[English] 日本語
Yorodumi
- PDB-7q5y: Structure of NADH:ubichinon oxidoreductase (complex I) of the hyp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q5y
TitleStructure of NADH:ubichinon oxidoreductase (complex I) of the hyperthermophilic eubacterium Aquifex aeolicus
Components
  • (NADH-quinone oxidoreductase subunit ...NADH dehydrogenase (quinone)) x 5
  • NADH dehydrogenase I chain G
KeywordsOXIDOREDUCTASE / complex I
Function / homology
Function and homology information


plasma membrane respiratory chain complex I / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / cellular respiration / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration ...plasma membrane respiratory chain complex I / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / cellular respiration / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding / plasma membrane
Similarity search - Function
NADH-quinone oxidoreductase subunit CD / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Soluble ligand binding domain / SLBB domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I ...NADH-quinone oxidoreductase subunit CD / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Soluble ligand binding domain / SLBB domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / NADH dehydrogenase I chain G / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit E / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit C/D 2 / NADH-quinone oxidoreductase subunit I
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsWarkentin, E. / Ermler, U. / Peng, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Structure of NADH:ubichinon oxidoreductase (complex I) of the hyperthermophilic eubacterium Aquifex aeolicus
Authors: Warkentin, E. / Ermler, U. / Peng, G.
History
DepositionNov 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADH dehydrogenase I chain G
B: NADH-quinone oxidoreductase subunit C/D 2
C: NADH-quinone oxidoreductase subunit F
D: NADH-quinone oxidoreductase subunit I
E: NADH-quinone oxidoreductase subunit E
F: NADH-quinone oxidoreductase subunit B
G: NADH dehydrogenase I chain G
H: NADH-quinone oxidoreductase subunit C/D 2
I: NADH-quinone oxidoreductase subunit F
J: NADH-quinone oxidoreductase subunit I
K: NADH-quinone oxidoreductase subunit E
L: NADH-quinone oxidoreductase subunit B
M: NADH dehydrogenase I chain G
N: NADH-quinone oxidoreductase subunit C/D 2
O: NADH-quinone oxidoreductase subunit F
P: NADH-quinone oxidoreductase subunit I
Q: NADH-quinone oxidoreductase subunit E
R: NADH-quinone oxidoreductase subunit B
S: NADH dehydrogenase I chain G
T: NADH-quinone oxidoreductase subunit C/D 2
U: NADH-quinone oxidoreductase subunit F
V: NADH-quinone oxidoreductase subunit I
W: NADH-quinone oxidoreductase subunit E
X: NADH-quinone oxidoreductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,015,90568
Polymers1,001,42124
Non-polymers14,48444
Water6,503361
1
A: NADH dehydrogenase I chain G
B: NADH-quinone oxidoreductase subunit C/D 2
C: NADH-quinone oxidoreductase subunit F
D: NADH-quinone oxidoreductase subunit I
E: NADH-quinone oxidoreductase subunit E
F: NADH-quinone oxidoreductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,97617
Polymers250,3556
Non-polymers3,62111
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27230 Å2
ΔGint-349 kcal/mol
Surface area75100 Å2
MethodPISA
2
G: NADH dehydrogenase I chain G
H: NADH-quinone oxidoreductase subunit C/D 2
I: NADH-quinone oxidoreductase subunit F
J: NADH-quinone oxidoreductase subunit I
K: NADH-quinone oxidoreductase subunit E
L: NADH-quinone oxidoreductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,97617
Polymers250,3556
Non-polymers3,62111
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27320 Å2
ΔGint-344 kcal/mol
Surface area75620 Å2
MethodPISA
3
M: NADH dehydrogenase I chain G
N: NADH-quinone oxidoreductase subunit C/D 2
O: NADH-quinone oxidoreductase subunit F
P: NADH-quinone oxidoreductase subunit I
Q: NADH-quinone oxidoreductase subunit E
R: NADH-quinone oxidoreductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,97617
Polymers250,3556
Non-polymers3,62111
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27480 Å2
ΔGint-347 kcal/mol
Surface area75380 Å2
MethodPISA
4
S: NADH dehydrogenase I chain G
T: NADH-quinone oxidoreductase subunit C/D 2
U: NADH-quinone oxidoreductase subunit F
V: NADH-quinone oxidoreductase subunit I
W: NADH-quinone oxidoreductase subunit E
X: NADH-quinone oxidoreductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,97617
Polymers250,3556
Non-polymers3,62111
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27410 Å2
ΔGint-352 kcal/mol
Surface area75190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.880, 240.240, 230.920
Angle α, β, γ (deg.)90.000, 95.566, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43
14
24
34
44
15
25
35
45
16
26
36
46

