7MIX

Human N-type voltage-gated calcium channel Cav2.2 in the presence of ziconotide at 3.0 Angstrom resolution


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 1.3 of the entry. See complete history


Literature

Structure of human Ca v 2.2 channel blocked by the painkiller ziconotide.

Gao, S.Yao, X.Yan, N.

(2021) Nature 596: 143-147

  • DOI: https://doi.org/10.1038/s41586-021-03699-6
  • Primary Citation of Related Structures:  
    7MIX

  • PubMed Abstract: 

    The neuronal-type (N-type) voltage-gated calcium (Ca v ) channels, which are designated Ca v 2.2, have an important role in the release of neurotransmitters 1-3 . Ziconotide is a Ca v 2.2-specific peptide pore blocker that has been clinically used for treating intractable pain 4-6 . Here we present cryo-electron microscopy structures of human Ca v 2.2 (comprising the core α1 and the ancillary α2δ-1 and β3 subunits) in the presence or absence of ziconotide. Ziconotide is thoroughly coordinated by helices P1 and P2, which support the selectivity filter, and the extracellular loops (ECLs) in repeats II, III and IV of α1. To accommodate ziconotide, the ECL of repeat III and α2δ-1 have to tilt upward concertedly. Three of the voltage-sensing domains (VSDs) are in a depolarized state, whereas the VSD of repeat II exhibits a down conformation that is stabilized by Ca v 2-unique intracellular segments and a phosphatidylinositol 4,5-bisphosphate molecule. Our studies reveal the molecular basis for Ca v 2.2-specific pore blocking by ziconotide and establish the framework for investigating electromechanical coupling in Ca v channels.


  • Organizational Affiliation

    Department of Molecular Biology, Princeton University, Princeton, NJ, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent N-type calcium channel subunit alpha-1B2,339Homo sapiensMutation(s): 0 
Gene Names: CACNA1BCACH5CACNL1A5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q00975 (Homo sapiens)
Explore Q00975 
Go to UniProtKB:  Q00975
PHAROS:  Q00975
GTEx:  ENSG00000148408 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00975
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Omega-conotoxin MVIIA25Conus magusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05484 (Conus magus)
Explore P05484 
Go to UniProtKB:  P05484
Entity Groups  
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UniProt GroupP05484
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent calcium channel subunit alpha-2/delta-1C [auth D]1,103Homo sapiensMutation(s): 0 
Gene Names: CACNA2D1CACNL2ACCHL2AMHS3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P54289 (Homo sapiens)
Explore P54289 
Go to UniProtKB:  P54289
PHAROS:  P54289
GTEx:  ENSG00000153956 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54289
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit beta-3D [auth C]484Homo sapiensMutation(s): 0 
Gene Names: CACNB3CACNLB3
UniProt & NIH Common Fund Data Resources
Find proteins for P54284 (Homo sapiens)
Explore P54284 
Go to UniProtKB:  P54284
PHAROS:  P54284
GTEx:  ENSG00000167535 
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UniProt GroupP54284
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranoseE [auth G]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
GlyGen:  G47362BJ
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth J],
H [auth P],
I [auth S]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth L]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G01361SX
GlyCosmos:  G01361SX
GlyGen:  G01361SX
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PT5 (Subject of Investigation/LOI)
Query on PT5

Download Ideal Coordinates CCD File 
U [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
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
S [auth A],
T [auth A]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
Y01 (Subject of Investigation/LOI)
Query on Y01

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L [auth A],
O [auth A]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A],
P [auth A],
Q [auth A],
R [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
J [auth A],
V [auth D],
W [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
K [auth A],
X [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM130762

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Structure summary
  • Version 1.2: 2021-07-28
    Changes: Database references
  • Version 1.3: 2021-08-18
    Changes: Database references