6KZP | pdb_00006kzp

calcium channel-ligand


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6KZP

This is version 1.3 of the entry. See complete history

Literature

Cryo-EM structures of apo and antagonist-bound human Cav3.1.

Zhao, Y.Huang, G.Wu, Q.Wu, K.Li, R.Lei, J.Pan, X.Yan, N.

(2019) Nature 576: 492-497

  • DOI: https://doi.org/10.1038/s41586-019-1801-3
  • Primary Citation Related Structures: 
    6KZO, 6KZP

  • PubMed Abstract: 

    Among the ten subtypes of mammalian voltage-gated calcium (Ca v ) channels, Ca v 3.1-Ca v 3.3 constitute the T-type, or the low-voltage-activated, subfamily, the abnormal activities of which are associated with epilepsy, psychiatric disorders and pain 1-5 . Here we report the cryo-electron microscopy structures of human Ca v 3.1 alone and in complex with a highly Ca v 3-selective blocker, Z944 6,7 , at resolutions of 3.3 Å and 3.1 Å, respectively. The arch-shaped Z944 molecule reclines in the central cavity of the pore domain, with the wide end inserting into the fenestration on the interface between repeats II and III, and the narrow end hanging above the intracellular gate like a plug. The structures provide the framework for comparative investigation of the distinct channel properties of different Ca v subfamilies.


  • Organizational Affiliation
    • Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.

Macromolecule Content 

  • Total Structure Weight: 247.67 kDa 
  • Atom Count: 8,557 
  • Modeled Residue Count: 1,014 
  • Deposited Residue Count: 2,146 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Voltage-dependent T-type calcium channel subunit alpha-1G,Voltage-dependent T-type calcium channel subunit alpha-1G2,146Homo sapiensMutation(s): 0 
Gene Names: CACNA1GKIAA1123
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O43497 (Homo sapiens)
Explore O43497 
Go to UniProtKB:  O43497
PHAROS:  O43497
GTEx:  ENSG00000006283 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43497
Glycosylation
Glycosylation Sites: 4Go to GlyGen: O43497-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
Y01

Query on Y01



Download:Ideal Coordinates CCD File
Q [auth A],
R [auth A],
S [auth A]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
DZR
(Subject of Investigation/LOI)

Query on DZR



Download:Ideal Coordinates CCD File
H [auth A]~{N}-[[1-[2-(~{tert}-butylamino)-2-oxidanylidene-ethyl]piperidin-4-yl]methyl]-3-chloranyl-5-fluoranyl-benzamide
C19 H27 Cl F N3 O2
JOCLITFYIMJMNK-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
DZR BindingDB:  6KZP IC50: 37 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2019-12-18 
  • Deposition Author(s): Yan, N.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31621092
National Natural Science Foundation of ChinaChina31800628
National Natural Science Foundation of ChinaChina81920108015
Ministry of Science and Technology (China)China2016YFA0500402
Ministry of Science and Technology (China)China2016YFA0501100

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary