HEADER VIRAL PROTEIN 25-FEB-15 4YG0 TITLE STRUCTURAL BASIS OF GLYCAN RECOGNITION IN NEONATE-SPECIFIC ROTAVIRUSES COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER CAPSID PROTEIN VP4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 64-225; COMPND 5 SYNONYM: P[11] HUMAN ROTAVIRUS N155 VP8*; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN ROTAVIRUS A; SOURCE 3 ORGANISM_TAXID: 10941; SOURCE 4 STRAIN: N155; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS ROTAVIRUS, STRUCTURAL BIOLOGY, GLYCAN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.HU,B.V.V.PRASAD REVDAT 6 27-SEP-23 4YG0 1 HETSYN LINK REVDAT 5 29-JUL-20 4YG0 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 11-DEC-19 4YG0 1 REMARK REVDAT 3 13-SEP-17 4YG0 1 REMARK REVDAT 2 14-OCT-15 4YG0 1 JRNL REVDAT 1 30-SEP-15 4YG0 0 JRNL AUTH L.HU,S.RAMANI,R.CZAKO,B.SANKARAN,Y.YU,D.F.SMITH, JRNL AUTH 2 R.D.CUMMINGS,M.K.ESTES,B.V.VENKATARAM PRASAD JRNL TITL STRUCTURAL BASIS OF GLYCAN SPECIFICITY IN NEONATE-SPECIFIC JRNL TITL 2 BOVINE-HUMAN REASSORTANT ROTAVIRUS. JRNL REF NAT COMMUN V. 6 8346 2015 JRNL REFN ESSN 2041-1723 JRNL PMID 26420502 JRNL DOI 10.1038/NCOMMS9346 REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 35194 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1755 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 31.0320 - 3.7046 0.97 2784 135 0.1538 0.1452 REMARK 3 2 3.7046 - 2.9411 0.93 2639 139 0.1551 0.2050 REMARK 3 3 2.9411 - 2.5696 0.94 2702 133 0.1740 0.2207 REMARK 3 4 2.5696 - 2.3347 0.99 2824 165 0.1816 0.1893 REMARK 3 5 2.3347 - 2.1674 0.85 2411 141 0.1878 0.2617 REMARK 3 6 2.1674 - 2.0397 0.86 2470 124 0.1532 0.1710 REMARK 3 7 2.0397 - 1.9375 0.84 2401 118 0.1502 0.1916 REMARK 3 8 1.9375 - 1.8532 0.60 1734 88 0.2049 0.2105 REMARK 3 9 1.8532 - 1.7819 1.00 2809 163 0.1610 0.1721 REMARK 3 10 1.7819 - 1.7204 1.00 2845 186 0.1669 0.1946 REMARK 3 11 1.7204 - 1.6666 1.00 2825 172 0.1587 0.1828 REMARK 3 12 1.6666 - 1.6190 1.00 2826 159 0.1576 0.1529 REMARK 3 13 1.6190 - 1.5763 1.00 2905 141 0.1622 0.2069 REMARK 3 14 1.5763 - 1.5379 1.00 2859 127 0.1626 0.2245 REMARK 3 15 1.5379 - 1.5029 0.74 2133 106 0.1683 0.1759 REMARK 3 16 1.5029 - 1.4709 0.71 2004 121 0.1710 0.2177 REMARK 3 17 1.4709 - 1.4415 0.69 1953 115 0.1957 0.2246 REMARK 3 18 1.4415 - 1.4143 0.99 2852 160 0.1842 0.2406 REMARK 3 19 1.4143 - 1.3891 1.00 2871 142 0.1671 0.1943 REMARK 3 20 1.3891 - 1.3655 0.99 2844 139 0.1760 0.2131 REMARK 3 21 1.3655 - 1.3435 0.99 2827 138 0.1841 0.2515 REMARK 3 22 1.3435 - 1.3228 0.99 2917 127 0.1872 0.2446 REMARK 3 23 1.3228 - 1.3034 1.00 2807 133 0.2083 0.2016 REMARK 3 24 1.3034 - 1.2850 0.97 2819 146 0.2971 0.3081 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1410 REMARK 3 ANGLE : 1.102 1934 REMARK 3 CHIRALITY : 0.046 222 REMARK 3 PLANARITY : 0.005 244 REMARK 3 DIHEDRAL : 11.480 586 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4YG0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207397. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977408 REMARK 200 MONOCHROMATOR : ASYMMETRIC CURVED CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35249 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.280 REMARK 200 RESOLUTION RANGE LOW (A) : 31.