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- PDB-5gpn: Architecture of mammalian respirasome -

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Entry
Database: PDB / ID: 5gpn
TitleArchitecture of mammalian respirasome
Components
  • (Cytochrome b-c1 complex subunit ...) x 9
  • (Cytochrome c oxidase subunit ...) x 13
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 10
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 3
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] 1 unknown subunit ...) x 6
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 6
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • Acyl carrier protein
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • Mitochondrial NADH dehydrogenase Fe-S protein 4
  • NADH-ubiquinone oxidoreductase 75 kDa subunit
KeywordsELECTRON TRANSPORT / OXIDOREDUCTASE / Respiratory / Respirasome / Mammalian
Function / homology
Function and homology information


ubiquinone-6 biosynthetic process / reproductive system development / NADH dehydrogenase complex / protein insertion into mitochondrial inner membrane / intrinsic component of mitochondrial membrane / oxidoreductase activity, acting on NAD(P)H / protein processing involved in protein targeting to mitochondrion / mitochondrial processing peptidase complex / electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity / NADH:ubiquinone reductase (H+-translocating) ...ubiquinone-6 biosynthetic process / reproductive system development / NADH dehydrogenase complex / protein insertion into mitochondrial inner membrane / intrinsic component of mitochondrial membrane / oxidoreductase activity, acting on NAD(P)H / protein processing involved in protein targeting to mitochondrion / mitochondrial processing peptidase complex / electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respirasome assembly / NADH dehydrogenase / mitochondrial respiratory chain complex III assembly / NADH dehydrogenase activity / integral component of mitochondrial membrane / mitochondrial respiratory chain complex I / respiratory chain complex IV / mitochondrial large ribosomal subunit / protein lipoylation / mitochondrial respiratory chain complex III / regulation of oxidative phosphorylation / mitochondrial respiratory chain complex I assembly / acyl carrier activity / mitochondrial electron transport, NADH to ubiquinone / acyl binding / mitochondrial respirasome / quinol-cytochrome-c reductase / multicellular organism aging / integral component of mitochondrial inner membrane / electron transport coupled proton transport / ubiquinol-cytochrome-c reductase activity / mitochondrial ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / cardiovascular system development / mitochondrial respiratory chain complex IV / cytochrome-c oxidase / electron transport chain / ATP synthesis coupled electron transport / anterograde axonal transport / mitochondrial ATP synthesis coupled proton transport / cytochrome-c oxidase activity / cellular response to interferon-beta / ubiquinone binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrion morphogenesis / iron-sulfur cluster binding / mitochondrial electron transport, ubiquinol to cytochrome c / quinone binding / respiratory electron transport chain / chloroplast thylakoid membrane / enzyme regulator activity / respirasome / mitochondrial membrane / axon cytoplasm / aerobic respiration / reactive oxygen species metabolic process / extrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / central nervous system development / muscle contraction / fatty acid metabolic process / cellular response to retinoic acid / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / 2 iron, 2 sulfur cluster binding / positive regulation of protein catabolic process / catalytic activity / mitochondrial intermembrane space / metalloendopeptidase activity / multicellular organism growth / negative regulation of cell growth / circadian rhythm / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / mitochondrial inner membrane / oxidation-reduction process / response to oxidative stress / nuclear body / copper ion binding / mitochondrial matrix / oxidoreductase activity / protein-containing complex binding / negative regulation of transcription, DNA-templated / ubiquitin protein ligase binding / heme binding / mitochondrion / membrane / integral component of membrane / nucleoplasm / plasma membrane / metal ion binding / cytosol / cytoplasm
Cytochrome C oxidase subunit II, transmembrane domain / Deoxynucleoside kinase domain / Cytochrome c oxidase, subunit Vb, zinc binding site / Cytochrome c1, transmembrane anchor, C-terminal / NAD(P)H-quinone oxidoreductase subunit D/H / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Cytochrome c oxidase-like, subunit I domain / Protein MGARP ...Cytochrome C oxidase subunit II, transmembrane domain / Deoxynucleoside kinase domain / Cytochrome c oxidase, subunit Vb, zinc binding site / Cytochrome c1, transmembrane anchor, C-terminal / NAD(P)H-quinone oxidoreductase subunit D/H / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Cytochrome c oxidase-like, subunit I domain / Protein MGARP / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Cytochrome b/b6-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / [NiFe]-hydrogenase, large subunit / Single alpha-helix domain superfamily / Cytochrome b / Protein MGARP, N-terminal / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase subunit 2, C-terminal / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome b/b6, C-terminal domain superfamily / Thioredoxin-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain superfamily / NAD(P)-binding domain superfamily / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Soluble ligand binding domain / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome c oxidase subunit IV / Cytochrome c-like domain / Phosphopantetheine binding ACP domain / GRIM-19 / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone oxidoreductase, subunit G / CHCH / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase subunit 5, C-terminal / Globular protein, non-globular alpha/beta subunit / Metalloenzyme, LuxS/M16 peptidase-like / NADH ubiquinone oxidoreductase, F subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / Cytochrome C oxidase subunit II, transmembrane domain / Peptidase M16, N-terminal / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Zinc finger, CHCC-type / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase, subunit 10 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / Cytochrome c oxidase, subunit VIa, conserved site / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Rieske [2Fe-2S] iron-sulphur domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / Cytochrome c oxidase, subunit II / Di-haem cytochrome, transmembrane / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH-quinone oxidoreductase, chain G, C-terminal / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Cytochrome b-c1 complex subunit 10 / Rieske iron-sulphur protein / Cytochrome c oxidase subunit IV superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome C oxidase, subunit VIIB / NADH dehydrogenase subunit 2 C-terminus / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Molybdopterin oxidoreductase / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Respiratory-chain NADH dehydrogenase 51 Kd subunit / SLBB domain / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH dehydrogenase / Proton-conducting membrane transporter / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / UcrQ family / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH dehydrogenase subunit 5 C-terminus / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NmrA-like family / Deoxynucleoside kinase / GRIM-19 protein / Cytochrome oxidase c subunit VIII / ETC complex I subunit conserved region / Zinc-finger domain / Cytochrome C and Quinol oxidase polypeptide I
NADH-ubiquinone oxidoreductase chain 5 / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / CHCH domain-containing protein / Oxidored_q6 domain-containing protein / NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 11 / NADH:ubiquinone oxidoreductase subunit B10 / Mitochondrial NADH dehydrogenase Fe-S protein 4 / Uncharacterized protein / un:f1sty1: ...NADH-ubiquinone oxidoreductase chain 5 / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / CHCH domain-containing protein / Oxidored_q6 domain-containing protein / NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 11 / NADH:ubiquinone oxidoreductase subunit B10 / Mitochondrial NADH dehydrogenase Fe-S protein 4 / Uncharacterized protein / un:f1sty1: / un:f1srg2: / Uncharacterized protein / un:f1sly2: / NADH:ubiquinone oxidoreductase subunit A9 / NADH:ubiquinone oxidoreductase subunit B9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / un:f1sif2: / NADH:ubiquinone oxidoreductase core subunit S1 / NADH dehydrogenase ubiquinone 1 beta subcomplex subunit 5, mitochondrial isoform 1 / Acyl carrier protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / AIF-MLS domain-containing protein / Uncharacterized protein / NADH:ubiquinone oxidoreductase subunit A1 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 4L / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome b-c1 complex subunit 10 / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 6B1 / NADH-ubiquinone oxidoreductase chain 2 / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome b / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome c1, heme protein, mitochondrial / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase ubiquinone iron-sulfur protein 2, mitochondrial isoform 1
Biological speciesBos taurus (cattle)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsGu, J. / Wu, M. / Guo, R. / Yang, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31030020 and 31170679 China
Ministry of Science and Technology2012CB911101 China
CitationJournal: Nature / Year: 2016
Title: The architecture of the mammalian respirasome.
Authors: Jinke Gu / Meng Wu / Runyu Guo / Kaige Yan / Jianlin Lei / Ning Gao / Maojun Yang /
Abstract: The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing ...The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing the proton gradient for ATP synthesis by complex V. The respiratory chain complexes can assemble into supercomplexes (SCs), but their precise arrangement is unknown. Here we report a 5.4 Å cryo-electron microscopy structure of the major 1.7 megadalton SCI1III2IV1 respirasome purified from porcine heart. The CIII dimer and CIV bind at the same side of the L-shaped CI, with their transmembrane domains essentially aligned to form a transmembrane disk. Compared to free CI, the CI in the respirasome is more compact because of interactions with CIII and CIV. The NDUFA11 and NDUFB9 supernumerary subunits of CI contribute to the oligomerization of CI and CIII. The structure of the respirasome provides information on the precise arrangements of the respiratory chain complexes in mitochondria.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Refinement description

