7XVF

Nav1.7 mutant class2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

VSD rotation and S4 unwinding during the electromechanical coupling in Nav1.7

Huang, G.Wu, Q.Li, Z.Pan, X.Yan, N.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium channel protein type 9 subunit alphaA2,022Homo sapiensMutation(s): 11 
Gene Names: SCN9ANENA
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15858 (Homo sapiens)
Explore Q15858 
Go to UniProtKB:  Q15858
PHAROS:  Q15858
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UniProt GroupQ15858
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium channel subunit beta-1B218Homo 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
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UniProt GroupQ07699
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium channel subunit beta-2C215Homo sapiensMutation(s): 0 
Gene Names: SCN2BUNQ326/PRO386
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O60939 (Homo sapiens)
Explore O60939 
Go to UniProtKB:  O60939
PHAROS:  O60939
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UniProt GroupO60939
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD, E 2N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P5S
Query on P5S

Download Ideal Coordinates CCD File 
JA [auth A]O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
 Ligand Interaction
PCW
Query on PCW

Download Ideal Coordinates CCD File 
HA [auth A],
IA [auth A],
N [auth A],
Q [auth A],
R [auth A],
HA [auth A],
IA [auth A],
N [auth A],
Q [auth A],
R [auth A],
S [auth A]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
 Ligand Interaction
LPE
Query on LPE

Download Ideal Coordinates CCD File 
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
J [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
J [auth A],
K [auth A],
KA [auth A],
M [auth A],
O [auth A],
P [auth A],
PA [auth B],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C26 H57 N O6 P
XKBJVQHMEXMFDZ-AREMUKBSSA-O
 Ligand Interaction
Y01
Query on Y01

Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
CA [auth A],
H [auth A],
Z [auth A]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
 Ligand Interaction
1PW
Query on 1PW

Download Ideal Coordinates CCD File 
L [auth A](2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
C20 H40 N O6 P
HWPZKJVGDYNEAW-QUDYQQOWSA-N
 Ligand Interaction
CLR
Query on CLR

Download Ideal Coordinates CCD File 
I [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
LA [auth B],
MA [auth B],
NA [auth B],
F [auth A],
G [auth A],
LA [auth B],
MA [auth B],
NA [auth B],
OA [auth B],
QA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Princeton UniversityUnited StatesShirley M. Tilghman endowed professorship
Beijing Municipal Science and Technology CommissionChinaZ191100001119127

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release