HEADER VIRAL PROTEIN 19-FEB-15 3J9S TITLE SINGLE PARTICLE CRYO-EM STRUCTURE OF ROTAVIRUS VP6 AT 2.6 ANGSTROM TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERMEDIATE CAPSID PROTEIN VP6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ROTAVIRUS VP6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOVINE ROTAVIRUS STRAIN UK/G6; SOURCE 3 ORGANISM_TAXID: 10934; SOURCE 4 EXPRESSION_SYSTEM: CHLOROCEBUS SABAEUS; SOURCE 5 EXPRESSION_SYSTEM_COMMON: GREEN MONKEY; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 60711 KEYWDS ROTAVIRUS, VIRUS, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR T.GRANT,N.GRIGORIEFF REVDAT 5 18-JUL-18 3J9S 1 REMARK REVDAT 4 02-SEP-15 3J9S 1 JRNL REVDAT 3 01-JUL-15 3J9S 1 REMARK REVDAT 2 10-JUN-15 3J9S 1 JRNL REVDAT 1 11-MAR-15 3J9S 0 JRNL AUTH T.GRANT,N.GRIGORIEFF JRNL TITL MEASURING THE OPTIMAL EXPOSURE FOR SINGLE PARTICLE CRYO-EM JRNL TITL 2 USING A 2.6 ANGSTROM RECONSTRUCTION OF ROTAVIRUS VP6. JRNL REF ELIFE V. 4 06980 2015 JRNL REFN ESSN 2050-084X JRNL PMID 26023829 JRNL DOI 10.7554/ELIFE.06980 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : COOT, COOT, FREALIGN, IMAGIC, TIGRIS REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1QHD REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : REFINEMENT PROTOCOL--FLEXIBLE DETAILS--MODEL REMARK 3 WAS REFINED BY REAL SPACE REFINEMENT USING COOT AND ALL REMARK 3 RESTRAINTS. REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 1.023 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.600 REMARK 3 NUMBER OF PARTICLES : 4000 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: FINAL MAP IS A 13-FOLD AVERAGE OF VP6 TRIMERS FROM REMARK 3 THE ASYMMETRIC UNIT OF THE RECONSTRUCTION OF THE WHOLE CAPSID. REMARK 3 DATA AT RESOLUTIONS HIGHER THAN 15A WERE NOT USED FOR ALIGNMENTS. REMARK 4 REMARK 4 3J9S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000160430. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : BOVINE ROTAVIRUS VP6 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.50 REMARK 245 SAMPLE SUPPORT DETAILS : C-FLAT 1.2/1.3 REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FOR 4-6 SECONDS BEFORE REMARK 245 PLUNGING INTO LIQUID ETHANE REMARK 245 (FEI VITROBOT MARK II). REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : NULL REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 13-AUG-14 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 100.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 29000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C3). 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 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 350 BIOMT1 2 -0.493942 0.867977 0.051358 -1.03074 REMARK 350 BIOMT2 2 -0.858367 -0.496189 0.130392 4.93395 REMARK 350 BIOMT3 2 0.138660 0.020322 0.990131 -0.18379 REMARK 350 BIOMT1 3 -0.493942 -0.858367 0.138660 3.75150 REMARK 350 BIOMT2 3 0.867977 -0.496189 0.020322 3.34657 REMARK 350 BIOMT3 3 0.051358 0.130392 0.990131 -0.40843 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 PRO A 251 C - N - CD ANGL. DEV. = 13.5 DEGREES REMARK 500 PRO A 251 CA - N - CD ANGL. DEV. = -8.6 DEGREES REMARK 500 PRO A 313 C - N - CD ANGL. DEV. = 17.4 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 ASP A 228 154.24 91.34 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 ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-6272 RELATED DB: EMDB DBREF 3J9S A 1 397 UNP P04509 VP6_ROTRF 1 397 SEQADV 3J9S ACE A 0 UNP P04509 ACETYLATION SEQRES 1 A 398 ACE MET ASP VAL LEU TYR SER LEU SER LYS THR LEU LYS SEQRES 2 A 398 ASP ALA ARG ASP LYS ILE VAL GLU GLY THR LEU TYR SER SEQRES 3 A 398 ASN VAL SER ASP LEU ILE GLN GLN PHE ASN GLN MET ILE SEQRES 4 A 398 ILE THR MET ASN GLY ASN GLU PHE GLN