HEADER VIRAL PROTEIN 26-JAN-04 1S6N TITLE NMR STRUCTURE OF DOMAIN III OF THE WEST NILE VIRUS ENVELOPE PROTEIN, TITLE 2 STRAIN 385-99 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAIN III; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: WEST NILE VIRUS; SOURCE 3 ORGANISM_TAXID: 307044; SOURCE 4 STRAIN: 385-99; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: C2X; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMAL C2X KEYWDS BETA BARREL, FLAVIVIRUS, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR D.E.VOLK,D.W.BEASLEY,D.A.KALLICK,M.R.HOLBROOK,A.D.BARRETT, AUTHOR 2 D.G.GORENSTEIN REVDAT 5 13-NOV-24 1S6N 1 REMARK REVDAT 4 13-JUL-11 1S6N 1 VERSN REVDAT 3 24-FEB-09 1S6N 1 VERSN REVDAT 2 28-SEP-04 1S6N 1 JRNL REVDAT 1 06-JUL-04 1S6N 0 JRNL AUTH D.E.VOLK,D.W.BEASLEY,D.A.KALLICK,M.R.HOLBROOK,A.D.BARRETT, JRNL AUTH 2 D.G.GORENSTEIN JRNL TITL SOLUTION STRUCTURE AND ANTIBODY BINDING STUDIES OF THE JRNL TITL 2 ENVELOPE PROTEIN DOMAIN III FROM THE NEW YORK STRAIN OF WEST JRNL TITL 3 NILE VIRUS JRNL REF J.BIOL.CHEM. V. 279 38755 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15190071 JRNL DOI 10.1074/JBC.M402385200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.E.VOLK,D.A.KALLICK,M.R.HOLBROOK,D.W.C.BEASLEY, REMARK 1 AUTH 2 A.D.T.BARRETT,D.G.GORENSTEIN REMARK 1 TITL LETTER TO THE EDITOR: 1H, 13C, AND 15N RESONANCE ASSIGNMENTS REMARK 1 TITL 2 FOR DOMAIN III OF THE WEST NILE VIRUS ENVELOPE PROTEIN REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 6 REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON, REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1S6N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021433. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 50MM PHOSPHATE, 100MM NACL, 10MM REMARK 210 NAN3 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7MM WND3 PROTEIN, 50MM K2HPO4, REMARK 210 100MM NACL, 10MM NAN3, 0.1MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_ 13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1B, SANE 1.0, FELIX 98, REMARK 210 AMBER 6 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: CHEMICAL SHIFTS WERE DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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 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 HG SER A 50 OD1 ASP A 57 1.31 REMARK 500 OD1 ASP A 90 HG SER A 111 1.32 REMARK 500 HG1 THR A 31 OE1 GLU A 83 1.33 REMARK 500 OD2 ASP A 90 HG SER A 112 1.38 REMARK 500 HH TYR A 38 O ASP A 42 1.51 REMARK 500 HG SER A 51 O GLU A 85 1.54 REMARK 500 HG SER A 2 O PRO A 60 1.56 REMARK 500 O LEU A 58 HG1 THR A 59 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 3 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 5 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 5 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 6 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 7 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 8 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 9 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 10 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 11 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 11 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 12 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 12 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 13 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 14 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 14 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 15 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES 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 THR A 9 62.11 -68.40 REMARK 500 1 SER A 