[English] 日本語
Yorodumi
- PDB-8bq6: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bq6
TitleCryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete conformation 2 composition)
Components
  • (Acyl carrier protein ...) x 2
  • (Cytochrome b-c1 complex subunit ...) x 6
  • (Gamma carbonic anhydrase ...) x 2
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 6
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 6
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 8
  • (NADH-ubiquinone oxidoreductase chain ...) x 6
  • (Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 2
  • (Probable mitochondrial-processing peptidase subunit ...) x 2
  • (Uncharacterized protein ...) x 2
  • AT3G07480.1
  • At2g46540/F11C10.23
  • At4g16450
  • B15 -- 1 beta subcomplex subunit 4
  • Cytochrome b
  • Cytochrome c1 2, heme protein, mitochondrial
  • ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
  • Excitatory amino acid transporter
  • Gamma carbonic anhydrase-like 2, mitochondrial
  • NADH dehydrogenase subunit 4L
  • Outer envelope pore protein 16-3, chloroplastic/mitochondrial
  • P1
  • Transmembrane protein
KeywordsMEMBRANE PROTEIN / Plant / Mitochondria / Complex
Function / homology
Function and homology information


plastid outer membrane / TIM22 mitochondrial import inner membrane insertion complex / anther dehiscence / vegetative to reproductive phase transition of meristem / chloroplast outer membrane / mitochondrial processing peptidase / plant-type cell wall / cold acclimation / respiratory chain complex III / NADH dehydrogenase complex ...plastid outer membrane / TIM22 mitochondrial import inner membrane insertion complex / anther dehiscence / vegetative to reproductive phase transition of meristem / chloroplast outer membrane / mitochondrial processing peptidase / plant-type cell wall / cold acclimation / respiratory chain complex III / NADH dehydrogenase complex / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / protein insertion into mitochondrial inner membrane / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / plant-type vacuole / mitochondrial respiratory chain complex III / vacuole / respiratory chain complex I / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / regulation of reactive oxygen species metabolic process / cobalt ion binding / response to osmotic stress / plastid / mitochondrial electron transport, ubiquinol to cytochrome c / acyl carrier activity / porin activity / NADH:ubiquinone reductase (H+-translocating) / pore complex / mitochondrial respiratory chain complex I / protein homotrimerization / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / monoatomic ion transport / response to salt stress / respiratory electron transport chain / chloroplast / mitochondrial membrane / carbonate dehydratase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / peroxisome / fatty acid biosynthetic process / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / mitochondrial outer membrane / electron transfer activity / oxidoreductase activity / carbohydrate metabolic process / mitochondrial matrix / copper ion binding / heme binding / nucleolus / protein homodimerization activity / mitochondrion / proteolysis / zinc ion binding / extracellular region / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Mitochondrial import inner membrane translocase subunit TIM22 / Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / At2g27730-like / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal ...Mitochondrial import inner membrane translocase subunit TIM22 / Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / At2g27730-like / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / Adrenodoxin / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome b / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Tim17/Tim22/Tim23/Pmp24 family / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / Soluble ligand binding domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / SLBB domain / Rieske iron-sulphur protein, C-terminal / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Zinc finger, CHCC-type / Zinc-finger domain / Hexapeptide repeat / Rieske iron-sulphur protein / GRIM-19 / GRIM-19 protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NDUFA6, LYR domain / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / Metalloenzyme, LuxS/M16 peptidase-like / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NDUFB9, LYR domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Bacterial transferase hexapeptide (six repeats) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / 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:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ
Similarity search - Domain/homology
Chem-8Q1 / CROTONYL COENZYME A / : / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / IRON/SULFUR CLUSTER / Chem-UQ5 / UBIQUINONE-7 ...Chem-8Q1 / CROTONYL COENZYME A / : / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / IRON/SULFUR CLUSTER / Chem-UQ5 / UBIQUINONE-7 / Ubiquinone-9 / (thale cress) hypothetical protein / (thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 6 / Cytochrome b / NADH-ubiquinone oxidoreductase chain 4L / (thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / Cytochrome b-c1 complex subunit 7-2, mitochondrial / NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / Outer envelope pore protein 16-3, chloroplastic/mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A / Acyl carrier protein 2, mitochondrial / Acyl carrier protein 1, mitochondrial / NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / Cytochrome b-c1 complex subunit 6-1, mitochondrial / Probable mitochondrial-processing peptidase subunit beta, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial / At4g16450 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / Uncharacterized protein At1g67785 / Transmembrane protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Excitatory amino acid transporter / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B / Cytochrome b-c1 complex subunit Rieske-1, mitochondrial / Cytochrome b-c1 complex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / Gamma carbonic anhydrase 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Cytochrome c1 2, heme protein, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Gamma carbonic anhydrase 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Cytochrome b-c1 complex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Cytochrome b-c1 complex subunit 8-1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein / Gamma carbonic anhydrase-like 2, mitochondrial / At2g46540/F11C10.23 / Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial / Uncharacterized protein At2g27730, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKlusch, N. / Kuehlbrandt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Plants / Year: 2023
Title: Cryo-EM structure of the respiratory I + III supercomplex from Arabidopsis thaliana at 2 Å resolution.
Authors: Niklas Klusch / Maximilian Dreimann / Jennifer Senkler / Nils Rugen / Werner Kühlbrandt / Hans-Peter Braun /
Abstract: Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis ...Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III with a co-purified ubiquinone in the Q site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.
History
DepositionNov 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADH-ubiquinone oxidoreductase chain 3
B: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3
D: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2
E: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
F: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
G: NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
H: NADH-ubiquinone oxidoreductase chain 1
I: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial
J: NADH-ubiquinone oxidoreductase chain 6
K: NADH dehydrogenase subunit 4L
L: NADH-ubiquinone oxidoreductase chain 5
M: NADH-ubiquinone oxidoreductase chain 4
N: NADH-ubiquinone oxidoreductase chain 2
O: AT3G07480.1
P: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
R: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
S: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
T: Acyl carrier protein 1, mitochondrial
U: Acyl carrier protein 2, mitochondrial
V: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial
W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
X: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
Y: Outer envelope pore protein 16-3, chloroplastic/mitochondrial
Z: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
a: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
b: At2g46540/F11C10.23
c: Transmembrane protein
d: Excitatory amino acid transporter
e: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B
f: At4g16450
g: ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
i: P1
j: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2
k: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A
l: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
m: B15 -- 1 beta subcomplex subunit 4
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B
q: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
u: Uncharacterized protein At1g67785
v: Uncharacterized protein At2g27730, mitochondrial
x: Gamma carbonic anhydrase-like 2, mitochondrial
y: Gamma carbonic anhydrase 2, mitochondrial
z: Gamma carbonic anhydrase 1, mitochondrial
AA: Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial
AB: Probable mitochondrial-processing peptidase subunit beta, mitochondrial
AC: Cytochrome b
AD: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
AE: Cytochrome c1 2, heme protein, mitochondrial
AF: Cytochrome b-c1 complex subunit 7-2, mitochondrial
AG: Cytochrome b-c1 complex subunit 8-1, mitochondrial
AH: Cytochrome b-c1 complex subunit 6-1, mitochondrial
AI: Cytochrome b-c1 complex subunit 9, mitochondrial
AJ: Cytochrome b-c1 complex subunit 10, mitochondrial
BA: Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial
BB: Probable mitochondrial-processing peptidase subunit beta, mitochondrial
BC: Cytochrome b
BD: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
BE: Cytochrome c1 2, heme protein, mitochondrial
BF: Cytochrome b-c1 complex subunit 7-2, mitochondrial
BG: Cytochrome b-c1 complex subunit 8-1, mitochondrial
BH: Cytochrome b-c1 complex subunit 6-1, mitochondrial
BI: Cytochrome b-c1 complex subunit 9, mitochondrial
BJ: Cytochrome b-c1 complex subunit 10, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,588,15398
Polymers1,575,18367
Non-polymers12,97131
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
NADH-ubiquinone oxidoreductase chain ... , 6 types, 6 molecules AHJLMN

#1: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 13969.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P92533, NADH:ubiquinone reductase (H+-translocating)
#8: Protein NADH-ubiquinone oxidoreductase chain 1


Mass: 36020.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: B5TM92, NADH:ubiquinone reductase (H+-translocating)
#10: Protein NADH-ubiquinone oxidoreductase chain 6


Mass: 23690.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: A0A2P2CLG1, NADH:ubiquinone reductase (H+-translocating)
#12: Protein NADH-ubiquinone oxidoreductase chain 5


Mass: 74497.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: B5TM94, NADH:ubiquinone reductase (H+-translocating)
#13: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 55995.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: B5TM93, NADH:ubiquinone reductase (H+-translocating)
#14: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 55486.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: O05000, NADH:ubiquinone reductase (H+-translocating)

+
NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 8 types, 8 molecules BCDGIQRe

#2: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial


Mass: 24071.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q42577, NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / NADH dehydrogenase subunit 9


Mass: 22910.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q95748, NADH:ubiquinone reductase (H+-translocating)
#4: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / NADH dehydrogenase subunit 7


Mass: 45062.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P93306, NADH:ubiquinone reductase (H+-translocating)
#7: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / Protein EMBRYO DEFECTIVE 1467


Mass: 81619.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9FGI6, NADH:ubiquinone reductase (H+-translocating)
#9: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial


Mass: 25536.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q42599, NADH:ubiquinone reductase (H+-translocating)
#17: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Protein FROSTBITE1


Mass: 17160.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FJW4
#18: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 12251.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M9M6
#31: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B


Mass: 9914.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LZI6

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

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


Mass: 28423.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: O22769, NADH:ubiquinone reductase (H+-translocating)
#6: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 53522.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9FNN5, NADH:ubiquinone reductase (H+-translocating)

+
Protein , 13 types, 15 molecules KOYbcdfgimxACBCAEBE

#11: Protein NADH dehydrogenase subunit 4L /


Mass: 11193.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A2P2CLH7
#15: Protein AT3G07480.1


Mass: 17626.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A384LA38
#25: Protein Outer envelope pore protein 16-3, chloroplastic/mitochondrial / Chloroplastic outer envelope pore protein of 16 kDa 3 / AtOEP16-3 / OEP16-3 / Mitochondrial complex ...Chloroplastic outer envelope pore protein of 16 kDa 3 / AtOEP16-3 / OEP16-3 / Mitochondrial complex I subunit B14.7


Mass: 17017.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O48528
#28: Protein At2g46540/F11C10.23 / Expressed protein / F11C10.23/F11C10.23 / Fiber


Mass: 6810.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZPY5
#29: Protein Transmembrane protein /


Mass: 9876.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8VZT9
#30: Protein Excitatory amino acid transporter


Mass: 9220.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94AL6
#32: Protein At4g16450 / NADH-ubiquinone oxidoreductase / Uncharacterized protein At4g16450


Mass: 11383.019 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q84W12
#33: Protein ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein


Mass: 12648.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SLC8
#34: Protein P1


Mass: 11808.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A178W1I8
#38: Protein B15 -- 1 beta subcomplex subunit 4


Mass: 8305.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A178VZI4
#45: Protein Gamma carbonic anhydrase-like 2, mitochondrial / GAMMA CAL2


Mass: 27985.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SMN1
#50: Protein Cytochrome b /


Mass: 44310.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A2P2CLG2
#52: Protein Cytochrome c1 2, heme protein, mitochondrial / / Complex III subunit 4-2 / Complex III subunit IV-2 / Cytochrome b-c1 complex subunit 4-2 / ...Complex III subunit 4-2 / Complex III subunit IV-2 / Cytochrome b-c1 complex subunit 4-2 / Ubiquinol-cytochrome c reductase complex cytochrome c1 subunit 2 / Cytochrome c-1 2


Mass: 33728.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FKS5

+
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 6 types, 6 molecules PSWXZa

#16: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial


Mass: 43988.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SK66
#19: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 10865.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FIJ2
#23: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6


Mass: 15102.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LHI0
#24: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B


Mass: 11985.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LGE7
#26: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / Protein MATERNAL EFFECT EMBRYO ARREST 4


Mass: 16145.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8RWA7
#27: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1


Mass: 7349.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9C9Z5

+
Acyl carrier protein ... , 2 types, 2 molecules TU

#20: Protein Acyl carrier protein 1, mitochondrial / MtACP-1 / ACP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 13735.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P53665
#21: Protein Acyl carrier protein 2, mitochondrial / MtACP-2 / ACP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 14183.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O80800

+
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 2 types, 2 molecules Vq

#22: Protein Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial


Mass: 19201.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FLX7
#42: Protein Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 18346.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M9M9

+
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 6 types, 6 molecules jklnop

#35: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2


Mass: 7582.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LDK3
#36: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A


Mass: 8064.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O64725
#37: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial


Mass: 13225.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FGK0
#39: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / B22 subunit of eukaryotic mitochondrial complex I / Complex I-B22 / CI-B22 / NADH-ubiquinone ...B22 subunit of eukaryotic mitochondrial complex I / Complex I-B22 / CI-B22 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 13638.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q945M1
#40: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7


Mass: 11757.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SKC9
#41: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B


Mass: 12462.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94C12

+
Uncharacterized protein ... , 2 types, 2 molecules uv

#43: Protein Uncharacterized protein At1g67785


Mass: 7546.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8VZ65
#44: Protein Uncharacterized protein At2g27730, mitochondrial


Mass: 11965.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZUX4

+
Gamma carbonic anhydrase ... , 2 types, 2 molecules yz

#46: Protein Gamma carbonic anhydrase 2, mitochondrial / GAMMA CA2 / Transcription factor APFI


Mass: 30102.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9C6B3, Lyases; Carbon-oxygen lyases; Hydro-lyases
#47: Protein Gamma carbonic anhydrase 1, mitochondrial / GAMMA CA1


Mass: 30010.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9FWR5, Lyases; Carbon-oxygen lyases; Hydro-lyases

+
Probable mitochondrial-processing peptidase subunit ... , 2 types, 4 molecules AABAABBB