THR GLY GLY ILE SEQRES 5 A 398 GLY ASN LEU PRO ILE ARG ASN TRP ASN PHE ASP PHE GLY SEQRES 6 A 398 LEU LEU GLY THR THR LEU LEU ASN LEU ASP ALA ASN TYR SEQRES 7 A 398 VAL GLU THR ALA ARG ASN THR ILE ASP TYR PHE VAL ASP SEQRES 8 A 398 PHE VAL ASP ASN VAL CYS MET ASP GLU MET VAL ARG GLU SEQRES 9 A 398 SER GLN ARG ASN GLY ILE ALA PRO GLN SER ASP SER LEU SEQRES 10 A 398 ILE LYS LEU SER GLY ILE LYS PHE LYS ARG ILE ASN PHE SEQRES 11 A 398 ASP ASN SER SER GLU TYR ILE GLU ASN TRP ASN LEU GLN SEQRES 12 A 398 ASN ARG ARG GLN ARG THR GLY PHE THR PHE HIS LYS PRO SEQRES 13 A 398 ASN ILE PHE PRO TYR SER ALA SER PHE THR LEU ASN ARG SEQRES 14 A 398 SER GLN PRO ALA HIS ASP ASN LEU MET GLY THR MET TRP SEQRES 15 A 398 LEU ASN ALA GLY SER GLU ILE GLN VAL ALA GLY PHE ASP SEQRES 16 A 398 TYR SER CYS ALA ILE ASN ALA PRO ALA ASN THR GLN GLN SEQRES 17 A 398 PHE GLU HIS ILE VAL GLN LEU ARG ARG VAL LEU THR THR SEQRES 18 A 398 ALA THR ILE THR LEU LEU PRO ASP ALA GLU ARG PHE SER SEQRES 19 A 398 PHE PRO ARG VAL ILE THR SER ALA ASP GLY ALA THR THR SEQRES 20 A 398 TRP TYR PHE ASN PRO VAL ILE LEU ARG PRO ASN ASN VAL SEQRES 21 A 398 GLU ILE GLU PHE LEU LEU ASN GLY GLN ILE ILE ASN THR SEQRES 22 A 398 TYR GLN ALA ARG PHE GLY THR ILE ILE ALA ARG ASN PHE SEQRES 23 A 398 ASP THR ILE ARG LEU SER PHE GLN LEU MET ARG PRO PRO SEQRES 24 A 398 ASN MET THR PRO ALA VAL ALA ALA LEU PHE PRO ASN ALA SEQRES 25 A 398 GLN PRO PHE GLU HIS HIS ALA THR VAL GLY LEU THR LEU SEQRES 26 A 398 ARG ILE GLU SER ALA VAL CYS GLU SER VAL LEU ALA ASP SEQRES 27 A 398 ALA SER GLU THR MET LEU ALA ASN VAL THR SER VAL ARG SEQRES 28 A 398 GLN GLU TYR ALA ILE PRO VAL GLY PRO VAL PHE PRO PRO SEQRES 29 A 398 GLY MET ASN TRP THR ASP LEU ILE THR ASN TYR SER PRO SEQRES 30 A 398 SER ARG GLU ASP ASN LEU GLN ARG VAL PHE THR VAL ALA SEQRES 31 A 398 SER ILE ARG SER MET LEU VAL LYS HET ACE A 0 3 HET ZN A 501 1 HET CL A 502 1 HET CA A 503 1 HET CA A 504 1 HETNAM ACE ACETYL GROUP HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM CA CALCIUM ION FORMUL 1 ACE C2 H4 O FORMUL 2 ZN ZN 2+ FORMUL 3 CL CL 1- FORMUL 4 CA 2(CA 2+) FORMUL 6 HOH *105(H2 O) HELIX 1 1 MET A 1 ILE A 18 1 18 HELIX 2 2 LEU A 23 ASN A 42 1 20 HELIX 3 3 ASP A 74 VAL A 101 1 28 HELIX 4 4 SER A 113 SER A 120 1 8 HELIX 5 5 ILE A 122 ASN A 128 5 7 HELIX 6 6 SER A 133 ARG A 144 1 12 HELIX 7 7 ALA A 201 ALA A 203 5 3 HELIX 8 8 THR A 301 PHE A 308 1 8 HELIX 9 9 THR A 341 TYR A 353 1 13 HELIX 10 10 PRO A 362 MET A 365 5 4 HELIX 11 11 ASN A 366 ASN A 373 1 8 HELIX 12 12 SER A 375 VAL A 396 1 22 SHEET 1 A 2 GLU A 45 THR A 48 0 SHEET 2 A 2 ARG A 57 ASN A 60 -1 O TRP A 59 N PHE A 46 SHEET 1 B 3 PHE A 150 HIS A 153 0 SHEET 2 B 3 HIS A 317 CYS A 331 -1 O CYS A 331 N PHE A 150 SHEET 3 B 3 PRO A 251 ILE A 253 1 N VAL A 252 O HIS A 317 SHEET 1 C 8 PHE A 158 ARG A 168 0 SHEET 2 C 8 MET A 177 GLY A 185 -1 O ASN A 183 N SER A 161 SHEET 3 C 8 GLU A 187 ASP A 194 -1 O ALA A 191 N MET A 180 SHEET 4 C 8 HIS A 317 CYS A 331 -1 O VAL A 320 N GLY A 192 SHEET 5 C 8 THR A 205 PRO A 227 -1 N THR A 222 O SER A 328 SHEET 6 C 8 GLY A 278 MET A 295 -1 O LEU A 294 N GLN A 206 SHEET 7 C 8 ASN A 257 LEU A 264 -1 N LEU A 264 O ASP A 286 SHEET 8 C 8 ILE A 269 GLN A 274 -1 O ILE A 270 N PHE A 263 SHEET 1 D 2 ARG A 236 THR A 239 0 SHEET 2 D 2 THR A 246 PHE A 249 -1 O PHE A 249 N ARG A 236 LINK C ACE A 0 N MET A 1 1555 1555 1.31 LINK NE2 HIS A 153 ZN ZN A 501 1555 1555 2.25 CISPEP 1 GLN A 312 PRO A 313 0 5.26 SITE 1 AC1 2 HIS A 153 CL A 502 SITE 1 AC2 2 LYS A 154 ZN A 501 SITE 1 AC3 2 VAL A 217 ASP A 286 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 HETATM 1 C ACE A 0 14.302 18.440 -25.134 1.00 20.00 C HETATM 2 O ACE A 0 14.305 17.303 -25.574 1.00 20.00 O HETATM 3 CH3 ACE A 0 15.117 19.519 -25.805 1.00 20.00 C