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Assembly

Deposited unit
A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: Cytochrome b-c1 complex subunit 9
K: Cytochrome b-c1 complex subunit 10
L: Cytochrome b-c1 complex subunit 9
M: Cytochrome b-c1 complex subunit 1, mitochondrial
N: Cytochrome b-c1 complex subunit 2, mitochondrial
O: Cytochrome b
P: Cytochrome c1, heme protein, mitochondrial
Q: Cytochrome b-c1 complex subunit Rieske, mitochondrial
R: Cytochrome b-c1 complex subunit 7
S: Cytochrome b-c1 complex subunit 8
T: Cytochrome b-c1 complex subunit 6, mitochondrial
U: Cytochrome b-c1 complex subunit Rieske, mitochondrial
V: Cytochrome b-c1 complex subunit 10
W: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3
Y: NADH-ubiquinone oxidoreductase 75 kDa subunit
Z: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2
a: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7
b: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8
c: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
d: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
e: NADH-ubiquinone oxidoreductase chain 1
f: NADH-ubiquinone oxidoreductase chain 2
g: NADH-ubiquinone oxidoreductase chain 3
h: NADH-ubiquinone oxidoreductase chain 4
i: NADH-ubiquinone oxidoreductase chain 4L
j: NADH-ubiquinone oxidoreductase chain 5
k: NADH-ubiquinone oxidoreductase chain 6
l: NADH-ubiquinone oxidoreductase chain 6
m: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
n: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
o: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
p: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9
q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
r: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
t: Acyl carrier protein
u: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5
v: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
w: Mitochondrial NADH dehydrogenase Fe-S protein 4
x: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
0: Cytochrome c oxidase subunit 3
1: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
2: Cytochrome c oxidase subunit 5A, mitochondrial
3: Cytochrome c oxidase subunit 5B, mitochondrial
4: Cytochrome c oxidase subunit 6A2, mitochondrial
5: Cytochrome c oxidase subunit 6B1
6: Cytochrome c oxidase subunit 6C
7: Cytochrome c oxidase subunit 7A1, mitochondrial
8: Cytochrome c oxidase subunit 7B, mitochondrial
9: Cytochrome c oxidase subunit 7C, mitochondrial
s: Cytochrome c oxidase subunit 8B, mitochondrial
y: Cytochrome c oxidase subunit 1
z: Cytochrome c oxidase subunit 2
Aa: Acyl carrier protein
Ab: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Ac: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
Ad: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Ae: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
Af: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Ag: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Ah: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Ai: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5
Aj: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
Ak: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
Al: NADH dehydrogenase [ubiquinone] 1 subunit C2
Am: NADH dehydrogenase [ubiquinone] 1 subunit C1
An: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Ao: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Ap: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Aq: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Ar: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
As: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
At: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Au: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Av: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Aw: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,741,771109
Polymers1,732,06784
Non-polymers9,70425
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Cytochrome b-c1 complex subunit ... , 9 types, 18 molecules AMBNEQFRGSHTIUJLKV

