5GJV

Structure of the mammalian voltage-gated calcium channel Cav1.1 complex at near atomic resolution

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Structure of the voltage-gated calcium channel Cav1.1 at 3.6 angstrom resolution

Wu, J.P., Yan, Z., Li, Z.Q., Qian, X.Y., Lu, S., Dong, M.Q., Zhou, Q., Yan, N.

(2016) Nature 537: 191-196

  • DOI: 10.1038/nature19321
  • Primary Citation of Related Structures:  
    5GJV, 5GJW

  • PubMed Abstract: 

    • The voltage-gated calcium (Ca v ) channels convert membrane electrical signals to intracellular Ca 2+ -mediated events. Among the ten subtypes of Ca v channel in mammals, Ca v 1.1 is specified for the excitation-contraction coupling of skeletal muscles ...

    The voltage-gated calcium (Ca v ) channels convert membrane electrical signals to intracellular Ca 2+ -mediated events. Among the ten subtypes of Ca v channel in mammals, Ca v 1.1 is specified for the excitation-contraction coupling of skeletal muscles. Here we present the cryo-electron microscopy structure of the rabbit Ca v 1.1 complex at a nominal resolution of 3.6 Å. The inner gate of the ion-conducting α1-subunit is closed and all four voltage-sensing domains adopt an 'up' conformation, suggesting a potentially inactivated state. The extended extracellular loops of the pore domain, which are stabilized by multiple disulfide bonds, form a windowed dome above the selectivity filter. One side of the dome provides the docking site for the α2δ-1-subunit, while the other side may attract cations through its negative surface potential. The intracellular I-II and III-IV linker helices interact with the β 1a -subunit and the carboxy-terminal domain of α1, respectively. Classification of the particles yielded two additional reconstructions that reveal pronounced displacement of β 1a and adjacent elements in α1. The atomic model of the Ca v 1.1 complex establishes a foundation for mechanistic understanding of excitation-contraction coupling and provides a three-dimensional template for molecular interpretations of the functions and disease mechanisms of Ca v and Na v channels.

    Organizational Affiliation: 

    Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit alpha-1SA1,873Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNA1S, CACH1, CACNL1A3
Membrane Entity: Yes 
UniProt
Find proteins for P07293 (Oryctolagus cuniculus)
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UniProt GroupP07293
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit beta-1B106Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNB1, CACNLB1
Membrane Entity: Yes 
UniProt
Find proteins for P19517 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit beta-1C199Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNB1, CACNLB1
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent calcium channel gamma-1 subunitD [auth E]222Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNG1, CACNLG
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent calcium channel subunit alpha-2/delta-1E [auth F]1,106Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNA2D1, CACNL2A, CCHL2A
Membrane Entity: Yes 
UniProt
Find proteins for P13806 (Oryctolagus cuniculus)
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Oligosaccharides

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Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth D],
G,
J,
K		2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH, I 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1
Download Ideal Coordinates CCD File 
AA [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
AA [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
DA [auth F],
EA [auth F],
FA [auth F],
GA [auth F],
HA [auth F],
DA [auth F],
EA [auth F],
FA [auth F],
GA [auth F],
HA [auth F],
IA [auth F],
JA [auth F],
M [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
BA [auth A],
CA [auth A],
KA [auth F]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXdev-2405
MODEL REFINEMENTREFMAC5.8
RECONSTRUCTIONRELION1.4

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
the Ministry of Science and Technology of ChinaChina2015CB9101012014, ZX09507003006
National Natural Science Foundation of ChinaChina31130002 and 31125009

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references, Other
  • Version 1.2: 2018-10-24
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 1.3: 2019-12-11
    Changes: Experimental preparation
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary