7W7F

Cryo-EM structure of human NaV1.3/beta1/beta2-ICA121431


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for modulation of human Na V 1.3 by clinical drug and selective antagonist.

Li, X.Xu, F.Xu, H.Zhang, S.Gao, Y.Zhang, H.Dong, Y.Zheng, Y.Yang, B.Sun, J.Zhang, X.C.Zhao, Y.Jiang, D.

(2022) Nat Commun 13: 1286-1286

  • DOI: https://doi.org/10.1038/s41467-022-28808-5
  • Primary Citation of Related Structures:  
    7W77, 7W7F

  • PubMed Abstract: 

    Voltage-gated sodium (Na V ) channels play fundamental roles in initiating and propagating action potentials. Na V 1.3 is involved in numerous physiological processes including neuronal development, hormone secretion and pain perception. Here we report structures of human Na V 1.3/β1/β2 in complex with clinically-used drug bulleyaconitine A and selective antagonist ICA121431. Bulleyaconitine A is located around domain I-II fenestration, providing the detailed view of the site-2 neurotoxin binding site. It partially blocks ion path and expands the pore-lining helices, elucidating how the bulleyaconitine A reduces peak amplitude but improves channel open probability. In contrast, ICA121431 preferentially binds to activated domain IV voltage-sensor, consequently strengthens the Ile-Phe-Met motif binding to its receptor site, stabilizes the channel in inactivated state, revealing an allosterically inhibitory mechanism of Na V channels. Our results provide structural details of distinct small-molecular modulators binding sites, elucidate molecular mechanisms of their action on Na V channels and pave a way for subtype-selective therapeutic development.


  • Organizational Affiliation

    Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel subunit beta-1A [auth B]218Homo sapiensMutation(s): 0 
Gene Names: SCN1B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q07699 (Homo sapiens)
Explore Q07699 
Go to UniProtKB:  Q07699
PHAROS:  Q07699
GTEx:  ENSG00000105711 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07699
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q07699-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel subunit beta-2B [auth C]215Homo sapiensMutation(s): 0 
Gene Names: SCN2B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O60939 (Homo sapiens)
Explore O60939 
Go to UniProtKB:  O60939
PHAROS:  O60939
GTEx:  ENSG00000149575 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60939
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel protein type 3 subunit alphaC [auth D]2,000Homo sapiensMutation(s): 0 
Gene Names: SCN3A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NY46 (Homo sapiens)
Explore Q9NY46 
Go to UniProtKB:  Q9NY46
PHAROS:  Q9NY46
GTEx:  ENSG00000153253 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NY46
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q9NY46-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth E]3N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth F]2N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6OU
Query on 6OU

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
K [auth D]
M [auth D]
AA [auth D],
BA [auth D],
CA [auth D],
K [auth D],
M [auth D],
N [auth D],
O [auth D],
P [auth D],
Q [auth D],
R [auth D],
S [auth D],
T [auth D],
U [auth D],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
C39 H76 N O8 P
FHQVHHIBKUMWTI-OTMQOFQLSA-N
9Z9
Query on 9Z9

Download Ideal Coordinates CCD File 
V [auth D](3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
C34 H56 O5
CEEBZAXXSRFQIC-GZSGZGDASA-N
8DE (Subject of Investigation/LOI)
Query on 8DE

Download Ideal Coordinates CCD File 
L [auth D]2,2-diphenyl-~{N}-[4-(1,3-thiazol-2-ylsulfamoyl)phenyl]ethanamide
C23 H19 N3 O3 S2
URSQNPPONHUJDL-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
8DE BindingDB:  7W7F IC50: min: 20, max: 240 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release