#1: Protein Cytochrome b-c1 complex subunit 1, mitochondrial


Mass: 49266.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P31800
#2: Protein Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2


Mass: 46575.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23004
#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / ...Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 29572.814 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: quinol-cytochrome-c reductase
#6: Protein Cytochrome b-c1 complex subunit 7 / Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex ...Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex 14 kDa protein


Mass: 13371.190 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#7: Protein Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa ...Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa protein / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


Mass: 9606.027 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13271
#8: Protein Cytochrome b-c1 complex subunit 6, mitochondrial / Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / ...Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c reductase complex 11 kDa protein


Mass: 9189.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00126
#9: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / ...Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 7964.259 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase
#10: Protein Cytochrome b-c1 complex subunit 9 / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol- ...Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol-cytochrome c reductase complex 7.2 kDa protein


Mass: 7209.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00130
#11: Protein Cytochrome b-c1 complex subunit 10 / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c reductase complex 6.4 kDa protein


Mass: 6527.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07552

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Protein , 5 types, 8 molecules CODPYtAaw

#3: Protein Cytochrome b / / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 42620.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00157
#4: Protein Cytochrome c1, heme protein, mitochondrial / / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol- ...Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1


Mass: 27323.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00125
#13: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit


Mass: 79627.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SHD7
#32: Protein Acyl carrier protein /


Mass: 17326.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SAB6
#34: Protein Mitochondrial NADH dehydrogenase Fe-S protein 4


Mass: 19718.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: G8IFA6

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 6 types, 6 molecules WZabox

#12: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3


Mass: 30241.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIF2
#14: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2


Mass: 52552.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S1A8
#15: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7


Mass: 23777.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LK43
#16: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8


Mass: 23893.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#28: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5


Mass: 12506.591 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SV23
#35: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 13348.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S031

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NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules cd

#17: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 50637.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RVN1
#18: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial


Mass: 27439.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SM98

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NADH-ubiquinone oxidoreductase chain ... , 7 types, 8 molecules efghijkl

#19: Protein NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35667.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79874, NADH:ubiquinone reductase (H+-translocating)
#20: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39077.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79875, NADH:ubiquinone reductase (H+-translocating)
#21: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 12998.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79880, NADH:ubiquinone reductase (H+-translocating)
#22: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 51859.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79881, NADH:ubiquinone reductase (H+-translocating)
#23: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10827.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: P56632, NADH:ubiquinone reductase (H+-translocating)
#24: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68695.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: Q9TDR1, NADH:ubiquinone reductase (H+-translocating)
#25: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 19021.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79882, NADH:ubiquinone reductase (H+-translocating)

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 10 types, 11 molecules mnpqvrAcAeAfAgAn

#26: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3


Mass: 9225.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RNI5
#27: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 11099.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: NADH:ubiquinone reductase (H+-translocating)
#29: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9


Mass: 42606.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SL07
#30: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 40476.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIS9
#31: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13


Mass: 16911.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S6Q1
#50: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1


Mass: 8088.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GR43
#52: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5


Mass: 13321.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SLY2
#53: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6


Mass: 14953.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SRG2
#54: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11


Mass: 14686.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM4
#59: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8


Mass: 20064.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SLR1

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 3 types, 4 molecules uAiAjAk

#33: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5


Mass: 21587.006 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SGC6
#55: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10


Mass: 20944.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LDC3
#56: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9


Mass: 21733.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GSE5

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Cytochrome c oxidase subunit ... , 13 types, 13 molecules 0123456789syz

#36: Protein Cytochrome c oxidase subunit 3 / / Cytochrome c oxidase polypeptide III