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A4 - 629
121chain 'A'A717
231chain 'G'G4 - 629
241chain 'G'G717
351chain 'M'M4 - 629
361chain 'M'M717
471chain 'S'S4 - 629
481chain 'S'S717
192chain 'B'B1 - 585
2102chain 'H'H1 - 585
3112chain 'N'N1 - 585
4122chain 'T'T1 - 585
1133chain 'C'C1 - 419
1143chain 'C'C500
2153chain 'I'I1 - 419
2163chain 'I'I500
3173chain 'O'O1 - 419
3183chain 'O'O500
4193chain 'U'U1 - 419
4203chain 'U'U500
1214chain 'D'D5 - 200
2224chain 'J'J5 - 200
3234chain 'P'P5 - 200
4244chain 'V'V5 - 200
1255chain 'E'E6 - 160
1265chain 'E'E720
2275chain 'K'K6 - 160
2285chain 'K'K720
3295chain 'Q'Q6 - 160
3305chain 'Q'Q720
4315chain 'W'W6 - 160
4325chain 'W'W720
1336chain 'F'F20 - 154
2346chain 'L'L20 - 154
3356chain 'R'R20 - 154
4366chain 'X'X20 - 154

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Protein , 1 types, 4 molecules AGMS

#1: Protein
NADH dehydrogenase I chain G


Mass: 72875.633 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5 / References: UniProt: O66748

-
NADH-quinone oxidoreductase subunit ... , 5 types, 20 molecules BHNTCIOUDJPVEKQWFLRX

#2: Protein
NADH-quinone oxidoreductase subunit C/D 2 / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit C/D 2 / NDH-1 subunit C/D 2


Mass: 67991.797 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5
References: UniProt: O67335, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#3: Protein
NADH-quinone oxidoreductase subunit F / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit F / NDH-1 subunit F


Mass: 47566.301 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5
References: UniProt: O66841, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#4: Protein
NADH-quinone oxidoreductase subunit I / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit I / NDH-1 subunit I


Mass: 23446.473 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5
References: UniProt: O67337, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#5: Protein
NADH-quinone oxidoreductase subunit E / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit E / NDH-1 subunit E


Mass: 18573.619 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5
References: UniProt: O66842, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#6: Protein
NADH-quinone oxidoreductase subunit B / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit B / NDH-1 subunit B


Mass: 19901.324 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5
References: UniProt: O67334, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

-
Non-polymers , 4 types, 405 molecules

#7: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe2S2
#9: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate (pH 5.0), 40% methylpentanediol (MPD), 0.05% decyl-beta-D-maltoside

