HEADER TRANSPORT PROTEIN 12-MAY-17 5VSN TITLE CRYSTAL STRUCTURE OF MOUSE RYANODINE RECEPTOR 2 SPRY2 DOMAIN (1080- TITLE 2 1253) DISEASE MUTANT P1124L COMPND MOL_ID: 1; COMPND 2 MOLECULE: RYANODINE RECEPTOR 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SPRY2 DOMAIN (UNP RESIDUES 1084-1252); COMPND 5 SYNONYM: RYR2, CARDIAC MUSCLE RYANODINE RECEPTOR, CARDIAC MUSCLE COMPND 6 RYANODINE RECEPTOR-CALCIUM RELEASE CHANNEL, TYPE 2 RYANODINE COMPND 7 RECEPTOR; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RYR2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RYANODINE RECEPTOR, DISEASE MUTANT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.YUCHI,F.VAN PETEGEM REVDAT 3 04-OCT-23 5VSN 1 LINK REVDAT 2 12-JUN-19 5VSN 1 JRNL REVDAT 1 23-MAY-18 5VSN 0 JRNL AUTH F.J.ALVARADO,J.M.BOS,Z.YUCHI,C.R.VALDIVIA,J.J.HERNANDEZ, JRNL AUTH 2 Y.T.ZHAO,D.S.HENDERLONG,Y.CHEN,T.R.BOOHER,C.A.MARCOU, JRNL AUTH 3 F.VAN PETEGEM,M.J.ACKERMAN,H.H.VALDIVIA JRNL TITL CARDIAC HYPERTROPHY AND ARRHYTHMIA IN MICE INDUCED BY A JRNL TITL 2 MUTATION IN RYANODINE RECEPTOR 2. JRNL REF JCI INSIGHT V. 5 2019 JRNL REFN ISSN 2379-3708 JRNL PMID 30835254 JRNL DOI 10.1172/JCI.INSIGHT.126544 REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 29666 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1480 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 24.6150 - 3.1991 1.00 2753 145 0.1547 0.1619 REMARK 3 2 3.1991 - 2.5401 1.00 2641 139 0.1746 0.2017 REMARK 3 3 2.5401 - 2.2192 1.00 2611 136 0.1799 0.2153 REMARK 3 4 2.2192 - 2.0164 1.00 2564 137 0.1680 0.1912 REMARK 3 5 2.0164 - 1.8719 1.00 2600 136 0.1792 0.1812 REMARK 3 6 1.8719 - 1.7616 1.00 2556 135 0.1863 0.2027 REMARK 3 7 1.7616 - 1.6734 1.00 2555 135 0.1925 0.2619 REMARK 3 8 1.6734 - 1.6006 1.00 2565 135 0.2009 0.1987 REMARK 3 9 1.6006 - 1.5390 1.00 2546 134 0.2200 0.2414 REMARK 3 10 1.5390 - 1.4859 1.00 2539 133 0.2565 0.2830 REMARK 3 11 1.4859 - 1.4394 0.89 2256 115 0.3006 0.2998 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.49 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 : 0.005 1445 REMARK 3 ANGLE : 0.757 1958 REMARK 3 CHIRALITY : 0.079 194 REMARK 3 PLANARITY : 0.004 264 REMARK 3 DIHEDRAL : 3.772 785 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 5VSN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227942. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29741 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.439 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.83000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.11.1_2575 REMARK 200 STARTING MODEL: PDB ENTRY 4P9I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M POTASSIUM THIOCYANATE, 30% REMARK 280 PEG2000 MME, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.11500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.49000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.11500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.49000 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 K K A1302 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1508 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A1084 CG CD NE CZ NH1 NH2 REMARK 470 PHE A1085 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A1123 CG CD OE1 NE2 REMARK 470 VAL A1209 CG1 CG2 REMARK 470 LYS A1225 CG CD CE NZ 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 NH1 ARG A 1119 O HOH A 1401 2.19 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 LEU A1124 59.56 -110.35 REMARK 500 ASP A1131 -157.95 -136.43 REMARK 500 ASP A1131 -159.69 -136.