7RNN | pdb_00007rnn

Human ASIC1a-Nb.C1 complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

Structure and analysis of nanobody binding to the human ASIC1a ion channel.

Wu, Y., Chen, Z., Sigworth, F.J., Canessa, C.M.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.67115
  • Primary Citation Related Structures: 
    7RNN

  • PubMed Abstract: 

    ASIC1a is a proton-gated sodium channel involved in modulation of pain, fear, addiction, and ischemia-induced neuronal injury. We report isolation and characterization of alpaca-derived nanobodies (Nbs) that specifically target human ASIC1a. Cryo-electron microscopy of the human ASIC1a channel at pH 7.4 in complex with one of these, Nb.C1, yielded a structure at 2.9 Å resolution. It is revealed that Nb.C1 binds to a site overlapping with that of the Texas coral snake toxin (MitTx1) and the black mamba venom Mambalgin-1; however, the Nb.C1-binding site does not overlap with that of the inhibitory tarantula toxin psalmotoxin-1 (PcTx1). Fusion of Nb.C1 with PcTx1 in a single polypeptide markedly enhances the potency of PcTx1, whereas competition of Nb.C1 and MitTx1 for binding reduces channel activation by the toxin. Thus, Nb.C1 is a molecular tool for biochemical and structural studies of hASIC1a; a potential antidote to the pain-inducing component of coral snake bite; and a candidate to potentiate PcTx1-mediated inhibition of hASIC1a in vivo for therapeutic applications.

    • Organizational Affiliation: 
    • Basic Sciences Department, Tsinghua University School of Medicine, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 73.21 kDa 
  • Atom Count: 4,000 
  • Modeled Residue Count: 540 
  • Deposited Residue Count: 644 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobodies Nb.C1A [auth C]116Vicugna pacosMutation(s): 0 
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Acid-sensing ion channel 1B [auth D]528Homo sapiensMutation(s): 0 
Gene Names: ASIC1, ACCN2, BNAC2
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: 2
Go to GlyGen: P78348-2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.18.2
MODEL REFINEMENTREFMAC5

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesR21 MH10107466402

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Refinement description, Structure summary