3J8H

Structure of the rabbit ryanodine receptor RyR1 in complex with FKBP12 at 3.8 Angstrom resolution

This is a large structure.

> Summary

Summary for 3J8H

EMDB informationEMD-2807
DescriptorRyanodine receptor 1, Peptidyl-prolyl cis-trans isomerase FKBP1A (E.C.5.2.1.8)
Functional Keywordsrabbit ryanodine receptor ryr1, high-conductance intracellular ca2+ channels, excitation-contraction coupling, transport protein-isomerase complex, transport protein/isomerase
Biological sourceOryctolagus cuniculus (rabbit)
Cellular locationCytoplasm  P62943
Total number of polymer chains8
Total molecular weight2048461.72
Authors
Yan, Z.,Bai, X.,Yan, C.,Wu, J.,Scheres, S.H.W.,Shi, Y.,Yan, N. (deposition date: 2014-10-26, release date: 2014-12-10, Last modification date: 2015-02-25)
Primary citation
Yan, Z.,Bai, X.C.,Yan, C.,Wu, J.,Li, Z.,Xie, T.,Peng, W.,Yin, C.C.,Li, X.,Scheres, S.H.,Shi, Y.,Yan, N.
Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution.
Nature, 517:50-55, 2015
PubMed: 25517095
DOI: 10.1038/nature14063
MImport into Mendeley
Experimental method
ELECTRON MICROSCOPY
?

Structure validation

ClashscoreRamachandran outliersSidechain outliers331.9%2.7%MetricValuePercentile RanksWorseBetterPercentile relative to all structuresPercentile relative to all EM structures

More Asymmetric unit images

Molmil generated image of 3j8h
no rotation
Molmil generated image of 3j8h
rotated about x axis by 90°
Molmil generated image of 3j8h
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, C, E, GRyanodine receptor 1polymer4599500213.44
UniProt (P11716)
Pfam (PF00520)
Pfam (PF00622)
Pfam (PF01365)
Pfam (PF02026)
Pfam (PF02815)
Pfam (PF06459)
Pfam (PF08454)
Pfam (PF08709)
Pfam (PF13833)
Oryctolagus cuniculus (rabbit)@PDBjRYR-1, RyR1, Skeletal muscle calcium release channel, Skeletal muscle ryanodine receptor, Skeletal muscle-type ryanodine receptor, Type 1 ryanodine receptor
B, D, F, HPeptidyl-prolyl cis-trans isomerase FKBP1Apolymer10711836.64
UniProt (P62943)
Pfam (PF00254)
Oryctolagus cuniculus (rabbit)@PDBjPPIase FKBP1A, 12 kDa FK506-binding protein, 12 kDa FKBP, FKBP-12, Calstabin-1, FK506-binding protein 1A, FKBP-1A, Immunophilin FKBP12, Rotamase
ZINC IONnon-polymer65.44

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains8
Total molecular weight2048200.2
Non-Polymers*Number of molecules4
Total molecular weight261.5
All*Total molecular weight2048461.7
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:ELECTRON MICROSCOPY

Cell axes1.0001.0001.000
Cell angles90.0090.0090.00
SpacegroupP 1
Resolution limits -
the highest resolution shell value -

Data Collection Statistics

Resolution limits -
the highest resolution shell value -

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

?

