOMAINS REMARK 3 ARE COMPLETELY INDEPENDENT AND WERE SOLVED SEPARATELY. THE REMARK 3 FIRST DOMAIN (CHAIN *N*, RESIDUES 1 - 17) WAS BASED ON 147 REMARK 3 APPROXIMATE INTERPROTON DISTANCE RESTRAINTS. THE SECOND REMARK 3 DOMAIN (CHAIN *C*, RESIDUES 22 - 39) WAS BASED ON 148 REMARK 3 APPROXIMATE INTERPROTON DISTANCE RESTRAINTS. THE LINKER REMARK 3 REGION IS HIGHLY FLEXIBLE AND CANNOT BE DEFINED FROM THE REMARK 3 NMR DATA. REMARK 3 REMARK 3 THE METHOD USED TO DETERMINE THE STRUCTURES IS THE HYBRID REMARK 3 METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED REMARK 3 ANNEALING METHOD (NILGES, CLORE, AND GRONENBORN, FEBS REMARK 3 LETT. 229, 317 (1988)). REMARK 3 REMARK 3 A TOTAL OF 15 SIMULATED ANNEALING STRUCTURES WAS CALCULATED REMARK 3 FOR EACH DOMAIN. THE COORDINATES OF THE DOMAINS WERE THEN REMARK 3 AVERAGED AND SUBJECTED TO RESTRAINED REGULARIZATION TO REMARK 3 YIELD THE RESTRAINED MINIMIZED STRUCTURES. ONLY THESE REMARK 3 COORDINATES ARE LISTED. THE FIRST CHAIN IS THE N-TERMINAL REMARK 3 DOMAIN, AND THE SECOND IS THE C-TERMINAL DOMAIN. REMARK 3 REMARK 3 THE FIELD PRESENTED IN COLUMNS 61 - 66 IN THIS COORDINATE REMARK 3 FILE REPRESENTS THE ATOMIC RMS DEVIATION OF THE INDIVIDUAL REMARK 3 STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS FOR EACH REMARK 3 DOMAIN. REMARK 3 REMARK 3 THE COORDINATES OF THE TWO DOMAINS HAVE BEEN BEST FITTED TO REMARK 3 EACH OTHER.

REMARK 4 REMARK 4 1NCP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 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 C 61 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS N 16 SG REMARK 620 2 CYS C 27 SG 107.5 REMARK 620 3 HIS C 32 NE2 110.4 109.3 REMARK 620 4 HIS N 11 NE2 117.9 105.7 7.5 REMARK 620 5 CYS N 6 SG 116.3 8.8 105.3 100.8 REMARK 620 6 CYS C 24 SG 112.8 109.0 107.8 103.5 103.7 REMARK 620 7 CYS N 3 SG 115.6 106.4 107.4 102.8 100.9 3.1 REMARK 620 8 CYS C 37 SG 3.2 110.3 110.3 117.8 119.1 110.1 112.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN N 60 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 27 SG REMARK 620 2 HIS C 32 NE2 115.9 REMARK 620 3 HIS N 11 NE2 113.3 8.1 REMARK 620 4 CYS N 6 SG 9.7 113.2 109.3 REMARK 620 5 CYS C 24 SG 116.9 114.2 110.8 112.4 REMARK 620 6 CYS N 3 SG 114.4 114.4 110.5 109.4 3.7 REMARK 620 7 CYS C 37 SG 103.0 100.6 108.7 112.7 102.8 106.2 REMARK 620 8 CYS N 16 SG 100.6 100.6 108.7 110.3 105.2 108.6 2.8 REMARK 620 N 1 2 3 4 5 6 7

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN N 60 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 61

DBREF 1NCP N 1 17 UNP P04585 POL_HV1H2 389 405 DBREF 1NCP C 22 39 UNP P24740 POL_HV1U4 410 427

SEQRES 1 N 17 VAL LYS CYS PHE ASN CYS GLY LYS GLU GLY HIS THR ALA SEQRES 2 N 17 ARG ASN CYS ARG SEQRES 1 C 18 LYS GLY CYS TRP LYS CYS GLY LYS GLU GLY HIS GLN MET SEQRES 2 C 18 LYS ASP CYS THR GLU

HET ZN N 60 1 HET ZN C 61 1

HETNAM ZN ZINC ION

FORMUL 3 ZN 2(ZN 2+)

SHEET 1 A 2 LYS N 2 CYS N 16 0 SHEET 2 A 2 CYS C 24 CYS C 37 1 N CYS C 24 O LYS N 2

SSBOND 1 CYS N 3 CYS C 24 1555 1555 0.18 SSBOND 2 CYS N 6 CYS C 27 1555 1555 0.39 SSBOND 3 CYS N 16 CYS C 37 1555 1555 0.34

LINK ZN ZN C 61 SG CYS N 16 1555 1555 1.98 LINK ZN ZN C 61 SG CYS C 27 1555 1555 2.30 LINK ZN ZN C 61 NE2 HIS C 32 1555 1555 2.00 LINK ZN ZN C 61 NE2 HIS N 11 1555 1555 2.10 LINK ZN ZN C 61 SG CYS N 6 1555 1555 2.45 LINK ZN ZN C 61 SG CYS C 24 1555 1555 2.29 LINK ZN ZN C 61 SG CYS N 3 1555 1555 2.42 LINK ZN ZN C 61 SG CYS C 37 1555 1555 2.30 LINK ZN ZN N 60 SG CYS C 27 1555 1555 2.20 LINK ZN ZN N 60 NE2 HIS C 32 1555 1555 1.94 LINK ZN ZN N 60 NE2 HIS N 11 1555 1555 2.00 LINK ZN ZN N 60 SG CYS N 6 1555 1555 2.30 LINK ZN ZN N 60 SG CYS C 24 1555 1555 2.19 LINK ZN ZN N 60 SG CYS N 3 1555 1555 2.30 LINK ZN ZN N 60 SG CYS C 37 1555 1555 2.62 LINK ZN ZN N 60 SG CYS N 16 1555 1555 2.30

SITE 1 AC1 8 CYS C 24 CYS C 27 HIS C 32 CYS C 37 SITE 2 AC1 8 CYS N 3 CYS N 6 HIS N 11 CYS N 16 SITE 1 AC2 8 CYS C 24 CYS C 27 HIS C 32 CYS C 37 SITE 2 AC2 8 CYS N 3 CYS N 6 HIS N 11 CYS N 16

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