HEADER VIRAL PROTEIN 25-FEB-15 4YG3 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 65-225; COMPND 5 SYNONYM: HEMAGGLUTININ; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ROTAVIRUS A; SOURCE 3 ORGANISM_COMMON: RV-A; SOURCE 4 ORGANISM_TAXID: 10930; 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 4YG3 1 REMARK REVDAT 5 11-DEC-19 4YG3 1 REMARK REVDAT 4 22-NOV-17 4YG3 1 REMARK REVDAT 3 13-SEP-17 4YG3 1 REMARK REVDAT 2 14-OCT-15 4YG3 1 JRNL REVDAT 1 30-SEP-15 4YG3 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. 2.29 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 5504 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.540 REMARK 3 FREE R VALUE TEST SET COUNT : 250 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 29.6450 - 2.8782 0.98 2640 128 0.1689 0.2203 REMARK 3 2 2.8782 - 2.2850 0.98 2614 122 0.2160 0.2868 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.620 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 : 0.003 1316 REMARK 3 ANGLE : 0.701 1806 REMARK 3 CHIRALITY : 0.028 197 REMARK 3 PLANARITY : 0.002 238 REMARK 3 DIHEDRAL : 11.809 455 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 4YG3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-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 : HKL-2000, MOSFLM REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5508 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.22300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.800 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 (%): 28.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, 1.6 M AMMONIUM SULFATE, PH REMARK 280 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 32.36700 REMARK 290 SMTRY3 2 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: 380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL 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 IN SAME ASYMMETRIC UNIT 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 O HOH A 407 O HOH A 460 2.03 REMARK 500 ND2 ASN A 197 O HOH A 401 2.11 REMARK 500 O4 SO4 A 301 O HOH A 479 2.16 REMARK 500 ND2 ASN A 127 O HOH A 402 2.18 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 SER A 99 -52.13 -136.14 REMARK 500 GLN A 183 -107.76 -114.47 REMARK 500 ASN A 203 44.63 -92.84 REMARK 500 GLN A 213 54.90 -115.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YFW RELATED DB: PDB REMARK 900 4YFW CONTAINS THE VP8* PROTEIN OF ANOTHER ROTAVIRUS STRAIN REMARK 900 RELATED ID: 4YE2 RELATED DB: PDB REMARK 900 RELATED ID: 4YEZ RELATED DB: PDB REMARK 900 RELATED ID: 4YG0 RELATED DB: PDB REMARK 900 RELATED ID: 4YG6 RELATED DB: PDB DBREF 4YG3 A 65 225 UNP P35746 VP4_ROTBB 65 225 SEQADV 4YG3 GLY A 63 UNP P35746 EXPRESSION TAG SEQADV 4YG3 SER A 64 UNP P35746 EXPRESSION TAG SEQRES 1 A 163 GLY SER LEU ASP GLY PRO TYR ALA PRO ASP SER SER ASN SEQRES 2 A 163 LEU PRO SER ASN CYS TRP TYR LEU VAL ASN PRO SER ASN SEQRES 3 A 163 ASP GLY VAL VAL PHE SER VAL THR ASP ASN SER THR PHE SEQRES 4 A 163 TRP MET PHE THR TYR LEU VAL LEU PRO ASN THR ALA GLN SEQRES 5 A 163 THR ASN VAL THR VAL ASN VAL MET ASN GLU THR VAL ASN SEQRES 6 A 163 ILE SER ILE ASP ASN SER GLY SER THR TYR ARG PHE VAL SEQRES 7 A 163 ASP TYR ILE LYS THR SER SER THR GLN ALA TYR GLY SER SEQRES 8 A 163 ARG ASN TYR LEU ASN THR ALA HIS ARG LEU GLN ALA TYR SEQRES 9 A 163 ARG ARG ASP GLY ASP GLY ASN ILE SER ASN TYR TRP GLY SEQRES 10 A 163 ALA ASP THR GLN GLY ASP LEU ARG VAL GLY THR TYR SER SEQRES 11 A 163 ASN PRO VAL PRO ASN ALA VAL ILE ASN LEU ASN ALA ASP SEQRES 12 A 163 PHE TYR VAL ILE PRO ASP SER GLN GLN GLU THR CYS THR SEQRES 13 A 163 GLU TYR ILE ARG GLY GLY LEU HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *81(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 PHE A 206 N TYR A 69 SHEET 3 AA1 6 CYS A 80 VAL 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 THR A 190 -1 O ARG A 187 N TRP A 178 SHEET 1 AA2 6 ASP A 72 SER A 74 0 SHEET 2 AA2 6 VAL A 199 LEU A 202 -1 O LEU A 202 N ASP A 72 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 VAL 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 VAL A 108 SHEET 6 AA2 6 GLY A 152 THR A 159 -1 O THR A 159 N TYR A 137 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 CISPEP 1 GLY A 67 PRO A 68 0 6.46 SITE 1 AC1 6 ASN A 85 HIS A 161 ARG A 162 PRO A 196 SITE 2 AC1 6 HOH A 410 HOH A 479 SITE 1 AC2 9 PRO A 86 SER A 87 ASN A 88 ARG A 154 SITE 2 AC2 9 ASN A 203 ALA A 204 HOH A 409 HOH A 430 SITE 3 AC2 9 HOH A 432 SITE 1 AC3 5 TYR A 156 ARG A 162 ASN A 197 HOH A 404 SITE 2 AC3 5 HOH A 417 CRYST1 28.812 64.734 36.752 90.00 114.87 90.00 P 1 21 1 2 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 0.034708 0.000000 0.016089 0.00000 SCALE2 0.000000 0.015448 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029991 0.00000