Functional Information from GO Data

ChainGOidnamespacecontents
B0043231cellular_componentintracellular membrane-bounded organelle
B0014802cellular_componentterminal cisterna
B0008144molecular_functiondrug binding
B0003755molecular_functionpeptidyl-prolyl cis-trans isomerase activity
B0010880biological_processregulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
B0060314biological_processregulation of ryanodine-sensitive calcium-release channel activity
D0043231cellular_componentintracellular membrane-bounded organelle
D0014802cellular_componentterminal cisterna
D0008144molecular_functiondrug binding
D0003755molecular_functionpeptidyl-prolyl cis-trans isomerase activity
D0010880biological_processregulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
D0060314biological_processregulation of ryanodine-sensitive calcium-release channel activity
F0043231cellular_componentintracellular membrane-bounded organelle
F0014802cellular_componentterminal cisterna
F0008144molecular_functiondrug binding
F0003755molecular_functionpeptidyl-prolyl cis-trans isomerase activity
F0010880biological_processregulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
F0060314biological_processregulation of ryanodine-sensitive calcium-release channel activity
H0043231cellular_componentintracellular membrane-bounded organelle
H0014802cellular_componentterminal cisterna
H0008144molecular_functiondrug binding
H0003755molecular_functionpeptidyl-prolyl cis-trans isomerase activity
H0010880biological_processregulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
H0060314biological_processregulation of ryanodine-sensitive calcium-release channel activity
A0016020cellular_componentmembrane
A1990425cellular_componentryanodine receptor complex
A0016529cellular_componentsarcoplasmic reticulum
A0033017cellular_componentsarcoplasmic reticulum membrane
A0014802cellular_componentterminal cisterna
A0005524molecular_functionATP binding
A0035381molecular_functionATP-gated ion channel activity
A0005262molecular_functioncalcium channel activity
A0005509molecular_functioncalcium ion binding
A0015278molecular_functioncalcium-release channel activity
A0005516molecular_functioncalmodulin binding
A0097718molecular_functiondisordered domain specific binding
A0008144molecular_functiondrug binding
A0042802molecular_functionidentical protein binding
A0044325molecular_functionion channel binding
A0005219molecular_functionryanodine-sensitive calcium-release channel activity
A0015643molecular_functiontoxic substance binding
A0005245molecular_functionvoltage-gated calcium channel activity
A0071313biological_processcellular response to caffeine
A0006936biological_processmuscle contraction
A0043931biological_processossification involved in bone maturation
A0003151biological_processoutflow tract morphogenesis
A0051209biological_processrelease of sequestered calcium ion into cytosol
A0014808biological_processrelease of sequestered calcium ion into cytosol by sarcoplasmic reticulum
A0048741biological_processskeletal muscle fiber development
A0043588biological_processskin development
C0016020cellular_componentmembrane
C1990425cellular_componentryanodine receptor complex
C0016529cellular_componentsarcoplasmic reticulum
C0033017cellular_componentsarcoplasmic reticulum membrane
C0014802cellular_componentterminal cisterna
C0005524molecular_functionATP binding
C0035381molecular_functionATP-gated ion channel activity
C0005262molecular_functioncalcium channel activity
C0005509molecular_functioncalcium ion binding
C0015278molecular_functioncalcium-release channel activity
C0005516molecular_functioncalmodulin binding
C0097718molecular_functiondisordered domain specific binding
C0008144molecular_functiondrug binding
C0042802molecular_functionidentical protein binding
C0044325molecular_functionion channel binding
C0005219molecular_functionryanodine-sensitive calcium-release channel activity
C0015643molecular_functiontoxic substance binding
C0005245molecular_functionvoltage-gated calcium channel activity
C0071313biological_processcellular response to caffeine
C0006936biological_processmuscle contraction
C0043931biological_processossification involved in bone maturation
C0003151biological_processoutflow tract morphogenesis
C0051209biological_processrelease of sequestered calcium ion into cytosol
C0014808biological_processrelease of sequestered calcium ion into cytosol by sarcoplasmic reticulum
C0048741biological_processskeletal muscle fiber development
C0043588biological_processskin development
E0016020cellular_componentmembrane
E1990425cellular_componentryanodine receptor complex
E0016529cellular_componentsarcoplasmic reticulum
E0033017cellular_componentsarcoplasmic reticulum membrane
E0014802cellular_componentterminal cisterna
E0005524molecular_functionATP binding
E0035381molecular_functionATP-gated ion channel activity
E0005262molecular_functioncalcium channel activity
E0005509molecular_functioncalcium ion binding
E0015278molecular_functioncalcium-release channel activity
E0005516molecular_functioncalmodulin binding
E0097718molecular_functiondisordered domain specific binding
E0008144molecular_functiondrug binding
E0042802molecular_functionidentical protein binding
E0044325molecular_functionion channel binding
E0005219molecular_functionryanodine-sensitive calcium-release channel activity
E0015643molecular_functiontoxic substance binding
E0005245molecular_functionvoltage-gated calcium channel activity
E0071313biological_processcellular response to caffeine
E0006936biological_processmuscle contraction
E0043931biological_processossification involved in bone maturation
E0003151biological_processoutflow tract morphogenesis
E0051209biological_processrelease of sequestered calcium ion into cytosol
E0014808biological_processrelease of sequestered calcium ion into cytosol by sarcoplasmic reticulum
E0048741biological_processskeletal muscle fiber development
E0043588biological_processskin development
G0016020cellular_componentmembrane
G1990425cellular_componentryanodine receptor complex
G0016529cellular_componentsarcoplasmic reticulum
G0033017cellular_componentsarcoplasmic reticulum membrane
G0014802cellular_componentterminal cisterna
G0005524molecular_functionATP binding
G0035381molecular_functionATP-gated ion channel activity
G0005262molecular_functioncalcium channel activity
G0005509molecular_functioncalcium ion binding
G0015278molecular_functioncalcium-release channel activity
G0005516molecular_functioncalmodulin binding
G0097718molecular_functiondisordered domain specific binding
G0008144molecular_functiondrug binding
G0042802molecular_functionidentical protein binding
G0044325molecular_functionion channel binding
G0005219molecular_functionryanodine-sensitive calcium-release channel activity
G0015643molecular_functiontoxic substance binding
G0005245molecular_functionvoltage-gated calcium channel activity
G0071313biological_processcellular response to caffeine
G0006936biological_processmuscle contraction
G0043931biological_processossification involved in bone maturation
G0003151biological_processoutflow tract morphogenesis
G0051209biological_processrelease of sequestered calcium ion into cytosol
G0014808biological_processrelease of sequestered calcium ion into cytosol by sarcoplasmic reticulum
G0048741biological_processskeletal muscle fiber development
G0043588biological_processskin development
?

Functional Information from PDB Data

site_idNumber of ResiduesDetails
?

Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
?

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
?

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
?

Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2017 Protein Data Bank Japan