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- PDB-8ad0: X-ray structure of Na+-NQR from Vibrio cholerae in different conf... -

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Basic information

Entry
Database: PDB / ID: 8ad0
TitleX-ray structure of Na+-NQR from Vibrio cholerae in different conformation at 3.1 A
Components(Na(+)-translocating NADH-quinone reductase subunit ...) x 6
KeywordsMEMBRANE PROTEIN / respiratory complex / NADH ubiquinone oxido reducatase / Na+ pump
Function / homology
Function and homology information


NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / respiratory electron transport chain / transmembrane transport / 2 iron, 2 sulfur cluster binding / FMN binding / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function
Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit D / NqrDE/RnfAE / Ion-translocating oxidoreductase NqrB/RnfD / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain / Rnf-Nqr subunit, membrane protein / NQR2, RnfD, RnfE family / Na(+)-translocating NADH-quinone reductase subunit A (NQRA) ...Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit D / NqrDE/RnfAE / Ion-translocating oxidoreductase NqrB/RnfD / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain / Rnf-Nqr subunit, membrane protein / NQR2, RnfD, RnfE family / Na(+)-translocating NADH-quinone reductase subunit A (NQRA) / NQRA C-terminal domain / Na(+)-translocating NADH-quinone reductase subunit C / Na(+)-translocating NADH-quinone reductase subunit F / FMN-binding / FMN-binding domain / FMN_bind / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / BROMIDE ION / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / : / RIBOFLAVIN / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit C / Na(+)-translocating NADH-quinone reductase subunit D ...1,2-Distearoyl-sn-glycerophosphoethanolamine / BROMIDE ION / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / : / RIBOFLAVIN / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit C / Na(+)-translocating NADH-quinone reductase subunit D / Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit F / Na(+)-translocating NADH-quinone reductase subunit A
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsFritz, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)311211092 Germany
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: X-ray structure of Na+-NQR from Vibrio cholerae at 3.4 A resolution
Authors: Fritz, G.
History
DepositionJul 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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: Na(+)-translocating NADH-quinone reductase subunit A
B: Na(+)-translocating NADH-quinone reductase subunit B
C: Na(+)-translocating NADH-quinone reductase subunit C
D: Na(+)-translocating NADH-quinone reductase subunit D
E: Na(+)-translocating NADH-quinone reductase subunit E
F: Na(+)-translocating NADH-quinone reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,46519
Polymers213,6176
Non-polymers4,84813
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.310, 142.150, 105.930
Angle α, β, γ (deg.)90.000, 109.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Na(+)-translocating NADH-quinone reductase subunit ... , 6 types, 6 molecules ABCDEF

#1: Protein Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-NQR subunit A / Na(+)-translocating NQR subunit A / NQR complex subunit A / NQR-1 subunit A


Mass: 51125.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag: MGSSHHHHHHSSGLEVLFQGPH / Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: nqrA, ERS013165_00619, ERS013186_02081, ERS013199_02394, ERS013202_01882, ERS013206_02986, ERS013207_01957
Production host: Vibrio cholerae (bacteria)
References: UniProt: A0A655PZA5, NADH:ubiquinone reductase (Na+-transporting)
#2: Protein Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-NQR subunit B / Na(+)-translocating NQR subunit B / NQR complex subunit B / NQR-1 subunit B


Mass: 45390.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: nqrB, D6U24_04465, ERS013186_02082, ERS013198_02508, ERS013199_02395, ERS013200_04117, ERS013202_01883, ERS013206_02987, ERS013207_01958, EYB64_17950, F0H40_10090, FLM02_04820, FLM12_12920, FXE67_12105, HPY07_02915
Production host: Vibrio cholerae (bacteria)
References: UniProt: A0A085SSI3, NADH:ubiquinone reductase (Na+-transporting)
#3: Protein Na(+)-translocating NADH-quinone reductase subunit C / Na(+)-NQR subunit C / Na(+)-translocating NQR subunit C / NQR complex subunit C / NQR-1 subunit C


