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- PDB-7pgi: NaVAb1p (bicelles) -

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Basic information

Entry
Database: PDB / ID: 7pgi
TitleNaVAb1p (bicelles)
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / ion channel membrane protein transport protein antibody complex
Function / homologyVoltage-gated cation channel calcium and sodium / voltage-gated sodium channel complex / voltage-gated sodium channel activity / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / identical protein binding / ACETATE ION / Ion transport protein
Function and homology information
Biological speciesAlcanivorax borkumensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.638 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 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 29, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ion transport protein
B: Ion transport protein
C: Ion transport protein
D: Ion transport protein
E: Ion transport protein
F: Ion transport protein
G: Ion transport protein
H: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,04519
Polymers135,5748
Non-polymers47111
Water00
1
A: Ion transport protein
B: Ion transport protein
C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0109
Polymers67,7874
Non-polymers2235
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-160 kcal/mol
Surface area30210 Å2
MethodPISA
2
E: Ion transport protein
F: Ion transport protein
G: Ion transport protein
H: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,03510
Polymers67,7874
Non-polymers2476
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14260 Å2
ΔGint-170 kcal/mol
Surface area29950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.180, 191.800, 192.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 134 through 135 or resid 138...
21(chain B and (resid 134 through 135 or resid 138...
31(chain C and (resid 134 through 135 or resid 138...
41(chain D and (resid 134 through 135 or resid 138...
51(chain E and (resid 134 through 135 or resid 138...
61(chain F and (resid 134 through 135 or resid 138...
71(chain G and (resid 134 through 135 or resid 138...
81(chain H and (resid 134 through 135 or resid 138...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 134 through 135 or resid 138...A134 - 135
121(chain A and (resid 134 through 135 or resid 138...A138 - 165
131(chain A and (resid 134 through 135 or resid 138...A167 - 190
141(chain A and (resid 134 through 135 or resid 138...A192
151(chain A and (resid 134 through 135 or resid 138...A133 - 278
161(chain A and (resid 134 through 135 or resid 138...A202 - 265
171(chain A and (resid 134 through 135 or resid 138...A267 - 268
181(chain A and (resid 134 through 135 or resid 138...A267 - 268
191(chain A and (resid 134 through 135 or resid 138...A274 - 275
1101(chain A and (resid 134 through 135 or resid 138...A277 - 278
211(chain B and (resid 134 through 135 or resid 138...B134 - 135
221(chain B and (resid 134 through 135 or resid 138...B138 - 165
231(chain B and (resid 134 through 135 or resid 138...B167 - 190
241(chain B and (resid 134 through 135 or resid 138...B192
251(chain B and (resid 134 through 135 or resid 138...B133 - 278
261(chain B and (resid 134 through 135 or resid 138...B202 - 265
271(chain B and (resid 134 through 135 or resid 138...B267 - 268
281(chain B and (resid 134 through 135 or resid 138...B267 - 268
291(chain B and (resid 134 through 135 or resid 138...B274 - 275
2101(chain B and (resid 134 through 135 or resid 138...B277 - 278
311(chain C and (resid 134 through 135 or resid 138...C134 - 135
321(chain C and (resid 134 through 135 or resid 138...C138 - 165
331(chain C and (resid 134 through 135 or resid 138...C133 - 278
341(chain C and (resid 134 through 135 or resid 138...C194
351(chain C and (resid 134 through 135 or resid 138...C192
361(chain C and (resid 134 through 135 or resid 138...C194 - 200
371(chain C and (resid 134 through 135 or resid 138...C208 - 200
381(chain C and (resid 134 through 135 or resid 138...C267 - 268
391(chain C and (resid 134 through 135 or resid 138...C274 - 275
3101(chain C and (resid 134 through 135 or resid 138...C277 - 278
411(chain D and (resid 134 through 135 or resid 138...D134 - 135
421(chain D and (resid 134 through 135 or resid 138...D138 - 165
431(chain D and (resid 134 through 135 or resid 138...D132 - 278
441(chain D and (resid 134 through 135 or resid 138...D194
451(chain D and (resid 134 through 135 or resid 138...D192
461(chain D and (resid 134 through 135 or resid 138...D198 - 200
471(chain D and (resid 134 through 135 or resid 138...D202 - 2652
481(chain D and (resid 134 through 135 or resid 138...D267 - 268
491(chain D and (resid 134 through 135 or resid 138...D270 - 272
4101(chain D and (resid 134 through 135 or resid 138...D274 - 275
4111(chain D and (resid 134 through 135 or resid 138...D277 - 278
511(chain E and (resid 134 through 135 or resid 138...E134 - 135
521(chain E and (resid 134 through 135 or resid 138...E138 - 165
531(chain E and (resid 134 through 135 or resid 138...E132 - 278
541(chain E and (resid 134 through 135 or resid 138...E194
551(chain E and (resid 134 through 135 or resid 138...E192
561(chain E and (resid 134 through 135 or resid 138...E194 - 200
571(chain E and (resid 134 through 135 or resid 138...E208 - 200
581(chain E and (resid 134 through 135 or resid 138...E267 - 268
591(chain E and (resid 134 through 135 or resid 138...E274 - 275
5101(chain E and (resid 134 through 135 or resid 138...E277 - 278
611(chain F and (resid 134 through 135 or resid 138...F134 - 135
621(chain F and (resid 134 through 135 or resid 138...F138 - 165
631(chain F and (resid 134 through 135 or resid 138...F167 - 190
641(chain F and (resid 134 through 135 or resid 138...F192
651(chain F and (resid 134 through 135 or resid 138...F133 - 278
661(chain F and (resid 134 through 135 or resid 138...F202 - 265
671(chain F and (resid 134 through 135 or resid 138...F267 - 268
681(chain F and (resid 134 through 135 or resid 138...F267 - 268
691(chain F and (resid 134 through 135 or resid 138...F274 - 275
6101(chain F and (resid 134 through 135 or resid 138...F277 - 278
711(chain G and (resid 134 through 135 or resid 138...G134 - 135
721(chain G and (resid 134 through 135 or resid 138...G138 - 165
731(chain G and (resid 134 through 135 or resid 138...G167 - 190
741(chain G and (resid 134 through 135 or resid 138...G198 - 200
751(chain G and (resid 134 through 135 or resid 138...G202 - 265
761(chain G and (resid 134 through 135 or resid 138...G267 - 268
771(chain G and (resid 134 through 135 or resid 138...G274 - 27
781(chain G and (resid 134 through 135 or resid 138...G274 - 275
791(chain G and (resid 134 through 135 or resid 138...G277 - 278
811(chain H and (resid 134 through 135 or resid 138...H134 - 135
821(chain H and (resid 134 through 135 or resid 138...H138 - 165
831(chain H and (resid 134 through 135 or resid 138...H167 - 190
841(chain H and (resid 134 through 135 or resid 138...H198 - 200
851(chain H and (resid 134 through 135 or resid 138...H202 - 265
861(chain H and (resid 134 through 135 or resid 138...H267 - 268
871(chain H and (resid 134 through 135 or resid 138...H274 - 27
881(chain H and (resid 134 through 135 or resid 138...H274 - 275
891(chain H and (resid 134 through 135 or resid 138...H277 - 278

