HEADER VIRAL PROTEIN 09-JAN-02 1KRI TITLE NMR SOLUTION STRUCTURES OF THE RHESUS ROTAVIRUS VP4 SIALIC ACID TITLE 2 BINDING DOMAIN WITHOUT LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: VP4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SIALIC ACID BINDING DOMAIN (RESIDUES 46-231); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHESUS ROTAVIRUS; SOURCE 3 ORGANISM_TAXID: 10969; SOURCE 4 GENE: SEGMENT 4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 & DL39; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-VP8(46-231) KEYWDS ROTAVIRUS, VP4, VP8*, SPIKE PROTEIN, OUTER CAPSID, SIALIC ACID, KEYWDS 2 HEMAGGLUTININ, CELL ATTACHMENT, NEUTRALIZATION ANTIGEN, LECTIN, KEYWDS 3 GALECTIN FOLD, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.R.DORMITZER,Z.-Y.J.SUN,G.WAGNER,S.C.HARRISON REVDAT 4 05-FEB-20 1KRI 1 REMARK REVDAT 3 27-JAN-16 1KRI 1 REMARK VERSN REVDAT 2 24-FEB-09 1KRI 1 VERSN REVDAT 1 27-MAR-02 1KRI 0 JRNL AUTH P.R.DORMITZER,Z.-Y.J.SUN,G.WAGNER,S.C.HARRISON JRNL TITL THE RHESUS ROTAVIRUS VP4 SIALIC ACID BINDING DOMAIN HAS A JRNL TITL 2 GALECTIN FOLD WITH A NOVEL CARBOHYDRATE BINDING SITE JRNL REF EMBO J. V. 21 885 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 11867517 JRNL DOI 10.1093/EMBOJ/21.5.885 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.R.DORMITZER,H.B.GREENBERG,S.C.HARRISON REMARK 1 TITL PROTEOLYSIS OF MONOMERIC RECOMBINANT ROTAVIRUS VP4 YIELDS AN REMARK 1 TITL 2 OLIGOMERIC VP5* CORE REMARK 1 REF J.VIROL. V. 75 7339 2001 REMARK 1 REFN ISSN 0022-538X REMARK 1 DOI 10.1128/JVI.75.16.7339-7350.2001 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROSA 3.7, CNS 1.0 REMARK 3 AUTHORS : GUNTERT, P., DOTSCH, V., WIDER, G., WUTHRICH, K. REMARK 3 (PROSA), BRUNGER, A.T., ADAMS, P.D., CLORE, G.M., REMARK 3 DELANO, W.L., GROS, P., GROSSE-KUNSTLEVE, R.W., REMARK 3 JIANG, J.S., KUSZEWSKI, J., NILGES, M., PANNU, REMARK 3 N.S., READ, R.J., RICE, L.M., SIMONSON, T., WARREN, REMARK 3 G.L. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE MODELS ARE BASED ON A TOTAL OF 1993 CONSTRAINTS (12.5 REMARK 3 CONSTRAINTS PER RESIDUE): REMARK 3 1793 NOE-DERIVED DISTANCE CONSTRAINTS; REMARK 3 116 TALOS-DERIVED DIHEDRAL ANGLE CONSTRAINTS; REMARK 3 AND 84 HYDROGEN BOND CONSTRAINTS, BASED ON THE IDENTIFICATION OF REMARK 3 SLOW EXCHANGE AMIDE PROTONS IN D2O NOESY AND TOCSY EXPERIMENTS, REMARK 3 ON CHARACTERISTIC NOE PATTERNS FOR ALPHA-HELICES AND BETA-SHEETS, REMARK 3 AND ON THE PROXIMITY AND ORIENTATION OF POTENTIAL HYDROGEN BOND REMARK 3 PARTNERS IN ANNEALED STRUCTURES. REMARK 3 THE FINAL SET OF 20 STRUCTURES CONTAINS NO VIOLATIONS OF NOE REMARK 3 DISTANCE CONSTRAINTS GREATER THAN 0.15 ANGSTROMS REMARK 3 AND NO VIOLATIONS OF DIHEDRAL ANGLE CONSTRAINTS GREATER THAN 5 REMARK 3 DEGREES. REMARK 4 REMARK 4 1KRI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015266. