HEADER MEMBRANE PROTEIN 05-DEC-25 9ZKD TITLE STRUCTURE OF RY12 DOMAIN OF RABBIT RYR1 COMPLEXED WITH ADP AND MG2+ TITLE 2 (MIMICKING MUSCLE FATIGUE) 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 9ZKD 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. 2.32 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) : 2.320 REMARK 3 NUMBER OF PARTICLES : 618878 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 9ZKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1000302883. 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 : RY12 DOMAIN OF RABBIT RYR1 REMARK 245 COMPLEXED WITH ADP AND MG2+ 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: 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 O1B ADP A 7602 MG MG A 7603 1.67 REMARK 500 O1A ADP A 7601 MG MG A 7603 1.69 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 GLN A 860 31.30 -96.75 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 MG A7603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A7601 O1B REMARK 620 2 ADP A7602 O2A 94.3 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-74364 RELATED DB: EMDB REMARK 900 STRUCTURE OF RY12 DOMAIN OF RABBIT RYR1 COMPLEXED WITH ADP AND MG2+ REMARK 900 (MIMICKING MUSCLE FATIGUE) DBREF 9ZKD A 850 1057 UNP P11716 RYR1_RABIT 850 1057 SEQRES 1 A 208 ASP PHE VAL PRO CYS PRO VAL ASP THR VAL GLN ILE VAL SEQRES 2 A 208 LEU PRO PRO HIS LEU GLU ARG ILE ARG GLU LYS LEU ALA SEQRES 3 A 208 GLU ASN ILE HIS GLU LEU TRP ALA LEU THR ARG ILE GLU SEQRES 4 A 208 GLN GLY TRP THR TYR GLY PRO VAL ARG ASP ASP ASN LYS SEQRES 5 A 208 ARG LEU HIS PRO CYS LEU VAL ASN PHE HIS SER LEU PRO SEQRES 6 A 208 GLU PRO GLU ARG ASN TYR ASN LEU GLN MET SER GLY GLU SEQRES 7 A 208 THR LEU LYS THR LEU LEU ALA LEU GLY CYS HIS VAL GLY SEQRES 8 A 208 MET ALA ASP GLU LYS ALA GLU ASP ASN LEU LYS LYS THR SEQRES 9 A 208 LYS LEU PRO LYS THR TYR MET MET SER ASN GLY TYR LYS SEQRES 10 A 208 PRO ALA PRO LEU ASP LEU SER HIS VAL ARG LEU THR PRO SEQRES 11 A 208 ALA GLN THR THR LEU VAL ASP ARG LEU ALA GLU ASN GLY SEQRES 12 A 208 HIS ASN VAL TRP ALA ARG ASP ARG VAL ALA GLN GLY TRP SEQRES 13 A 208 SER TYR SER ALA VAL GLN ASP ILE PRO ALA ARG ARG ASN SEQRES 14 A 208 PRO ARG LEU VAL PRO TYR ARG LEU LEU ASP GLU ALA THR SEQRES 15 A 208 LYS ARG SER ASN ARG ASP SER LEU CYS GLN ALA VAL ARG SEQRES 16 A 208 THR LEU LEU GLY TYR GLY TYR ASN ILE GLU PRO PRO ASP HET ADP A7601 27 HET ADP A7602 27 HET MG A7603 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 MG MG 2+ FORMUL 5 HOH *51(H2 O) HELIX 1 AA1 PRO A 864 ARG A 869 1 6 HELIX 2 AA2 ILE A 870 GLN A 889 1 20 HELIX 3 AA3 ASN A 909 LEU A 913 5 5 HELIX 4 AA4 PRO A 914 LEU A 935 1 22 HELIX 5 AA5 LYS A 945 LEU A 950 1 6 HELIX 6 AA6 PRO A 956 MET A 960 5 5 HELIX 7 AA7 THR A 978 GLN A 1003 1 26 HELIX 8 AA8 PRO A 1023 LEU A 1027 5 5 HELIX 9 AA9 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 MET A 941 0 SHEET 2 AA2 2 TYR A1051 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 LINK O1B ADP A7601 MG MG A7603 1555 1555 1.73 LINK O2A ADP A7602 MG MG A7603 1555 1555 1.80 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 1674 1675 1676 1677 1681 CONECT 1675 1674 1728 CONECT 1676 1674 CONECT 1677 1674 CONECT 1678 1679 1680 1681 1682 CONECT 1679 1678 CONECT 1680 1678 CONECT 1681 1674 1678 CONECT 1682 1678 1683 CONECT 1683 1682 1684 CONECT 1684 1683 1685 1686 CONECT 1685 1684 1690 CONECT 1686 1684 1687 1688 CONECT 1687 1686 CONECT 1688 1686 1689 1690 CONECT 1689 1688 CONECT 1690 1685 1688 1691 CONECT 1691 1690 1692 1700 CONECT 1692 1691 1693 CONECT 1693 1692 1694 CONECT 1694 1693 1695 1700 CONECT 1695 1694 1696 1697 CONECT 1696 1695 CONECT 1697 1695 1698 CONECT 1698 1697 1699 CONECT 1699 1698 1700 CONECT 1700 1691 1694 1699 CONECT 1701 1702 1703 1704 1708 CONECT 1702 1701 CONECT 1703 1701 CONECT 1704 1701 CONECT 1705 1706 1707 1708 1709 CONECT 1706 1705 CONECT 1707 1705 1728 CONECT 1708 1701 1705 CONECT 1709 1705 1710 CONECT 1710 1709 1711 CONECT 1711 1710 1712 1713 CONECT 1712 1711 1717 CONECT 1713 1711 1714 1715 CONECT 1714 1713 CONECT 1715 1713 1716 1717 CONECT 1716 1715 CONECT 1717 1712 1715 1718 CONECT 1718 1717 1719 1727 CONECT 1719 1718 1720 CONECT 1720 1719 1721 CONECT 1721 1720 1722 1727 CONECT 1722 1721 1723 1724 CONECT 1723 1722 CONECT 1724 1722 1725 CONECT 1725 1724 1726 CONECT 1726 1725 1727 CONECT 1727 1718 1721 1726 CONECT 1728 1675 1707 MASTER 140 0 3 9 6 0 0 6 1778 1 55 16 END