Mass: 27652.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: nqrC, BC353_01370, D6U24_04470, ERS013165_00616, ERS013186_02083, ERS013198_02507, ERS013199_02396, ERS013200_04118, ERS013201_01110, ERS013202_01884, ERS013206_02988, ERS013207_01959, F0H40_ ...Gene: nqrC, BC353_01370, D6U24_04470, ERS013165_00616, ERS013186_02083, ERS013198_02507, ERS013199_02396, ERS013200_04118, ERS013201_01110, ERS013202_01884, ERS013206_02988, ERS013207_01959, F0H40_10095, FLM02_04815, FLM12_12915
Production host: Vibrio cholerae (bacteria)
References: UniProt: A0A085R7S2, NADH:ubiquinone reductase (Na+-transporting)
#4: Protein Na(+)-translocating NADH-quinone reductase subunit D / Na(+)-NQR subunit D / Na(+)-translocating NQR subunit D / NQR complex subunit D / NQR-1 subunit D


Mass: 22853.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: nqrD, BC353_01365, D6U24_04475, ERS013165_00615, ERS013186_02084, ERS013198_02506, ERS013199_02397, ERS013200_04119, ERS013201_01111, ERS013202_01885, ERS013206_02989, ERS013207_01960, EYB64_ ...Gene: nqrD, BC353_01365, D6U24_04475, ERS013165_00615, ERS013186_02084, ERS013198_02506, ERS013199_02397, ERS013200_04119, ERS013201_01111, ERS013202_01885, ERS013206_02989, ERS013207_01960, EYB64_17940, F0315_08345, F0H40_10100, F0M16_14020, FLM02_04810, FLM12_12910, HPY07_02925
Production host: Vibrio cholerae (bacteria)
References: UniProt: A0A085RHY8, NADH:ubiquinone reductase (Na+-transporting)
#5: Protein Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-NQR subunit E / Na(+)-translocating NQR subunit E / NQR complex subunit E / NQR-1 subunit E


Mass: 21481.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: nqrE, BC353_01360, D6U24_04480, ERS013165_00614, ERS013186_02085, ERS013198_02505, ERS013199_02398, ERS013200_04120, ERS013201_01112, ERS013202_01886, ERS013206_02990, ERS013207_01961, EYB64_ ...Gene: nqrE, BC353_01360, D6U24_04480, ERS013165_00614, ERS013186_02085, ERS013198_02505, ERS013199_02398, ERS013200_04120, ERS013201_01112, ERS013202_01886, ERS013206_02990, ERS013207_01961, EYB64_17935, F0315_08350, F0H40_10105, F0M16_14025, FLM02_04805, FLM12_12905, HPY07_02930
Production host: Vibrio cholerae (bacteria)
References: UniProt: A0A085QWM0, NADH:ubiquinone reductase (Na+-transporting)
#6: Protein Na(+)-translocating NADH-quinone reductase subunit F / Na(+)-NQR subunit F / Na(+)-translocating NQR subunit F / NQR complex subunit F / NQR-1 subunit F


Mass: 45113.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: nqrF, D6U24_04485, ERS013198_02504, ERS013199_02399, ERS013201_01113, ERS013202_01887, ERS013206_02991, EYB64_17930, FLM12_12900
Production host: Vibrio cholerae (bacteria)
References: UniProt: A0A085ST13, NADH:ubiquinone reductase (Na+-transporting)

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Sugars , 1 types, 3 molecules

#9: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 9 types, 15 molecules

#7: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#8: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 / Riboflavin


