7VFU

Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to ziconotide

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Closed-state inactivation and pore-blocker modulation mechanisms of human Ca V 2.2.

Dong, Y., Gao, Y., Xu, S., Wang, Y., Yu, Z., Li, Y., Li, B., Yuan, T., Yang, B., Zhang, X.C., Jiang, D., Huang, Z., Zhao, Y.

(2021) Cell Rep 37: 109931-109931

  • DOI: https://doi.org/10.1016/j.celrep.2021.109931
  • Primary Citation of Related Structures:  
    7VFS, 7VFU, 7VFV, 7VFW

  • PubMed Abstract: 

    • N-type voltage-gated calcium (Ca V ) channels mediate Ca 2+ influx at presynaptic terminals in response to action potentials and play vital roles in synaptogenesis, release of neurotransmitters, and nociceptive transmission. Here, we elucidate a cryo-electron microscopy (cryo-EM) structure of the human Ca V 2 ...

    N-type voltage-gated calcium (Ca V ) channels mediate Ca 2+ influx at presynaptic terminals in response to action potentials and play vital roles in synaptogenesis, release of neurotransmitters, and nociceptive transmission. Here, we elucidate a cryo-electron microscopy (cryo-EM) structure of the human Ca V 2.2 complex in apo, ziconotide-bound, and two Ca V 2.2-specific pore blockers-bound states. The second voltage-sensing domain (VSD) is captured in a resting-state conformation, trapped by a phosphatidylinositol 4,5-bisphosphate (PIP 2 ) molecule, which is distinct from the other three VSDs of Ca V 2.2, as well as activated VSDs observed in previous structures of Ca V channels. This structure reveals the molecular basis for the unique inactivation process of Ca V 2.2 channels, in which the intracellular gate formed by S6 helices is closed and a W-helix from the domain II-III linker stabilizes closed-state inactivation. The structures of this inactivated, drug-bound complex lay a solid foundation for developing new state-dependent blockers for treatment of chronic pain.

    Organizational Affiliation: 

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: zhaoy@ibp.ac.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent N-type calcium channel subunit alpha-1BA2,339Homo sapiensMutation(s): 0 
Gene Names: CACNA1B, CACH5, CACNL1A5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q00975 (Homo sapiens)
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Go to UniProtKB:  Q00975
PHAROS:  Q00975
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UniProt GroupQ00975
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Omega-conotoxin MVIIAB [auth E]25Conus magusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05484 (Conus magus)
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Go to UniProtKB:  P05484
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UniProt GroupP05484
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit beta-1C [auth D]598Homo sapiensMutation(s): 0 
Gene Names: CACNB1, CACNLB1
Membrane Entity: Yes 
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Find proteins for Q02641 (Homo sapiens)
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PHAROS:  Q02641
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UniProt GroupQ02641
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent calcium channel subunit alpha-2/delta-1D [auth B]1,103Homo sapiensMutation(s): 0 
Gene Names: CACNA2D1, CACNL2A, CCHL2A, MHS3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P54289 (Homo sapiens)
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PHAROS:  P54289
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Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C],
F		3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G44266EX
GlyCosmos:  G44266EX
GlyGen:  G44266EX
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT5
Query on PT5
Download Ideal Coordinates CCD File 
CA [auth A][(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
C47 H85 O19 P3
CNWINRVXAYPOMW-HJBQCNPJSA-N		 Ligand Interaction
Y01
Query on Y01
Download Ideal Coordinates CCD File 
BA [auth A],
K [auth A],
S [auth A]		CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N		 Ligand Interaction
R16
Query on R16
Download Ideal Coordinates CCD File 
AA [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth A],
AA [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B]
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 
DA [auth A],
EA [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB37030304

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references