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 20 MM NAPO4, 10 MM NACL, 0.02% REMARK 210 NA AZIDE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM ECVP8(46-231) U-15N; 1 MM REMARK 210 ECVP8(46-231) U-15N, 13C, 2D; REMARK 210 0.1 MM ECVP8(46-231) U-15N-ILE REMARK 210 OR U-15N-LEU OR U-15N-PHE OR U- REMARK 210 15N-TYR OR U-15N-VAL; 1 MM REMARK 210 ECVP8(46-231) U-15N, 13C; 1 MM REMARK 210 ECVP8(46-231) U-10% 13C; 1 MM REMARK 210 ECVP8(46-231) REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HSQC; HNCA; HN(CO)CA; HNCACB; REMARK 210 HN(CO)CACB; HNCO; HN(CA)CO; REMARK 210 HCCCONH; HNHA; HNHB; 3D-15N- REMARK 210 SEPARATED TOCHSQC; HCCH-TOCSY; REMARK 210 13C-HSQC; 2D-D2O-TOCSY; 3D-13C- REMARK 210 SEPARATED NOESY; 3D-15N- REMARK 210 SEPARATED NOEHSQC; 2D-D2O-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : UNITY; AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1.3.13, DYANA 1.5, TALOS, REMARK 210 CNS 1.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: THE N-TERMINAL 19 RESIDUES (A46 TO V64 OF VP4) REMARK 210 AND THE C-TERMINAL 7 RESIDUES (P225 TO R231 OF VP4) ARE DISORDERED REMARK 210 AND ARE NOT INCLUDED IN THE MODELS. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 ALA A 46 REMARK 465 PRO A 47 REMARK 465 VAL A 48 REMARK 465 ASN A 49 REMARK 465 TRP A 50 REMARK 465 GLY A 51 REMARK 465 PRO A 52 REMARK 465 GLY A 53 REMARK 465 GLU A 54 REMARK 465 THR A 55 REMARK 465 ASN A 56 REMARK 465 ASP A 57 REMARK 465 SER A 58 REMARK 465 THR A 59 REMARK 465 THR A 60 REMARK 465 VAL A 61 REMARK 465 GLU A 62 REMARK 465 PRO A 63 REMARK 465 VAL A 64 REMARK 465 PRO A 225 REMARK 465 PRO A 226 REMARK 465 ILE A 227 REMARK 465 GLN A 228 REMARK 465 ASN A 229 REMARK 465 THR A 230 REMARK 465 ARG A 231 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 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 ASP A 66 -66.74 -98.43 REMARK 500 1 PRO A 68 80.26 -68.67 REMARK 500 1 PRO A 77 -160.86 -57.35 REMARK 500 1 ALA A 89 -175.17 -64.90 REMARK 500 1 THR A 99 -53.13 -139.99 REMARK 500 1 ASP A 100 42.56 -167.39 REMARK 500 1 ARG A 101 118.20 -175.64 REMARK 500 1 ASN A 111 95.18 56.08 REMARK 500 1 SER A 114 98.29 51.94 REMARK 500 1 SER A 151 -177.21 -68.17 REMARK 500 1 TYR A 152 85.36 -171.14 REMARK 500 1 LYS A 163 97.74 69.06 REMARK 500 1 LEU A 164 137.33 -175.60 REMARK 500 1 ASN A 183 54.61 -145.38 REMARK 500 1 THR A 192 -57.94 -136.98 REMARK 500 1 GLU A 212 42.49 -93.43 REMARK 500 1 ASN A 222 40.68 -150.33 REMARK 500 2 GLN A 70 175.98 -55.06 REMARK 500 2 THR A 72 157.24 177.20 REMARK 500 2 PRO A 77 174.37 -50.43 REMARK 500 2 THR A 99 -67.41 -143.50 REMARK 500 2 ASP A 100 39.98 -152.37 REMARK 500 2 ARG A 101 127.44 -170.32 REMARK 500 2 ASN A 111 85.35 54.48 REMARK 500 2 SER A 114 94.70 56.85 REMARK 500 2 ASN A 132 141.90 -172.68 REMARK 500 2 LYS A 163 79.72 61.74 REMARK 500 2 ASN A 171 -71.07 65.98 REMARK 500 2 CYS A 203 -158.94 -131.36 REMARK 500 2 GLU A 212 