Mass: 29943.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#37: Protein Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / / Cytochrome c oxidase polypeptide IV / Cytochrome c oxidase subunit IV isoform 1 / COX IV-1


Mass: 17179.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00423
#38: Protein Cytochrome c oxidase subunit 5A, mitochondrial /


Mass: 12453.081 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 44-152 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00426
#39: Protein Cytochrome c oxidase subunit 5B, mitochondrial / / Cytochrome c oxidase polypeptide VIa / Cytochrome c oxidase polypeptide Vb


Mass: 10684.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00428
#40: Protein Cytochrome c oxidase subunit 6A2, mitochondrial / / Cytochrome c oxidase polypeptide VIa-heart / COXVIAH / Cytochrome c oxidase polypeptide VIb


Mass: 9452.687 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 13-96 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07471
#41: Protein Cytochrome c oxidase subunit 6B1 / / Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase ...Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase subunit VIb isoform 1 / COX VIb-1


Mass: 10039.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00429
#42: Protein Cytochrome c oxidase subunit 6C / / Cytochrome c oxidase polypeptide VIc / Cytochrome c oxidase subunit STA


Mass: 8494.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P04038
#43: Protein Cytochrome c oxidase subunit 7A1, mitochondrial / / Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c ...Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c oxidase subunit VIIa-H / Cytochrome c oxidase subunit VIIa-muscle / Cytochrome c oxidase subunit VIIa-M


Mass: 6682.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07470
#44: Protein Cytochrome c oxidase subunit 7B, mitochondrial / / Cytochrome c oxidase polypeptide VIIb / IHQ


Mass: 6365.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13183
#45: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial / / Cytochrome c oxidase polypeptide VIIIA / Cytochrome c oxidase polypeptide VIIc


Mass: 5449.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00430
#46: Protein/peptide Cytochrome c oxidase subunit 8B, mitochondrial / / Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c ...Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c oxidase subunit 8H / IX / VIIIb


Mass: 4967.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P10175
#47: Protein Cytochrome c oxidase subunit 1 / / Cytochrome c oxidase polypeptide I


Mass: 57065.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00396, cytochrome-c oxidase
#48: Protein Cytochrome c oxidase subunit 2 / / Cytochrome c oxidase polypeptide II


Mass: 26040.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P68530

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NADH dehydrogenase [ubiquinone] 1 unknown subunit ... , 6 types, 12 molecules AbAhAdAoApAvAqAsAwArAtAu

#49: Protein NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment


Mass: 11422.071 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#51: Protein/peptide
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment


Mass: 3677.524 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#60: Protein NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment


Mass: 6485.986 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#61: Protein/peptide NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment


Mass: 2911.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#62: Protein/peptide NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment


Mass: 1464.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#63: Protein/peptide NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment


Mass: 1124.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)

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NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules AlAm

#57: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14327.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1STY1
#58: Protein NADH dehydrogenase [ubiquinone] 1 subunit C1


Mass: 8630.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RRC9

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Non-polymers , 10 types, 25 molecules

#64: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme


Mass: 616.487 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#65: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H34FeN4O4
#66: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Fe2S2
#67: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Fe4S4
#68: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#69: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#70: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#71: Chemical ChemComp-HEA / HEME-A / Heme A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C49H56FeN4O6
#72: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cu
#73: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg

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Details

Sequence detailsAuthor does not know the sequences of chains Ab, Ah, Ad, Ao, Ap, Av, Aq, As, Aw, Ar, At, Au

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Respirasome / Type: COMPLEX / Details: Mammalian, respirasome
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73
Source: NATURAL
Molecular weightValue: 1.7 MDa / Experimental value: YES
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.7 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1EMAN2.1particle selection
2RELION1.4image acquisition
4CTFFIND3CTF correction
7COOT8.01model fitting
9EMAN2.1initial Euler assignment
10EMAN2.1final Euler assignment
11EMAN2.1classification
12EMAN2.13D reconstruction
13PHENIX1.9model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139996 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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