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 393067 / % possible obs: 98.1 % / Redundancy: 2.7 % / Biso Wilson estimate: 64.94 Å2 / Rrim(I) all: 0.128 / Net I/σ(I): 8.03
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.7 % / Num. unique obs: 20959 / Rrim(I) all: 1.689 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
XDSdata scaling
SHARPv2006/3phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→29.95 Å / SU ML: 0.3537 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.6686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2087 19447 5.02 %
Rwork0.1694 367799 -
obs0.1714 387246 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.51 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms68252 0 412 361 69025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008770603
X-RAY DIFFRACTIONf_angle_d1.298895668
X-RAY DIFFRACTIONf_chiral_restr0.072710320
X-RAY DIFFRACTIONf_plane_restr0.008520616
X-RAY DIFFRACTIONf_dihedral_angle_d14.803942204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.3556170.319712189X-RAY DIFFRACTION98.12
2.73-2.760.33856760.305212253X-RAY DIFFRACTION98.58
2.76-2.80.33926520.312210X-RAY DIFFRACTION98.85
2.8-2.830.33086440.288512368X-RAY DIFFRACTION98.85
2.83-2.870.30835990.273712324X-RAY DIFFRACTION99.06
2.87-2.910.31686490.271912280X-RAY DIFFRACTION99.14
2.91-2.950.31396940.268312329X-RAY DIFFRACTION99.13
2.95-2.990.29316610.25512303X-RAY DIFFRACTION99.17
2.99-3.040.28696120.24912380X-RAY DIFFRACTION99.11
3.04-3.090.29955920.239212382X-RAY DIFFRACTION99.22
3.09-3.140.28786220.236512299X-RAY DIFFRACTION99.11
3.14-3.20.27536600.221412354X-RAY DIFFRACTION99.25
3.2-3.260.26186380.208812380X-RAY DIFFRACTION99.28
3.26-3.330.24886360.204812335X-RAY DIFFRACTION99.2
3.33-3.40.23226250.193212395X-RAY DIFFRACTION99.29
3.4-3.480.23226810.185312270X-RAY DIFFRACTION99.28
3.48-3.570.2196510.176212379X-RAY DIFFRACTION99.35
3.57-3.660.2166710.168312369X-RAY DIFFRACTION99.31
3.66-3.770.20626350.160412326X-RAY DIFFRACTION99.18
3.77-3.890.1966880.151712312X-RAY DIFFRACTION99.16
3.89-4.030.18436640.146912362X-RAY DIFFRACTION99
4.03-4.190.17596520.141212291X-RAY DIFFRACTION98.94
4.19-4.380.17346670.133412295X-RAY DIFFRACTION98.75
4.38-4.610.17146590.130812290X-RAY DIFFRACTION98.56
4.61-4.90.17726410.133912296X-RAY DIFFRACTION98.3
4.9-5.280.18236840.140712124X-RAY DIFFRACTION97.77
5.28-5.80.18696570.151312145X-RAY DIFFRACTION97.5
5.8-6.640.18396730.147412115X-RAY DIFFRACTION96.88
6.64-8.330.17236580.140412012X-RAY DIFFRACTION95.77
8.33-29.950.15665890.12911432X-RAY DIFFRACTION90.42
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4026027548740.0666180823773-0.101496080080.62294878641-0.02619253021020.7801558586190.07805890184580.02953948410140.243316511610.0218796063756-0.01919902362960.141216624477-0.493268520114-0.133213486276-0.02902795441980.5824300493690.1051739562140.06174848183960.4834438846250.03822571620630.466958378452142.208665589237.009855897220.938076379
20.9411007716140.360201089145-0.2473714014830.475035626565-0.06067988546890.716924096261-0.1992486703290.117104893701-0.705718047272-0.09672230459280.00841315016881-0.3492989724520.391676778230.1142813465890.04815718772570.5096028159450.1150426848910.1086920381910.48509122401-0.0979414153620.83209642065199.9532681653143.916566622197.978979308
30.794988221224-0.098047782221-0.2053255399770.3301737681750.02803013171021.15598167928-0.119577132405-0.18331507992-0.2614599147070.05916307617230.09730226168380.01621826166110.5398596694420.1268329208950.007405817371680.6286323931110.04945680067110.009981441794830.6350947959470.1143492646050.42817714043164.5457773631137.984905018145.719883292
40.4127433346830.0472088968316-0.01264032255280.133818579044-0.2276555461930.7427948430020.043441794073-0.01655648358420.235205215075-0.009958838105250.06234232796160.069016100598-0.667480370671-0.22693779713-0.03147125047231.275746622330.2202368634380.1657725499860.698902211843-0.02822920429330.54744034860423.2209237451233.409613328119.428164773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' or chain 'B' or chain 'C' or (chain 'D' and ((resid 27 through 201) or (resid 301 through 302))) or chain 'E' or chain 'F' )
2X-RAY DIFFRACTION2((chain 'G' ) or (chain 'H' ) or (chain 'I' ) or (chain 'J' and ((resid 27 through 201) or (resid 301 through 302))) or chain 'K' or chain 'L' )
3X-RAY DIFFRACTION3((chain 'M' ) or (chain 'N' ) or (chain 'O' ) or (chain 'P' and ((resid 27 through 201) or (resid 301 through 302))) or chain 'Q' or chain 'R' )
4X-RAY DIFFRACTION4(chain 'S' or chain 'T' or chain 'U' or (chain 'V' and ((resid 27 through 201) or (resid 301 through 302))) or chain 'W' or chain 'X' )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more