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Components

#1: Protein
Ion transport protein


Mass: 16946.805 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcanivorax borkumensis (strain ATCC 700651 / DSM 11573 / NCIMB 13689 / SK2) (bacteria)
Strain: ATCC 700651 / DSM 11573 / NCIMB 13689 / SK2 / Gene: ABO_1668 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0VNY2
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 6.06 Å3/Da / Density % sol: 79.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium acetate, 0.1 M HEPES pH 7.5, 20% PEG 3000, 8% Bicelles

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.638→19.98 Å / Num. obs: 36662 / % possible obs: 98.41 % / Redundancy: 4.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.157 / Net I/σ(I): 5.2
Reflection shellResolution: 3.64→3.769 Å / Rmerge(I) obs: 1 / Num. unique obs: 3616 / CC1/2: 0.172

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PGG

7pgg


Resolution: 3.638→14.993 Å / SU ML: 0.69 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3035 1755 4.83 %
Rwork0.2872 34602 -
obs0.2879 36357 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 363.98 Å2 / Biso mean: 130.7106 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.638→14.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9246 0 29 0 9275
Biso mean--104.68 --
Num. residues----1170
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1047X-RAY DIFFRACTIONPOSITIONAL0.666
12B1047X-RAY DIFFRACTIONPOSITIONAL0.666
13C1047X-RAY DIFFRACTIONPOSITIONAL0.681
14D1047X-RAY DIFFRACTIONPOSITIONAL0.627
15E1047X-RAY DIFFRACTIONPOSITIONAL0.654
16F1047X-RAY DIFFRACTIONPOSITIONAL0.771
17G1047X-RAY DIFFRACTIONPOSITIONAL0.541
18H1047X-RAY DIFFRACTIONPOSITIONAL0.802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.638-3.73490.40411700.37042515268598
3.7349-3.8430.33881310.37092673280499
3.843-3.96490.37251570.35392637279499
3.9649-4.10380.33541350.35372617275299
4.1038-4.26450.38451370.32352657279499
4.2645-4.45370.28891530.30352617277099
4.4537-4.68170.30141570.26592637279499
4.6817-4.9650.2881180.26782656277499
4.965-5.33230.28321210.28142694281599
5.3323-5.83990.2961320.28226762808100
5.8399-6.62050.3241320.28782706283899
6.6205-8.11470.2906980.27782751284999
8.1147-14.9930.24811140.25162766288098

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