7CFS | pdb_00007cfs

Cryo-EM strucutre of human acid-sensing ion channel 1a at pH 8.0


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7CFS

This is version 1.1 of the entry. See complete history

Literature

Structural insights into human acid-sensing ion channel 1a inhibition by snake toxin mambalgin1.

Sun, D.Liu, S.Li, S.Zhang, M.Yang, F.Wen, M.Shi, P.Wang, T.Pan, M.Chang, S.Zhang, X.Zhang, L.Tian, C.Liu, L.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.57096
  • Primary Citation Related Structures: 
    7CFS, 7CFT

  • PubMed Abstract: 

    Acid-sensing ion channels (ASICs) are proton-gated cation channels that are involved in diverse neuronal processes including pain sensing. The peptide toxin Mambalgin1 (Mamba1) from black mamba snake venom can reversibly inhibit the conductance of ASICs, causing an analgesic effect. However, the detailed mechanism by which Mamba1 inhibits ASIC1s, especially how Mamba1 binding to the extracellular domain affects the conformational changes of the transmembrane domain of ASICs remains elusive. Here, we present single-particle cryo-EM structures of human ASIC1a (hASIC1a) and the hASIC1a-Mamba1 complex at resolutions of 3.56 and 3.90 Å, respectively. The structures revealed the inhibited conformation of hASIC1a upon Mamba1 binding. The combination of the structural and physiological data indicates that Mamba1 preferentially binds hASIC1a in a closed state and reduces the proton sensitivity of the channel, representing a closed-state trapping mechanism.


  • Organizational Affiliation
    • Hefei National Laboratory of Physical Sciences at Microscale, Anhui Laboratory of Advanced Photonic Science and Technology and School of Life Sciences, University of Science and Technology of China, Hefei, China.

Macromolecule Content 

  • Total Structure Weight: 166.91 kDa 
  • Atom Count: 9,974 
  • Modeled Residue Count: 1,278 
  • Deposited Residue Count: 1,431 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acid-sensing ion channel 1
A, B, C
477Homo sapiensMutation(s): 0 
Gene Names: ASIC1ACCN2BNAC2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P78348 (Homo sapiens)
Explore P78348 
Go to UniProtKB:  P78348
PHAROS:  P78348
GTEx:  ENSG00000110881 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78348
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P78348-2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01

Query on Y01



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B],
M [auth C]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
H [auth B]
I [auth B]
K [auth C]
D [auth A],
E [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31600601
National Natural Science Foundation of China (NSFC)China21778051
National Natural Science Foundation of China (NSFC)China91753205
National Natural Science Foundation of China (NSFC)China21532004
Ministry of Science and Technology (MoST, China)China2017YFA0505200
Ministry of Science and Technology (MoST, China)China2016YFA0400903
Ministry of Science and Technology (MoST, China)China2017YFA0505201
Ministry of Science and Technology (MoST, China)China2017YFA0505403

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references, Refinement description, Structure summary