[English] 日本語
Yorodumi
- PDB-5gup: Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gup
TitleCryo-EM structure of mammalian respiratory supercomplex I1III2IV1
Components
  • (Cytochrome b-c1 complex subunit ...) x 9
  • (Cytochrome c oxidase subunit ...) x 13
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 12
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 7
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • Acyl carrier protein, mitochondrial
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
KeywordsELECTRON TRANSPORT / Cryo-EM / Mammalian / Respiratory / Supercomplex
Function / homology
Function and homology information


ubiquinone-6 biosynthetic process / pons development / subthalamus development / respiratory chain complex III / reproductive system development / NADH dehydrogenase complex / protein insertion into mitochondrial inner membrane / oxidoreductase activity, acting on NAD(P)H / cerebellar Purkinje cell layer development / NADH:ubiquinone reductase (H+-translocating) ...ubiquinone-6 biosynthetic process / pons development / subthalamus development / respiratory chain complex III / reproductive system development / NADH dehydrogenase complex / protein insertion into mitochondrial inner membrane / oxidoreductase activity, acting on NAD(P)H / cerebellar Purkinje cell layer development / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase / mitochondrial respiratory chain complex III assembly / NADH dehydrogenase activity / mitochondrial respiratory chain complex I / mitochondrial large ribosomal subunit / protein lipoylation / pyramidal neuron development / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex I assembly / acyl carrier activity / mitochondrial electron transport, NADH to ubiquinone / acyl binding / quinol-cytochrome-c reductase / multicellular organism aging / thalamus development / 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 / electron transport chain / ATP synthesis coupled electron transport / anterograde axonal 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 / midbrain development / quinone binding / chloroplast thylakoid membrane / hypothalamus development / respirasome / mitochondrial membrane / axon cytoplasm / aerobic respiration / reactive oxygen species metabolic process / extrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / muscle contraction / fatty acid metabolic process / cellular response to retinoic acid / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / hippocampus development / 2 iron, 2 sulfur cluster binding / positive regulation of protein catabolic process / catalytic activity / mitochondrial intermembrane space / multicellular organism growth / negative regulation of cell growth / circadian rhythm / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / oxidation-reduction process / response to oxidative stress / mitochondrial matrix / electron transfer activity / oxidoreductase activity / protein-containing complex binding / negative regulation of transcription, DNA-templated / ubiquitin protein ligase binding / mitochondrion / membrane / integral component of membrane / nucleoplasm / metal ion binding / cytosol / cytoplasm
CHCH domain / Cytochrome b/b6-like domain superfamily / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-ubiquinone oxidoreductase, subunit 10 / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NAD(P)H-quinone oxidoreductase subunit D/H / Ubiquinol-cytochrome C reductase hinge domain ...CHCH domain / Cytochrome b/b6-like domain superfamily / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-ubiquinone oxidoreductase, subunit 10 / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NAD(P)H-quinone oxidoreductase subunit D/H / Ubiquinol-cytochrome C reductase hinge domain / Protein MGARP / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / P-loop containing nucleoside triphosphate hydrolase / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / [NiFe]-hydrogenase, large subunit / Single alpha-helix domain superfamily / Cytochrome b / Deoxynucleoside kinase domain / Protein MGARP, N-terminal / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Cytochrome b/b6, C-terminal domain superfamily / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Ubiquinol-cytochrome C reductase hinge domain superfamily / Peptidase M16, N-terminal / GRIM-19 / NADH:ubiquinone oxidoreductase subunit B14.5a / 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 / NADH:ubiquinone oxidoreductase, MNLL subunit / Rieske [2Fe-2S] iron-sulphur domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Rieske iron-sulphur protein / Cytochrome b-c1 complex subunit 10 / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Di-haem cytochrome, transmembrane / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / ACP-like superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / ETC complex I subunit conserved region / NADH ubiquinone oxidoreductase subunit NDUFA12 / NmrA-like family / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NADH-ubiquinone oxidoreductase MWFE subunit / Deoxynucleoside kinase / Tim17/Tim22/Tim23/Pmp24 family / GRIM-19 protein / NADH-ubiquinone oxidoreductase B12 subunit family / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH-ubiquinone oxidoreductase subunit 10 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / Proton-conducting membrane transporter / NADH dehydrogenase subunit 2 C-terminus / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / 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 / MNLL subunit / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Molybdopterin oxidoreductase / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Rieske [2Fe-2S] domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-quinone oxidoreductase subunit E, N-terminal / NuoE domain / Ubiquinol-cytochrome C reductase hinge protein
NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 11 / NADH dehydrogenase 1 beta subcomplex 6 / Cytochrome b-c1 complex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / un:f1sif2: / NADH:ubiquinone oxidoreductase subunit B3 / NADH:ubiquinone oxidoreductase core subunit S1 / NADH dehydrogenase ubiquinone 1 beta subcomplex subunit 5, mitochondrial isoform 1 / Cytochrome b-c1 complex subunit 10 ...NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 11 / NADH dehydrogenase 1 beta subcomplex 6 / Cytochrome b-c1 complex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / un:f1sif2: / NADH:ubiquinone oxidoreductase subunit B3 / NADH:ubiquinone oxidoreductase core subunit S1 / NADH dehydrogenase ubiquinone 1 beta subcomplex subunit 5, mitochondrial isoform 1 / Cytochrome b-c1 complex subunit 10 / Uncharacterized protein / Acyl carrier protein / Uncharacterized protein / NADH dehydrogenase ubiquinone iron-sulfur protein 2, mitochondrial isoform 1 / Ubiquinol-cytochrome c reductase core protein 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / un:f1rwv4: / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / AIF-MLS domain-containing protein / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Uncharacterized protein / Ubiquinol-cytochrome c reductase complex III subunit VII / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Cytochrome c oxidase subunit 5A / NADH:ubiquinone oxidoreductase subunit A9 / Ubiquinol-cytochrome c reductase complex / un:i3lpw0: / Cytochrome b / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 1 / NADH:ubiquinone oxidoreductase subunit B9 / NADH:ubiquinone oxidoreductase subunit A1 / Oxidored_q6 domain-containing protein / CHCH domain-containing protein / NADH:ubiquinone oxidoreductase subunit B10 / Mitochondrial NADH dehydrogenase Fe-S protein 4 / Uncharacterized protein / un:f1sty1: / Uncharacterized protein / un:f1srg2: / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Uncharacterized protein / un:f1sly2: / Uncharacterized protein
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsGu, J. / Wu, M. / Guo, R. / Yang, M.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2016YFA0501100 and 2012CB911101 China
National Outstanding Young Scholar Science Foundation China
National Natural Science Foundation of China3162500065, 31030020 and 31170679 China
CitationJournal: Cell / Year: 2016
Title: Structure of Mammalian Respiratory Supercomplex IIIIIV.
Authors: Meng Wu / Jinke Gu / Runyu Guo / Yushen Huang / Maojun Yang /
Abstract: The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to ...The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to synthesize ATP. The precise arrangement of SCs is largely unknown. Here, we report a 4.0-Å cryo-electron microscopy (cryo-EM) structure of the major SC in porcine heart, the 1.7-MDa SCIIIIIV. The complex III (CIII) dimer and complex IV (CIV) bind at the same side of the L-shaped complex I (CI). Several accessory or supernumerary subunits of CI, such as NDUFA11, NDUFB4, NDUFB8, and NDUFB9, directly contribute to the oligomerization of CI, CIII, and CIV. COX7C and COX7A of CIV attach CIV to the concave surface formed by CIII and the distal end of membrane arm of CI. The structure suggests a possible mechanism by which electrons are transferred from NADH to cytochrome c and provides a platform for future functional dissection of respiration.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: cell / em_image_scans / em_software / Item: _cell.Z_PDB / _em_software.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9539
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c oxidase subunit 6C
B: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
D: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
E: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
F: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
G: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
H: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
I: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
J: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
K: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
L: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
M: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
N: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
O: Acyl carrier protein, mitochondrial
P: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
R: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
S: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
T: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
U: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
V: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
X: Acyl carrier protein, mitochondrial
Y: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
Z: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
a: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
b: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
c: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
d: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
e: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
f: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
g: NADH dehydrogenase [ubiquinone] 1 subunit C2
h: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
i: NADH-ubiquinone oxidoreductase chain 2
j: NADH-ubiquinone oxidoreductase chain 3
k: NADH-ubiquinone oxidoreductase chain 4L
l: NADH-ubiquinone oxidoreductase chain 5
m: NADH-ubiquinone oxidoreductase chain 6
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
q: NADH-ubiquinone oxidoreductase chain 4
r: NADH-ubiquinone oxidoreductase chain 1
s: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
t: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
u: Cytochrome b-c1 complex subunit 1, mitochondrial
v: Cytochrome b-c1 complex subunit 2, mitochondrial
w: Cytochrome b
x: Cytochrome c1, heme protein, mitochondrial
y: Cytochrome b-c1 complex subunit 7
z: Cytochrome b-c1 complex subunit 8
0: Cytochrome b-c1 complex subunit 6, mitochondrial
1: Cytochrome b-c1 complex subunit 9
2: Cytochrome b-c1 complex subunit Rieske, mitochondrial
3: Cytochrome b-c1 complex subunit 10
4: Cytochrome b-c1 complex subunit Rieske, mitochondrial
5: Cytochrome b-c1 complex subunit 1, mitochondrial
6: Cytochrome b-c1 complex subunit 2, mitochondrial
7: Cytochrome b
8: Cytochrome c1, heme protein, mitochondrial
9: Cytochrome b-c1 complex subunit 7
Aa: Cytochrome b-c1 complex subunit 8
Ab: Cytochrome b-c1 complex subunit 6, mitochondrial
Ac: Cytochrome b-c1 complex subunit 9
Ad: Cytochrome b-c1 complex subunit 10
Ae: Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial
Af: Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial
Ag: Cytochrome c oxidase subunit 8B, mitochondrial
Ah: Cytochrome c oxidase subunit 7A1, mitochondrial
Ai: Cytochrome c oxidase subunit 7B, mitochondrial
Aj: Cytochrome c oxidase subunit 7C, mitochondrial
Ak: Cytochrome c oxidase subunit 1
Al: Cytochrome c oxidase subunit 2
Am: Cytochrome c oxidase subunit 3
An: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
Ao: Cytochrome c oxidase subunit 5A, mitochondrial
Ap: Cytochrome c oxidase subunit 5B, mitochondrial
Aq: Cytochrome c oxidase subunit 6A, mitochondrial
Ar: Cytochrome c oxidase subunit 6B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,818,749132
Polymers1,781,94180
Non-polymers36,80852
Water0
1