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6
#10: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#11: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#12: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#13: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#14: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#15: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#16: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 40 mM KSCN, 21.0% PEG 2000MME, 100 mM Tris-acetic acid, 8% 1-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 3.1→48.12 Å / Num. obs: 44650 / % possible obs: 98.7 % / Redundancy: 3.445 % / Biso Wilson estimate: 115.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.104 / Χ2: 0.836 / Net I/σ(I): 9.01 / Num. measured all: 153823 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.33.4321.9950.725093772673120.322.36594.6
3.3-3.53.5370.9441.5421205600659960.6481.11299.8
3.5-43.4080.3443.833512510339103070.9250.40999.7
4-63.4770.09212.015139514846147820.9910.10999.6
6-103.3920.03724.1816599494248930.9980.04499
10-48.123.240.02638.624406139813600.9980.03197.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P6V

4p6v
PDB Unreleased entry


Resolution: 3.11→48.12 Å / SU ML: 0.62 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2878 2233 5 %
Rwork0.2485 42398 -
obs0.2505 44631 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 328.14 Å2 / Biso mean: 149.7109 Å2 / Biso min: 79.06 Å2
Refinement stepCycle: final / Resolution: 3.11→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14096 0 615 5 14716
Biso mean--142.61 110.67 -
Num. residues----1839
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.11-3.170.51331330.50222520265395
3.17-3.250.44491380.440126332771100
3.25-3.330.4081410.39526772818100
3.33-3.420.37481410.35926652806100
3.42-3.520.38431380.346126282766100
3.52-3.630.39571400.340426572797100
3.63-3.760.36281400.31226522792100
3.76-3.910.33371390.275526472786100
3.91-4.090.25481400.235826622802100
4.09-4.310.25591400.235326632803100
4.31-4.580.29281390.219226322771100
4.58-4.930.25481400.202226752815100
4.93-5.420.23471410.216826662807100
5.43-6.210.25241400.237826642804100
6.21-7.820.27781400.24032657279799
7.82-48.120.26011430.20842700284398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.63940.3055-0.32953.02430.51161.9596-0.02760.1173-0.01040.01440.1211-0.05920.4910.117-0.080.9095-0.11230.06610.98650.04411.0343-3.2465-30.486317.1812
26.5115-0.80850.55632.9426-2.12263.54380.2019-0.16281.32570.7927-0.5059-0.25170.10290.9970.2670.8083-0.06160.26130.8669-0.12961.343414.3304-10.771223.309
33.5016-0.9287-1.01693.331-0.19867.9946-0.69290.79131.56660.6776-0.01130.3094-0.0608-0.84790.21570.5190.0175-0.08171.18440.13431.33077.8637-11.421817.8393
43.28512.65994.16731.03310.96462.82880.2348-0.06980.58681.5293-0.45650.13180.4716-0.11190.43451.6870.24450.23171.4834-0.19681.43429.327317.365544.8611
52.12131.29450.10912.1883-1.59031.8515-0.4125-0.04340.33560.60430.04211.08830.212-0.04710.31141.37830.3492-0.29750.785-0.14811.885913.581921.022636.333
62.23390.58060.59674.03090.61135.22770.2989-0.0901-0.10040.7834-0.34130.22070.4024-0.59860.20510.73140.0683-0.02080.7951-0.08310.843827.84846.512643.0275
