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- PDB-7pgh: NaVAe1/Sp1CTDp (DDM) -

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Basic information

Entry
Database: PDB / ID: 7pgh
TitleNaVAe1/Sp1CTDp (DDM)
ComponentsIon transport protein,Voltage-gated sodium channel subunit
KeywordsMEMBRANE PROTEIN / ion channel membrane protein transport protein antibody complex
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / sodium ion transport / metal ion binding / identical protein binding
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
DODECANE / N-OCTANE / Ion transport protein / Voltage-gated sodium channel subunit
Similarity search - Component
Biological speciesAlkalilimnicola ehrlichii (bacteria)
Ruegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 4.194 Å
AuthorsLolicato, M. / Arrigoni, C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2022
Title: Quaternary structure independent folding of voltage-gated ion channel pore domain subunits.
Authors: Arrigoni, C. / Lolicato, M. / Shaya, D. / Rohaim, A. / Findeisen, F. / Fong, L.K. / Colleran, C.M. / Dominik, P. / Kim, S.S. / Schuermann, J.P. / DeGrado, W.F. / Grabe, M. / Kossiakoff, A.A. / Minor Jr., D.L.
History
DepositionAug 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Ion transport protein,Voltage-gated sodium channel subunit
A: Ion transport protein,Voltage-gated sodium channel subunit
B: Ion transport protein,Voltage-gated sodium channel subunit
C: Ion transport protein,Voltage-gated sodium channel subunit
D: Ion transport protein,Voltage-gated sodium channel subunit
E: Ion transport protein,Voltage-gated sodium channel subunit
G: Ion transport protein,Voltage-gated sodium channel subunit
H: Ion transport protein,Voltage-gated sodium channel subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,95127
Polymers130,8498
Non-polymers6,10219
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21830 Å2
ΔGint-151 kcal/mol
Surface area71200 Å2
Unit cell
Length a, b, c (Å)123.465, 134.696, 155.545
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules FABCDEGH

#1: Protein
Ion transport protein,Voltage-gated sodium channel subunit


Mass: 16356.166 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkalilimnicola ehrlichii (strain ATCC BAA-1101 / DSM 17681 / MLHE-1) (bacteria), (gene. exp.) Ruegeria pomeroyi (bacteria)
Strain: ATCC BAA-1101 / DSM 17681 / MLHE-1 / Gene: Mlg_0322 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0ABW0, UniProt: Q6TMY8

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Non-polymers , 5 types, 19 molecules

#2: Chemical
ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26
#4: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.94 Å3/Da / Density % sol: 75.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Purified NaVAe1Sp1CTDp was concentrated to 13-13.5 mg ml-1 and crystallized in 22% PEG3350, 0.3 M KI, 8 mM sarcosine. Crystals were harvested in 30% PEG3350, 0.3 M KI, 8 mM sarcosine and 1mM ...Details: Purified NaVAe1Sp1CTDp was concentrated to 13-13.5 mg ml-1 and crystallized in 22% PEG3350, 0.3 M KI, 8 mM sarcosine. Crystals were harvested in 30% PEG3350, 0.3 M KI, 8 mM sarcosine and 1mM Fos-choline 12 (FC-12), Anatrace).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1, 0.97698, 0.97953, 0.95368
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.976981
30.979531
40.953681
ReflectionResolution: 4.194→15 Å / Num. obs: 18983 / % possible obs: 96.53 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.6
Reflection shellResolution: 4.194→4.342 Å / Rmerge(I) obs: 1 / Num. unique obs: 1766 / CC1/2: 0.404

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: MAD / Resolution: 4.194→14.989 Å / SU ML: 1.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 50.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3369 851 4.5 %
Rwork0.3175 18062 -
obs0.3184 18913 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 650.8 Å2 / Biso mean: 317.5867 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 4.194→14.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8288 0 415 0 8703
Biso mean--277.06 --
Num. residues----1043
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.194-4.44990.4414135281594
4.4499-4.78310.47951450.4722997100
4.7831-5.24560.46611662977100
5.2456-5.96240.44051323043100
5.9624-7.36090.44261420.41723063100
7.3609-14.9890.23181310.22353167100

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