HEADER MEMBRANE PROTEIN 08-DEC-25 9ZLF TITLE STRUCTURE OF RY12 DOMAIN OF RABBIT RYR1 COMPLEXED WITH DANTROLENE AND TITLE 2 ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RYANODINE RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RYR-1,RYR1,SKELETAL MUSCLE CALCIUM RELEASE CHANNEL,SKELETAL COMPND 5 MUSCLE RYANODINE RECEPTOR,SKELETAL MUSCLE-TYPE RYANODINE RECEPTOR, COMPND 6 TYPE 1 RYANODINE RECEPTOR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986 KEYWDS SARCOPLASMIC RETICULUM, INTRACELLULAR CALCIUM CHANNEL, EXCITATION- KEYWDS 2 CONTRACTION COUPLING, COMPLEX, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR K.KIM,O.B.CLARKE REVDAT 1 16-SEP-26 9ZLF 0 JRNL AUTH K.KIM,H.LI,Q.YUAN,Z.MELVILLE,R.ZALK,A.DES GEORGES,J.FRANK, JRNL AUTH 2 W.A.HENDRICKSON,A.R.MARKS,O.B.CLARKE JRNL TITL STRUCTURAL IDENTIFICATION OF THE RY12 DOMAIN OF RYR1 AS AN JRNL TITL 2 ADP SENSOR AND THE TARGET OF THE MALIGNANT HYPERTHERMIA JRNL TITL 3 THERAPEUTIC DANTROLENE JRNL REF NAT COMMUN 2026 JRNL REFN ESSN 2041-1723 JRNL DOI 10.1038/S41467-026-76519-Y REMARK 2 REMARK 2 RESOLUTION. 2.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.710 REMARK 3 NUMBER OF PARTICLES : 282476 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9ZLF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1000303020. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : RYR1 COMPLEXED WITH FKBP12.6 REMARK 245 AND CALMODULIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5800.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL 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 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 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 ALA A 942 -118.84 59.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-74402 RELATED DB: EMDB REMARK 900 STRUCTURE OF RY12 DOMAIN OF RABBIT RYR1 COMPLEXED WITH DANTROLENE REMARK 900 AND ATP DBREF 9ZLF A 850 1055 UNP P11716 RYR1_RABIT 850 1055 SEQRES 1 A 206 ASP PHE VAL PRO CYS PRO VAL ASP THR VAL GLN ILE VAL SEQRES 2 A 206 LEU PRO PRO HIS LEU GLU ARG ILE ARG GLU LYS LEU ALA SEQRES 3 A 206 GLU ASN ILE HIS GLU LEU TRP ALA LEU THR ARG ILE GLU SEQRES 4 A 206 GLN GLY TRP THR TYR GLY PRO VAL ARG ASP ASP ASN LYS SEQRES 5 A 206 ARG LEU HIS PRO CYS LEU VAL ASN PHE HIS SER LEU PRO SEQRES 6 A 206 GLU PRO GLU ARG ASN TYR ASN LEU GLN MET SER GLY GLU SEQRES 7 A 206 THR LEU LYS THR LEU LEU ALA LEU GLY CYS HIS VAL GLY SEQRES 8 A 206 MET ALA ASP GLU LYS ALA GLU ASP ASN LEU LYS LYS THR SEQRES 9 A 206 LYS LEU PRO LYS THR TYR MET MET SER ASN GLY TYR LYS SEQRES 10 A 206 PRO ALA PRO LEU ASP LEU SER HIS VAL ARG LEU THR PRO SEQRES 11 A 206 ALA GLN