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

-
Components

+
Cytochrome c oxidase subunit ... , 13 types, 13 molecules AAgAhAiAjAkAlAmAnAoApAqAr

#1: Protein Cytochrome c oxidase subunit 6C /


Mass: 8494.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#56: Protein/peptide Cytochrome c oxidase subunit 8B, mitochondrial /


Mass: 4967.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#57: Protein Cytochrome c oxidase subunit 7A1, mitochondrial /


Mass: 6682.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#58: Protein Cytochrome c oxidase subunit 7B, mitochondrial /


Mass: 6365.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#59: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial /


Mass: 5449.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#60: Protein Cytochrome c oxidase subunit 1 /


Mass: 57065.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#61: Protein Cytochrome c oxidase subunit 2 /


Mass: 26040.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#62: Protein Cytochrome c oxidase subunit 3 /


Mass: 29943.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#63: Protein Cytochrome c oxidase subunit 4 isoform 1, mitochondrial /


Mass: 17179.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#64: Protein Cytochrome c oxidase subunit 5A, mitochondrial /


Mass: 12453.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SJ34
#65: Protein Cytochrome c oxidase subunit 5B, mitochondrial /


Mass: 10684.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#66: Protein Cytochrome c oxidase subunit 6A, mitochondrial /


Mass: 9452.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#67: Protein Cytochrome c oxidase subunit 6B1 /


Mass: 10039.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)

+
NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules BE

#2: 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
#5: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial


Mass: 26301.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SM98

+
NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules CDFHIJh

#3: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial


Mass: 52552.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S1A8
#4: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial


Mass: 30241.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIF2
#6: 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
#8: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial


Mass: 23893.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#9: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial