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.28300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4YFW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NACL, 0.1M IMIDAZOLE, 1.0M REMARK 280 POTASIUM/SODIUM TARTRATE, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 16.10500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.46000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.02500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.46000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.10500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.02500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 11.0 KCAL/MOL 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: 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 ASN A 88 -123.65 -108.73 REMARK 500 SER A 99 -57.15 -141.20 REMARK 500 ARG A 154 -122.30 -122.34 REMARK 500 ASN A 193 80.99 -150.47 REMARK 500 VAL A 195 50.14 -142.19 REMARK 500 ASN A 203 55.93 -95.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YFZ RELATED DB: PDB REMARK 900 4YFZ CONTAINS THE SAME PROTEIN COMPLEXED WITH LNT REMARK 900 RELATED ID: 4YE2 RELATED DB: PDB REMARK 900 RELATED ID: 4YFW RELATED DB: PDB REMARK 900 RELATED ID: 4YG3 RELATED DB: PDB REMARK 900 RELATED ID: 4YG6 RELATED DB: PDB DBREF 4YG0 A 64 225 UNP B6RGK2 B6RGK2_9REOV 64 225 SEQADV 4YG0 GLY A 62 UNP B6RGK2 EXPRESSION TAG SEQADV 4YG0 SER A 63 UNP B6RGK2 EXPRESSION TAG SEQRES 1 A 164 GLY SER ALA LEU ASP GLY PRO TYR THR PRO ASP SER SER SEQRES 2 A 164 ASN LEU PRO SER ASN TYR TRP TYR LEU ILE ASN PRO LEU SEQRES 3 A 164 ASN ASP GLY VAL VAL PHE SER VAL THR ASN ASN SER THR SEQRES 4 A 164 PHE TRP MET PHE THR TYR LEU ILE LEU PRO ASN THR ALA SEQRES 5 A 164 GLN THR ASN VAL THR VAL ASN VAL MET ASN GLU THR VAL SEQRES 6 A 164 ASN ILE SER ILE ASP ASN SER GLY SER THR TYR ARG PHE SEQRES 7 A 164 VAL ASP TYR PHE LYS THR SER SER THR GLN SER TYR ARG SEQRES 8 A 164 GLN ARG ASN TYR LEU ILE THR GLU HIS ARG LEU GLN ALA SEQRES 9 A 164 TYR ARG ARG ASP GLU SER GLY ASN ILE SER ASN TYR TRP SEQRES 10 A 164 GLY SER SER THR TYR GLY ASP LEU ARG VAL GLY THR TYR SEQRES 11 A 164 PHE ASN PRO VAL LEU ASN ALA VAL ILE ASN LEU ASN ALA SEQRES 12 A 164 ASP PHE TYR ILE ILE PRO ASP SER GLN GLN GLU LYS CYS SEQRES 13 A 164 THR GLU TYR ILE LYS GLY GLY LEU HET BGC B 1 12 HET GAL B 2 11 HET NAG B 3 14 HET GAL B 4 11 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 BGC C6 H12 O6 FORMUL 2 GAL 2(C6 H12 O6) FORMUL 2 NAG C8 H15 N O6 FORMUL 3 HOH *286(H2 O) HELIX 1 AA1 GLN A 213 GLY A 224 1 12 SHEET 1 AA1 6 ASP A 66 TYR A 69 0 SHEET 2 AA1 6 PHE A 206 PRO A 210 -1 O ILE A 208 N ASP A 66 SHEET 3 AA1 6 TYR A 80 ILE A 84 -1 N TRP A 81 O ILE A 209 SHEET 4 AA1 6 GLN A 164 ARG A 168 -1 O TYR A 166 N TYR A 82 SHEET 5 AA1 6 ILE A 174 TRP A 178 -1 O SER A 175 N ARG A 167 SHEET 6 AA1 6 ARG A 187 TYR A 191 -1 O ARG A 187 N TRP A 178 SHEET 1 AA2 6 ASP A 72 SER A 74 0 SHEET 2 AA2 6 ILE A 200 LEU A 202 -1 O ILE A 200 N SER A 74 SHEET 3 AA2 6 GLY A 90 THR A 96 -1 N SER A 94 O ASN A 201 SHEET 4 AA2 6 TRP A 102 ILE A 108 -1 O LEU A 107 N GLY A 90 SHEET 5 AA2 6 TYR A 137 LYS A 144 -1 O ARG A 138 N ILE A 108 SHEET 6 AA2 6 ARG A 152 THR A 159 -1 O ARG A 154 N ASP A 141 SHEET 1 AA3 2 THR A 112 VAL A 121 0 SHEET 2 AA3 2 GLU A 124 ASN A 132 -1 O GLU A 124 N VAL A 121 LINK O4 BGC B 1 C1 GAL B 2 1555 1555 1.44 LINK O3 GAL B 2 C1 NAG B 3 1555 1555 1.42 LINK O4 NAG B 3 C1 GAL B 4 1555 1555 1.43 CISPEP 1 GLY A 67 PRO A 68 0 1.88 CRYST1 32.210 64.050 70.920 90.00 90.00 90.00 P 21 21 21 4 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 0.031046 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015613 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014100 0.00000