THR THR LEU VAL ASP ARG LEU ALA GLU ASN GLY SEQRES 12 A 206 HIS ASN VAL TRP ALA ARG ASP ARG VAL ALA GLN GLY TRP SEQRES 13 A 206 SER TYR SER ALA VAL GLN ASP ILE PRO ALA ARG ARG ASN SEQRES 14 A 206 PRO ARG LEU VAL PRO TYR ARG LEU LEU ASP GLU ALA THR SEQRES 15 A 206 LYS ARG SER ASN ARG ASP SER LEU CYS GLN ALA VAL ARG SEQRES 16 A 206 THR LEU LEU GLY TYR GLY TYR ASN ILE GLU PRO HET U1C A1101 23 HET ATP A1102 31 HETNAM U1C DANTROLENE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETSYN U1C 1-[(Z)-{[5-(4-NITROPHENYL)FURAN-2- HETSYN 2 U1C YL]METHYLIDENE}AMINO]IMIDAZOLIDINE-2,4-DIONE FORMUL 2 U1C C14 H10 N4 O5 FORMUL 3 ATP C10 H16 N5 O13 P3 FORMUL 4 HOH *44(H2 O) HELIX 1 AA1 PRO A 864 ARG A 869 1 6 HELIX 2 AA2 ILE A 870 GLY A 890 1 21 HELIX 3 AA3 PRO A 914 LEU A 935 1 22 HELIX 4 AA4 LYS A 945 LEU A 950 1 6 HELIX 5 AA5 PRO A 956 MET A 960 5 5 HELIX 6 AA6 THR A 978 GLY A 1004 1 27 HELIX 7 AA7 PRO A 1023 LEU A 1027 5 5 HELIX 8 AA8 ASP A 1028 TYR A 1049 1 22 SHEET 1 AA1 2 THR A 892 TYR A 893 0 SHEET 2 AA1 2 LEU A 903 HIS A 904 1 O HIS A 904 N THR A 892 SHEET 1 AA2 2 HIS A 938 GLY A 940 0 SHEET 2 AA2 2 ASN A1052 GLU A1054 -1 O GLU A1054 N HIS A 938 SHEET 1 AA3 2 SER A1006 TYR A1007 0 SHEET 2 AA3 2 ARG A1017 ASN A1018 1 O ASN A1018 N SER A1006 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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 CONECT 1659 1672 1673 CONECT 1660 1661 1675 CONECT 1661 1660 1662 CONECT 1662 1661 1663 1679 CONECT 1663 1662 1664 CONECT 1664 1663 1665 CONECT 1665 1664 1674 1679 CONECT 1666 1669 1674 CONECT 1667 1670 1671 CONECT 1668 1672 1675 CONECT 1669 1666 1670 CONECT 1670 1667 1669 1676 CONECT 1671 1667 1674 CONECT 1672 1659 1668 1677 CONECT 1673 1659 1675 1678 CONECT 1674 1665 1666 1671 CONECT 1675 1660 1668 1673 CONECT 1676 1670 1680 1681 CONECT 1677 1672 CONECT 1678 1673 CONECT 1679 1662 1665 CONECT 1680 1676 CONECT 1681 1676 CONECT 1682 1683 1684 1685 1689 CONECT 1683 1682 CONECT 1684 1682 CONECT 1685 1682 CONECT 1686 1687 1688 1689 1693 CONECT 1687 1686 CONECT 1688 1686 CONECT 1689 1682 1686 CONECT 1690 1691 1692 1693 1694 CONECT 1691 1690 CONECT 1692 1690 CONECT 1693 1686 1690 CONECT 1694 1690 1695 CONECT 1695 1694 1696 CONECT 1696 1695 1697 1698 CONECT 1697 1696 1702 CONECT 1698 1696 1699 1700 CONECT 1699 1698 CONECT 1700 1698 1701 1702 CONECT 1701 1700 CONECT 1702 1697 1700 1703 CONECT 1703 1702 1704 1712 CONECT 1704 1703 1705 CONECT 1705 1704 1706 CONECT 1706 1705 1707 1712 CONECT 1707 1706 1708 1709 CONECT 1708 1707 CONECT 1709 1707 1710 CONECT 1710 1709 1711 CONECT 1711 1710 1712 CONECT 1712 1703 1706 1711 MASTER 118 0 2 8 6 0 0 6 1755 1 54 16 END