Mass: 23777.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LK43
#10: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial


Mass: 19718.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: G8IFA6
#32: 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

+
Protein , 4 types, 7 molecules GOXw7x8

#7: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial


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


Mass: 17326.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SAB6
#47: Protein Cytochrome b /


Mass: 42840.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q1HBG9
#48: Protein Cytochrome c1, heme protein, mitochondrial /


Mass: 35488.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)

+
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12 types, 13 molecules KRLMNPQSTUVWs

#11: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 17162.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SQP4
#12: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial


Mass: 42606.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SL07
#13: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7


Mass: 12648.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SA62
#14: 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
#16: 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: UniProt: F1RGE3
#17: 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
#18: 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
#19: 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
#20: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 40476.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIS9
#21: 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
#22: 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
#43: 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

+
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules YZabcdenopt

#23: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial


Mass: 11939.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SRQ0
#24: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3


Mass: 11128.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SI50
#25: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial


Mass: 21587.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SGC6
#26: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6


Mass: 15603.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2EN80
#27: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 21702.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWL7
#28: 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
#29: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial


Mass: 17384.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWV4
#38: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1


Mass: 7044.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SD73
#39: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4


Mass: 15117.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LPW0
#40: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9


Mass: 21864.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GSE5
#44: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7


Mass: 16487.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)

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

#30: Protein NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial


Mass: 8630.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RRC9
#31: 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

+
NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules ijklmqr

#33: 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
#34: 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
#35: 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
#36: 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
#37: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 19021.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79882
#41: 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
#42: 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

+
Cytochrome b-c1 complex subunit ... , 9 types, 18 molecules u5v6y9zAa0Ab1Ac243AdAeAf

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


Mass: 52756.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKM0
#46: Protein Cytochrome b-c1 complex subunit 2, mitochondrial


Mass: 48264.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#49: Protein Cytochrome b-c1 complex subunit 7


Mass: 13587.549 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#50: Protein Cytochrome b-c1 complex subunit 8


Mass: 9784.339 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RI18
#51: Protein Cytochrome b-c1 complex subunit 6, mitochondrial


Mass: 10685.803 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S3W0
#52: Protein Cytochrome b-c1 complex subunit 9


Mass: 7412.530 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2EN79
#53: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 29492.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RNZ1
#54: Protein Cytochrome b-c1 complex subunit 10


Mass: 6560.654 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SDI2
#55: Protein Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial


Mass: 7900.107 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RNZ1

+
Non-polymers , 14 types, 52 molecules

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


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#69: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#70: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#71: Chemical
ChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C42H89NO8P
#72: 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
#73: Chemical ChemComp-ZMP / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate


Mass: 568.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49N2O8PS
#74: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#75: Chemical
ChemComp-PEE / 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 749.073 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C41H83NO8P / Comment: DOPE, phospholipid*YM
#76: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#77: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#78: Chemical ChemComp-HEA / HEME-A / Heme A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#79: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#80: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#81: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

+
Details

Sequence detailsTHE SEQUENCE OF RESIDUE 1-47 OF CHAIN E IS MFLTAALRARATGFTAQWGRHVRNLHKTAVQNGAGGALFVHRDTPEN. THE ...THE SEQUENCE OF RESIDUE 1-47 OF CHAIN E IS MFLTAALRARATGFTAQWGRHVRNLHKTAVQNGAGGALFVHRDTPEN. THE AUTHOR COULD OBSERVE SOME CONNECTED RESIDUES AND ASSIGNED UNK TO THESE RESIDUES. THE AUTHOR IS NOT SURE WHCIH PART OF RESIDUE 1-47 CORRESPONDS WITH THIS PEPTIDE OF UNK. SO THE RESIDUE NUMBERS OF UNK IS MEANINGLESS.

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Respiratory supercomplex I1III2IV1 / Type: COMPLEX / Details: Supercomplex generated by complex I, III and IV.
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
Source: NATURAL
Molecular weightValue: 1.7 MDa / Experimental value: YES
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1EMAN2.1particle selection
2AutoEMation2image acquisition
4CTFFIND3CTF correction
7Coot0.8.2model fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13PHENIX1.9model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161912 / Symmetry type: POINT

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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