15 -44.91 -167.27 REMARK 500 1 LYS A 16 -76.09 61.99 REMARK 500 1 ALA A 17 77.06 -102.49 REMARK 500 1 PRO A 44 95.79 -55.11 REMARK 500 1 SER A 54 27.99 -152.93 REMARK 500 1 LEU A 55 17.66 55.47 REMARK 500 1 ASN A 56 52.15 -68.37 REMARK 500 1 ALA A 76 14.31 -66.35 REMARK 500 1 ASN A 77 16.65 -62.22 REMARK 500 1 PRO A 87 167.66 -47.40 REMARK 500 1 SER A 109 70.68 52.41 REMARK 500 2 SER A 15 -44.57 -160.03 REMARK 500 2 LYS A 16 -70.62 64.46 REMARK 500 2 ALA A 17 78.60 -100.81 REMARK 500 2 THR A 39 32.21 -72.72 REMARK 500 2 PRO A 44 87.91 -54.69 REMARK 500 2 SER A 54 36.05 -155.32 REMARK 500 2 LEU A 55 10.03 58.17 REMARK 500 2 ASN A 56 46.28 -68.78 REMARK 500 2 THR A 75 0.66 -63.68 REMARK 500 2 ASN A 77 18.26 -61.63 REMARK 500 2 PRO A 87 150.89 -45.76 REMARK 500 2 SER A 109 -0.22 119.68 REMARK 500 2 SER A 111 -154.77 -88.32 REMARK 500 3 THR A 9 68.96 -62.82 REMARK 500 3 SER A 15 -22.49 -151.14 REMARK 500 3 LYS A 16 -62.41 56.58 REMARK 500 3 PRO A 44 109.01 -51.94 REMARK 500 3 SER A 54 30.84 -154.78 REMARK 500 3 ASN A 56 46.48 -69.52 REMARK 500 3 ALA A 76 12.82 -67.07 REMARK 500 3 ASN A 77 18.04 -65.38 REMARK 500 4 THR A 9 72.57 -67.52 REMARK 500 4 SER A 15 -21.90 -141.00 REMARK 500 4 LYS A 16 -77.75 45.36 REMARK 500 4 PRO A 44 99.18 -50.17 REMARK 500 4 SER A 54 34.75 -154.04 REMARK 500 4 LEU A 55 12.77 57.71 REMARK 500 4 ASN A 56 45.83 -67.01 REMARK 500 4 VAL A 71 89.65 -69.11 REMARK 500 4 ALA A 76 12.80 -65.04 REMARK 500 4 ASN A 77 13.46 -62.75 REMARK 500 4 SER A 109 84.60 59.39 REMARK 500 5 SER A 2 -178.96 -69.05 REMARK 500 5 SER A 15 -3.22 -150.42 REMARK 500 5 LYS A 16 -75.95 53.98 REMARK 500 5 THR A 39 43.33 -77.43 REMARK 500 5 PRO A 44 107.00 -48.04 REMARK 500 5 SER A 54 30.84 -152.17 REMARK 500 REMARK 500 THIS ENTRY HAS 162 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 79 VAL A 80 2 -148.60 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 2 ARG A 63 0.13 SIDE CHAIN REMARK 500 2 ARG A 97 0.09 SIDE CHAIN REMARK 500 5 TYR A 92 0.07 SIDE CHAIN REMARK 500 9 ARG A 63 0.08 SIDE CHAIN REMARK 500 9 TYR A 92 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 1-5 AND 113-115 ARE NOT IN THE NATIVE SEQUENCE. REMARK 999 THEY WERE ADDED TO INCREASE SOLUBILITY. DBREF 1S6N A 6 112 UNP Q913C7 Q913C7_WNV 297 403 SEQADV 1S6N ILE A 1 UNP Q913C7 SEE REMARK 999 SEQADV 1S6N SER A 2 UNP Q913C7 SEE REMARK 999 SEQADV 1S6N GLU A 3 UNP Q913C7 SEE REMARK 999 SEQADV 1S6N PHE A 4 UNP Q913C7 SEE REMARK 999 SEQADV 1S6N GLN A 5 UNP Q913C7 SEE REMARK 999 SEQADV 1S6N ILE A 113 UNP Q913C7 SEE REMARK 999 SEQADV 1S6N GLY A 114 UNP Q913C7 SEE REMARK 999 SEQADV 1S6N LYS A 115 UNP Q913C7 SEE REMARK 999 SEQRES 1 A 115 ILE SER GLU PHE GLN LEU LYS GLY THR THR TYR GLY VAL SEQRES 2 A 115 CYS SER LYS ALA PHE LYS PHE LEU GLY THR PRO ALA ASP SEQRES 3 A 115 THR GLY HIS GLY THR VAL VAL LEU GLU LEU GLN TYR THR SEQRES 4 A 115 GLY THR ASP GLY PRO CYS LYS VAL PRO ILE SER SER VAL SEQRES 5 A 115 ALA SER LEU ASN ASP LEU THR PRO VAL GLY ARG LEU VAL SEQRES 6 A 115 THR VAL ASN PRO PHE VAL SER VAL ALA THR ALA ASN ALA SEQRES 7 A 115 LYS VAL LEU ILE GLU LEU GLU PRO PRO PHE GLY ASP SER SEQRES 8 A 115 TYR ILE VAL VAL GLY ARG GLY GLU GLN GLN ILE ASN HIS SEQRES 9 A 115 HIS TRP HIS LYS SER GLY SER SER ILE GLY LYS SHEET 1 A 4 PHE A 18 ASP A 26 0 SHEET 2 A 4 VAL A 32 TYR A 38 -1 O GLU A 35 N GLY A 22 SHEET 3 A 4 LYS A 79 GLU A 85 -1 O ILE A 82 N LEU A 34 SHEET 4 A 4 ARG A 63 LEU A 64 -1 N ARG A 63 O GLU A 85 SHEET 1 B 3 ILE A 49 VAL A 52 0 SHEET 2 B 3 GLY A 89 ARG A 97 -1 O TYR A 92 N VAL A 52 SHEET 3 B 3 GLN A 100 LYS A 108 -1 O HIS A 104 N ILE A 93 SSBOND 1 CYS A 14 CYS A 45 1555 1555 2.04 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