33.36 -96.13 REMARK 500 2 ASN A 222 61.43 -159.87 REMARK 500 3 PRO A 71 -81.71 -81.90 REMARK 500 3 THR A 72 -164.02 44.18 REMARK 500 3 PRO A 86 -169.55 -71.86 REMARK 500 3 THR A 87 25.22 -152.82 REMARK 500 3 ALA A 88 156.70 178.79 REMARK 500 3 THR A 99 -63.16 -152.17 REMARK 500 3 ASP A 100 42.45 -156.33 REMARK 500 3 ASN A 111 74.11 59.25 REMARK 500 3 LYS A 163 82.95 61.99 REMARK 500 3 ASN A 183 52.53 -142.49 REMARK 500 3 THR A 186 96.05 -69.55 REMARK 500 3 THR A 192 -56.63 -132.69 REMARK 500 3 GLU A 212 31.68 -95.56 REMARK 500 4 PRO A 68 81.27 -63.77 REMARK 500 4 THR A 72 -176.46 -170.08 REMARK 500 4 PRO A 77 -168.07 -75.70 REMARK 500 4 ALA A 85 67.90 -115.97 REMARK 500 4 THR A 99 -57.39 -143.99 REMARK 500 4 ASP A 100 49.24 -166.21 REMARK 500 REMARK 500 THIS ENTRY HAS 331 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KQR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RHESUS ROTAVIRUS VP4 SIALIC ACID BINDING REMARK 900 DOMAIN IN COMPLEX WITH 2-O-METHYL-ALPHA-D-N-ACETYL NEURAMINIC ACID REMARK 900 RELATED ID: 5275 RELATED DB: BMRB DBREF 1KRI A 46 231 UNP P12473 VP4_ROTRH 46 231 SEQRES 1 A 186 ALA PRO VAL ASN TRP GLY PRO GLY GLU THR ASN ASP SER SEQRES 2 A 186 THR THR VAL GLU PRO VAL LEU ASP GLY PRO TYR GLN PRO SEQRES 3 A 186 THR THR PHE ASN PRO PRO VAL ASP TYR TRP MET LEU LEU SEQRES 4 A 186 ALA PRO THR ALA ALA GLY VAL VAL VAL GLU GLY THR ASN SEQRES 5 A 186 ASN THR ASP ARG TRP LEU ALA THR ILE LEU VAL GLU PRO SEQRES 6 A 186 ASN VAL THR SER GLU THR ARG SER TYR THR LEU PHE GLY SEQRES 7 A 186 THR GLN GLU GLN ILE THR ILE ALA ASN ALA SER GLN THR SEQRES 8 A 186 GLN TRP LYS PHE ILE ASP VAL VAL LYS THR THR GLN ASN SEQRES 9 A 186 GLY SER TYR SER GLN TYR GLY PRO LEU GLN SER THR PRO SEQRES 10 A 186 LYS LEU TYR ALA VAL MET LYS HIS ASN GLY LYS ILE TYR SEQRES 11 A 186 THR TYR ASN GLY GLU THR PRO ASN VAL THR THR LYS TYR SEQRES 12 A 186 TYR SER THR THR ASN TYR ASP SER VAL ASN MET THR ALA SEQRES 13 A 186 PHE CYS ASP PHE TYR ILE ILE PRO ARG GLU GLU GLU SER SEQRES 14 A 186 THR CYS THR GLU TYR ILE ASN ASN GLY LEU PRO PRO ILE SEQRES 15 A 186 GLN ASN THR ARG HELIX 1 1 ASN A 193 VAL A 197 5 5 HELIX 2 2 GLU A 212 GLY A 223 1 12 SHEET 1 A 6 THR A 72 ASN A 75 0 SHEET 2 A 6 MET A 199 PHE A 202 -1 O ALA A 201 N THR A 72 SHEET 3 A 6 GLY A 90 ASN A 97 -1 N GLU A 94 O THR A 200 SHEET 4 A 6 ARG A 101 VAL A 108 -1 O LEU A 107 N GLY A 90 SHEET 5 A 6 TRP A 138 LYS A 145 -1 O LYS A 139 N VAL A 108 SHEET 6 A 6 SER A 153 SER A 160 -1 O LEU A 158 N PHE A 140 SHEET 1 B 5 ASP A 204 ILE A 208 0 SHEET 2 B 5 TYR A 80 ALA A 85 -1 N ALA A 85 O ASP A 204 SHEET 3 B 5 LEU A 164 HIS A 170 -1 O TYR A 165 N LEU A 84 SHEET 4 B 5 LYS A 173 THR A 181 -1 N TYR A 175 O MET A 168 SHEET 5 B 5 THR A 185 THR A 191 -1 N TYR A 189 O ILE A 174 SHEET 1 C 2 SER A 114 LEU A 121 0 SHEET 2 C 2 THR A 124 ALA A 131 -1 O ILE A 130 N GLU A 115 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