71.19971.1431.45281.38220.07132.304-0.54040.1414-0.43070.87170.09210.35720.18830.97930.26751.1661-0.04570.39971.28470.07851.642568.758629.654221.8368
84.3423-2.4112-0.56723.8219-1.32565.27320.666-1.0488-0.3277-0.9692-0.68590.8974-1.54860.3341-0.0141.8949-0.3216-0.18921.18220.31231.431260.392629.277344.615
92.25711.14351.46274.7642-0.8352.5221-1.1591.2914-0.497-1.8810.3123-2.026-0.37540.39720.38980.5778-0.2380.15521.37060.13641.719643.049122.41974.5235
101.46410.4094-0.20525.31133.75439.1743-0.1715-0.228-0.20190.8431.4168-0.50520.0535-0.7907-1.05760.74880.0474-0.09111.34150.24061.202555.108520.57829.7028
113.77310.8336-1.33952.4183-0.94250.5053-0.32520.2217-0.1468-0.54850.0965-0.39110.03640.15750.39991.27640.097-0.30621.18660.20451.393136.184726.184414.287
125.54623.24973.75523.39071.68915.49480.155-1.07890.1897-0.7366-0.90390.7133-0.0848-2.06880.41791.1120.4964-0.33122.1426-0.061.480522.041515.41074.3751
132.54860.6083-0.92742.847-0.84151.3173-0.27680.7988-0.10020.55420.3927-0.9525-0.16451.4357-0.40910.6250.252-0.13771.0195-0.23161.098343.77323.860322.8342
141.48590.3826-1.98952.224-0.60972.7508-1.1794-1.0391-1.18420.21460.6618-0.033-1.0925-0.71420.38170.91980.0498-0.03471.1653-0.35911.955868.712210.17618.5204
152.4331-2.3429-1.55746.3991.53064.52570.92740.2919-0.46050.45370.9053-0.0051-0.3313-1.4403-0.58791.2642-0.1326-0.26031.18550.22051.365455.93555.0779.1095
163.6162-2.8838-0.78613.07160.00971.95860.2490.1454-1.38630.8351-0.2401-0.1089-0.0667-0.4705-0.25811.07890.2606-0.11241.4576-0.11511.220442.3933-0.50456.6733
179.57-1.21010.10526.07791.1413.11151.05850.2478-0.8544-0.22140.028-0.11080.5892-0.0075-0.71710.85980.0637-0.05851.01980.03091.010639.90497.659623.3048
182.741.13231.8810.2236-0.18970.97750.497-0.4742-0.2107-0.3738-0.13260.14290.2022-0.2464-0.56821.54990.06930.00241.1391-0.20111.306141.3629-7.3537-7.6168
192.95760.30050.05285.8433-2.39135.53930.2750.216-0.1368-0.7399-0.12670.10470.6068-0.052-0.10970.98820.1241-0.08770.8015-0.0240.96455.0975-1.7824-27.6388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 327 )A1 - 327
2X-RAY DIFFRACTION2chain 'A' and (resid 328 through 414 )A328 - 414
3X-RAY DIFFRACTION3chain 'A' and (resid 415 through 446 )A415 - 446
4X-RAY DIFFRACTION4chain 'B' and (resid 31 through 117 )B31 - 117
5X-RAY DIFFRACTION5chain 'B' and (resid 118 through 187 )B118 - 187
6X-RAY DIFFRACTION6chain 'B' and (resid 188 through 414 )B188 - 414
7X-RAY DIFFRACTION7chain 'C' and (resid 7 through 92 )C7 - 92
8X-RAY DIFFRACTION8chain 'C' and (resid 93 through 253 )C93 - 253
9X-RAY DIFFRACTION9chain 'D' and (resid 8 through 65 )D8 - 65
10X-RAY DIFFRACTION10chain 'D' and (resid 66 through 111 )D66 - 111
11X-RAY DIFFRACTION11chain 'D' and (resid 112 through 200 )D112 - 200
12X-RAY DIFFRACTION12chain 'D' and (resid 201 through 209 )D201 - 209
13X-RAY DIFFRACTION13chain 'E' and (resid 2 through 50 )E2 - 50
14X-RAY DIFFRACTION14chain 'E' and (resid 51 through 75 )E51 - 75
15X-RAY DIFFRACTION15chain 'E' and (resid 76 through 99 )E76 - 99
16X-RAY DIFFRACTION16chain 'E' and (resid 100 through 119 )E100 - 119
17X-RAY DIFFRACTION17chain 'E' and (resid 120 through 198 )E120 - 198
18X-RAY DIFFRACTION18chain 'F' and (resid 1 through 130 )F1 - 130
19X-RAY DIFFRACTION19chain 'F' and (resid 131 through 406 )F131 - 406

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