#48: Protein Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial / Alpha-MPP 1 / Complex III subunit II / Core protein II / Cytochrome b-c1 complex subunit 2-1 / ...Alpha-MPP 1 / Complex III subunit II / Core protein II / Cytochrome b-c1 complex subunit 2-1 / mitochondrial / Inactive zinc metalloprotease alpha-1 / Ubiquinol-cytochrome c oxidoreductase core protein 2-1


Mass: 54459.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZU25
#49: Protein Probable mitochondrial-processing peptidase subunit beta, mitochondrial / Beta-MPP / Complex III subunit I / Core protein I / Cytochrome b-c1 complex subunit 1 / ...Beta-MPP / Complex III subunit I / Core protein I / Cytochrome b-c1 complex subunit 1 / mitochondrial / Ubiquinol-cytochrome c oxidoreductase core protein 1


Mass: 59234.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q42290, mitochondrial processing peptidase

+
Cytochrome b-c1 complex subunit ... , 6 types, 12 molecules ADBDAFBFAGBGAHBHAIBIAJBJ

#51: Protein Cytochrome b-c1 complex subunit Rieske-1, mitochondrial / Complex III subunit 5-1 / Rieske iron-sulfur protein 1 / RISP1 / Ubiquinol-cytochrome c reductase ...Complex III subunit 5-1 / Rieske iron-sulfur protein 1 / RISP1 / Ubiquinol-cytochrome c reductase iron-sulfur subunit 1


Mass: 29645.584 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94JS0, quinol-cytochrome-c reductase
#53: Protein Cytochrome b-c1 complex subunit 7-2, mitochondrial / Complex III subunit 7-2 / Complex III subunit VII / Ubiquinol-cytochrome c oxidoreductase subunit 7-2


Mass: 14620.021 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4JWS8
#54: Protein Cytochrome b-c1 complex subunit 8-1, mitochondrial / Complex III subunit 8-1 / Complex III subunit VIII / Ubiquinol-cytochrome c oxidoreductase subunit ...Complex III subunit 8-1 / Complex III subunit VIII / Ubiquinol-cytochrome c oxidoreductase subunit 8-1 / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


Mass: 8517.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SG91
#55: Protein Cytochrome b-c1 complex subunit 6-1, mitochondrial / Complex III subunit 6-1 / Complex III subunit VI / Mitochondrial hinge protein / Ubiquinol- ...Complex III subunit 6-1 / Complex III subunit VI / Mitochondrial hinge protein / Ubiquinol-cytochrome c oxidoreductase subunit 6-1


Mass: 7997.315 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q0WWE3
#56: Protein Cytochrome b-c1 complex subunit 9, mitochondrial / Complex III subunit 9 / Complex III subunit X / Ubiquinol-cytochrome c oxidoreductase subunit 9


Mass: 8461.634 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LXJ2
#57: Protein Cytochrome b-c1 complex subunit 10, mitochondrial / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c oxidoreductase subunit 10


Mass: 5980.947 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94K78

+
Non-polymers , 12 types, 31 molecules

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


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#59: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#60: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#61: Chemical ChemComp-UQ9 / Ubiquinone-9 / 2,3-dimethoxy-5-methyl-6-[(2E,6E,10E,14Z,18E,22E,26E,30Z)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18 ,22,26,30,34-nonaen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 795.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H82O4 / Feature type: SUBJECT OF INVESTIGATION
#62: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#63: 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 / Feature type: SUBJECT OF INVESTIGATION
#64: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#65: Chemical ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H45N2O8PS / Feature type: SUBJECT OF INVESTIGATION
#66: Chemical ChemComp-COO / CROTONYL COENZYME A


Mass: 835.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#67: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#68: Chemical ChemComp-UQ5 / 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE


Mass: 522.758 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H50O4 / Feature type: SUBJECT OF INVESTIGATION
#69: Chemical ChemComp-UQ7 / UBIQUINONE-7


Mass: 658.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H66O4 / Feature type: SUBJECT OF INVESTIGATION

+
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Complete conformation 2 composition)
Type: COMPLEX / Entity ID: #1-#57 / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.4
SpecimenConc.: 0.18 mg/ml / Embedding 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 283.15 K

-
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 215000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
4CTFFIND4.1.13CTF correction
7Coot0.9.5model fitting
9PHENIX1.20.1-4487model refinement
10RELION3.1.3initial Euler assignment
11RELION3.1.3final Euler assignment
12RELION3.1.3classification
13RELION3.1.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1215138
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50886 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008100957
ELECTRON MICROSCOPYf_angle_d0.88136767
ELECTRON MICROSCOPYf_dihedral_angle_d10.16614552
ELECTRON MICROSCOPYf_chiral_restr0.04614997
ELECTRON MICROSCOPYf_plane_restr0.00617166

+
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