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1302 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A1094 OH REMARK 620 2 TYR A1094 OH 0.0 REMARK 620 3 THR A1243 O 73.0 73.0 REMARK 620 4 THR A1243 O 73.0 73.0 0.0 REMARK 620 5 HOH A1459 O 106.5 106.5 81.5 81.5 REMARK 620 6 HOH A1459 O 142.0 142.0 77.6 77.6 92.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 1302 DBREF 5VSN A 1084 1252 UNP E9Q401 RYR2_MOUSE 1084 1252 SEQADV 5VSN LEU A 1124 UNP E9Q401 PRO 1124 ENGINEERED MUTATION SEQRES 1 A 169 ARG PHE ARG ILE PHE ARG ALA GLU LYS THR TYR ALA VAL SEQRES 2 A 169 LYS ALA GLY ARG TRP TYR PHE GLU PHE GLU ALA VAL THR SEQRES 3 A 169 ALA GLY ASP MET ARG VAL GLY TRP SER ARG PRO GLY CYS SEQRES 4 A 169 GLN LEU ASP LEU GLU LEU GLY SER ASP ASP ARG ALA PHE SEQRES 5 A 169 ALA PHE ASP GLY PHE LYS ALA GLN ARG TRP HIS GLN GLY SEQRES 6 A 169 ASN GLU HIS TYR GLY ARG SER TRP GLN ALA GLY ASP VAL SEQRES 7 A 169 VAL GLY CYS MET VAL ASP MET ASN GLU HIS THR MET MET SEQRES 8 A 169 PHE THR LEU ASN GLY GLU ILE LEU LEU ASP ASP SER GLY SEQRES 9 A 169 SER GLU LEU ALA PHE LYS ASP PHE ASP VAL GLY ASP GLY SEQRES 10 A 169 PHE ILE PRO VAL CYS SER LEU GLY VAL ALA GLN VAL GLY SEQRES 11 A 169 ARG MET ASN PHE GLY LYS ASP VAL SER THR LEU LYS TYR SEQRES 12 A 169 PHE THR ILE CYS GLY LEU GLN GLU GLY TYR GLU PRO PHE SEQRES 13 A 169 ALA VAL ASN THR ASN ARG ASP ILE THR MET TRP LEU SER HET GOL A1301 6 HET K A1302 1 HETNAM GOL GLYCEROL HETNAM K POTASSIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 K K 1+ FORMUL 4 HOH *111(H2 O) HELIX 1 AA1 GLU A 1091 ALA A 1095 5 5 HELIX 2 AA2 ASP A 1220 LEU A 1224 5 5 HELIX 3 AA3 ALA A 1240 THR A 1243 5 4 SHEET 1 AA1 6 ARG A1086 ARG A1089 0 SHEET 2 AA1 6 ILE A1202 LEU A1207 -1 O LEU A1207 N ARG A1086 SHEET 3 AA1 6 MET A1113 SER A1118 -1 N SER A1118 O ILE A1202 SHEET 4 AA1 6 ALA A1134 ASP A1138 -1 O PHE A1137 N VAL A1115 SHEET 5 AA1 6 GLN A1143 TRP A1145 -1 O TRP A1145 N ALA A1136 SHEET 6 AA1 6 ASN A1149 HIS A1151 -1 O GLU A1150 N ARG A1144 SHEET 1 AA2 5 GLU A1180 ILE A1181 0 SHEET 2 AA2 5 THR A1172 LEU A1177 -1 N LEU A1177 O GLU A1180 SHEET 3 AA2 5 VAL A1161 ASP A1167 -1 N ASP A1167 O THR A1172 SHEET 4 AA2 5 ARG A1100 ALA A1107 -1 N PHE A1103 O CYS A1164 SHEET 5 AA2 5 GLY A1213 ASN A1216 -1 O ASN A1216 N GLU A1104 SHEET 1 AA3 5 PHE A1192 LYS A1193 0 SHEET 2 AA3 5 THR A1172 LEU A1177 -1 N MET A1173 O PHE A1192 SHEET 3 AA3 5 VAL A1161 ASP A1167 -1 N ASP A1167 O THR A1172 SHEET 4 AA3 5 ARG A1100 ALA A1107 -1 N PHE A1103 O CYS A1164 SHEET 5 AA3 5 GLU A1237 PRO A1238 1 O GLU A1237 N TYR A1102 LINK OH TYR A1094 K K A1302 1555 1555 2.93 LINK OH TYR A1094 K K A1302 1555 2555 2.93 LINK O THR A1243 K K A1302 1555 1555 2.72 LINK O THR A1243 K K A1302 1555 2555 2.72 LINK K K A1302 O HOH A1459 1555 1555 2.74 LINK K K A1302 O HOH A1459 1555 2555 2.74 SITE 1 AC1 8 ARG A1086 SER A1188 GLU A1189 LEU A1207 SITE 2 AC1 8 VAL A1212 GLY A1213 ARG A1214 HOH A1479 SITE 1 AC2 3 TYR A1094 THR A1243 HOH A1459 CRYST1 36.290 66.230 66.980 90.00 90.00 90.00 P 2 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 0.027556 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015099 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014930 0.00000