HEADER ANTIVIRAL PROTEIN 24-APR-01 1IIY TITLE SOLUTION NMR STRUCTURE OF COMPLEX OF 1:2 CYANOVIRIN-N:MAN-ALPHA1,2- TITLE 2 MAN-ALPHA RESTRAINED REGULARIZED MEAN COORDINATES COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYANOVIRIN-N; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOSTOC ELLIPSOSPORUM; SOURCE 3 ORGANISM_TAXID: 45916 KEYWDS HIV-INACTIVATING PROTEIN, MAN-ALPHA1, 2-MAN-ALPHA, ANTIVIRAL PROTEIN EXPDTA SOLUTION NMR AUTHOR C.A.BEWLEY REVDAT 3 29-JUL-20 1IIY 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 24-FEB-09 1IIY 1 VERSN REVDAT 1 24-OCT-01 1IIY 0 JRNL AUTH C.A.BEWLEY JRNL TITL SOLUTION STRUCTURE OF A CYANOVIRIN-N:MAN ALPHA 1-2MAN ALPHA JRNL TITL 2 COMPLEX. STRUCTURAL BASIS FOR HIGH AFFINITY JRNL TITL 3 CARBOHYDRATE-MEDIATED BINDING TO GP120 JRNL REF STRUCTURE V. 9 931 2001 JRNL REFN ISSN 0969-2126 JRNL PMID 11591348 JRNL DOI 10.1016/S0969-2126(01)00653-0 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE OF THE 1:1 COMPLEX IN REMARK 3 WHICH DISACCHARIDE IS BOUND EXCLUSIVELY THROUGH THE HIGH REMARK 3 AFFINITY SITE WAS CALCULATED USING CONJOINED RIGID BODY/TORSION REMARK 3 ANGLE DYNAMICS (BEWLEY AND CLORE (2000) J.AM.CHEM.SOC. 122, 6009- REMARK 3 6016; WANG ET AL. (2001) EMBO. J., 19, 5635-5649 & REFS THEREIN) REMARK 3 IN WHICH THE PROTEIN BACKBONE AND NON-INTERFACIAL SIDE CHAINS REMARK 3 ARE HELD FIXED AND THE DISACCHARIDE AND INTERFACIAL SIDE CHAINS REMARK 3 ARE FREE TO TRANSLATE AND ROTATE SUBJECT TO EXPERIMENTAL REMARK 3 DISTANCE AND TORSION ANGLE RESTRAINTS. THE STRUCTURE OF THE REMARK 3 DISACCHARIDE BOUND THROUGH THE LOW AFFINITY SITE IS A MODEL REMARK 3 CALCULATED FROM A COMBINATION OF EXPERIMENTAL DISTANCE AND REMARK 3 TORSION ANGLE RESTRAINTS, AND ADDITIONAL RESTRAINTS INTRODUCED REMARK 3 ON THE BASIS OF SYMMETRY PRESENT BETWEEN THE TWO DOMAINS (HIGH REMARK 3 AND LOW AFFINITY). THE NMR COORDINATES FOR MONOMERIC CVN (PDB REMARK 3 ACC. 2EZM) WERE USED FOR THE STARTING COORDINATES WITH 2 EQ. OF REMARK 3 MAN-ALPHA-1,2-MAN-ALPHA POSITIONED WITHIN 10 A OF THE PREVIOUSLY REMARK 3 MAPPED CARBOHYDRATE BINDING SITES (BEWLEY & OTERO-QUINTERO (2001) REMARK 3 J.AM.CHEM.SOC. IN PRESS). REMARK 4 REMARK 4 1IIY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013314. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TRIPLE RESONANCE FOR ASSIGNMENT REMARK 210 OF PROTEIN: CBCA(CO)NH; CBCANH; REMARK 210 HCCH-COSY; HCCH-TOCSY; 15N- REMARK 210 SEPARATED HOHAHA; QUANTITATIVE J REMARK 210 CORRELATION FOR COUPLING REMARK 210 CONSTANTS; DIPOLAR COUPLINGS REMARK 210 OBTAINED BY TAKING THE REMARK 210 DIFFERENCE IN THE J SPLITTINGS REMARK 210 IN ISOTROPIC MEDIUM AND IN A REMARK 210 LIQUID CRYSTALLINE MEDIUM (5% REMARK 210 C12E5, R=0.96) (RUCKERT & OTTING REMARK 210 (2000) J.AM.CHEM.SOC. 122, 7793- REMARK 210 7797) MEASURED IN 2D IPAP (15N, REMARK 210 1H)-HSQC EXPERIMENTS (OTTIGER ET REMARK 210 AL (1998) J.AM.CHEM.SOC. 131, REMARK 210 373-378); INTERMOLECULAR REMARK 210 DISTANCE RESTRAINTS OBTAINED REMARK 210 FROM 12C-FILTERED/13C-SEPARATED REMARK 210 AND 15N-SEPARATED NOE REMARK 210 EXPERIMENTS ON COMPLEXES REMARK 210 COMPRISING 1:1 AND 1:2 CVN:MAN- REMARK 210 ALPHA-(1,2)-MAN-ALPHA; INTRA- REMARK 210 DISACCHARIDE AND INTER- REMARK 210 MANNOPYRANOSE DISTANCE REMARK 210 RESTRAINTS OBTAINED FROM 12C- REMARK 210 FILTERED NOE AND HOHAHA REMARK 210 EXPERIMENTS ON COMPLEXES REMARK 210 COMPRISING 1:1 AND 1:2 CVN:MAN- REMARK 210 ALPHA-(1,2)-MAN-ALPHA. REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX500; DMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : CONJOINED RIGID BODY/TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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: REMARK 210 THIS STRUCTURE IS THE RESTRAINED REGULARIZED MEAN STRUCTURE. REMARK 210 REMARK 210 REMARK 210 IN THIS ENTRY THE ELEVENTH COLUMN OF THE COORDINATES (WITH "ATOM" REMARK 210 AS THE FIRST COLUMN) REPRESENTS THE AVERAGE RMS REMARK 210 DIFFERENCE BETWEEN THE 50 INDIVIDUAL SIMULATED ANNEALING REMARK 210 STRUCTURES HAVING ZERO DISTANCE VIOLATIONS GREATER THAN REMARK 210 0.2 A AND ZERO DIHEDRAL ANGLE VIOLATIONS GREATER THAN 5 DEG. REMARK 210 THE AVERAGE STRUCTURE WAS GENERATED BY BEST FITTING TO REMARK 210 THE BACKBONE OF RESIDUES 1-101. NOTE THE OCCUPANCY FIELD IN THE REMARK 210 TENTH COLUMN HAS NO MEANING. REMARK 210 AVE.RMS DIFF. TO MEAN FOR INTERFACIAL SIDE CHAINS AND REMARK 210 DISACCHARIDE OF THE HIGH AFFINITY SITE=0.36. REMARK 210 AVE.RMS DIFF. TO MEAN FOR INTERFACIAL SIDE CHAINS AND REMARK 210 DISACCHARIDE OF THE LOW AFFINITY SITE=0.58. REMARK 210 RMS DEVIATIONS FOR BONDS, ANGLES, IMPROPERS, NOE, CDIH REMARK 210 6.389414E-03 0.717363 0.693234 8.897236E-03 9.181435E-02. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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: 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 SER A 52 12.36 174.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 RESIDUE NUMBERING: REMARK 600 CVN:1-101 REMARK 600 MAN:201/202 (CHAIN B) CORRESPONDS TO REMARK 600 MAN-ALPHA-1,2-MAN-ALPHA BOUND THROUGH THE REMARK 600 HIGH AFFINITY SITE WITH C1-C6 OF MAN 201 CORRESPONDING REMARK 600 TO THE REDUCING MANNOPYRANOSE RING AND C1-C6 OF MAN 202 REMARK 600 CORRESPONDING TO C1-C6 OF THE NONREDUCING PYRANOSE. REMARK 600 MAN:203/204 (CHAIN C) CORRESPONDS TO REMARK 600 MAN-ALPHA-1,2-MAN-ALPHA BOUND THROUGH THE LOW AFFINITY REMARK 600 SITE WITH C1-C6 OF MAN 203 CORRESPONDING TO THE REDUCING REMARK 600 MANNOPYRANOSE RING AND C1-C6 OF MAN 204 CORRESPONDING REMARK 600 TO C1-C6 OF THE NONREDUCING PYRANOSE. DBREF 1IIY A 1 101 UNP P81180 CVN_NOSEL 1 101 SEQRES 1 A 101 LEU GLY LYS PHE SER GLN THR CYS TYR ASN SER ALA ILE SEQRES 2 A 101 GLN GLY SER VAL LEU THR SER THR CYS GLU ARG THR ASN SEQRES 3 A 101 GLY GLY TYR ASN THR SER SER ILE ASP LEU ASN SER VAL SEQRES 4 A 101 ILE GLU ASN VAL ASP GLY SER LEU LYS TRP GLN PRO SER SEQRES 5 A 101 ASN PHE ILE GLU THR CYS ARG ASN THR GLN LEU ALA GLY SEQRES 6 A 101 SER SER GLU LEU ALA ALA GLU CYS LYS THR ARG ALA GLN SEQRES 7 A 101 GLN PHE VAL SER THR LYS ILE ASN LEU ASP ASP HIS ILE SEQRES 8 A 101 ALA ASN ILE ASP GLY THR LEU LYS TYR GLU HET MAN B 1 23 HET MAN B 2 22 HET MAN C 1 23 HET MAN C 2 22 HETNAM MAN ALPHA-D-MANNOPYRANOSE FORMUL 2 MAN 4(C6 H12 O6) HELIX 1 1 LYS A 3 GLN A 6 5 4 HELIX 2 2 ASN A 53 GLU A 56 5 4 SHEET 1 A 3 CYS A 8 GLN A 14 0 SHEET 2 A 3 VAL A 17 GLU A 23 -1 N VAL A 17 O GLN A 14 SHEET 3 A 3 TYR A 29 ASP A 35 -1 N ASN A 30 O CYS A 22 SHEET 1 B 2 ILE A 40 VAL A 43 0 SHEET 2 B 2 SER A 46 TRP A 49 -1 O SER A 46 N VAL A 43 SHEET 1 C 3 CYS A 58 ALA A 64 0 SHEET 2 C 3 GLU A 68 LYS A 74 -1 O GLU A 68 N ALA A 64 SHEET 3 C 3 PHE A 80 ASN A 86 -1 N VAL A 81 O CYS A 73 SHEET 1 D 2 ILE A 91 ILE A 94 0 SHEET 2 D 2 THR A 97 TYR A 100 -1 O THR A 97 N ILE A 94 SSBOND 1 CYS A 8 CYS A 22 1555 1555 2.02 SSBOND 2 CYS A 58 CYS A 73 1555 1555 2.02 LINK O2 MAN B 1 C1 MAN B 2 1555 1555 1.44 LINK O2 MAN C 1 C1 MAN C 2 1555 1555 1.44 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