8IBC

Respiratory complex CIII2, focus-refined of type IB, Wild type mouse under cold temperature

PDB DOI: https://doi.org/10.2210/pdb8IBC/pdb
EM Map EMD-35339: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2023-02-10 Released: 2024-09-18
Deposition Author(s): Shin, Y.-C., Liao, M.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Respiratory complex CIII2, focus-refined of type IB, Wild type mouse under cold temperature

Shin, Y.-C., Liao, M.

To be published.

Macromolecule Content

Total Structure Weight: 556.01 kDa
Atom Count: 31,431
Modelled Residue Count: 3,915
Deposited Residue Count: 4,904
Unique protein chains: 10

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 1, mitochondrial	A [auth AA], L [auth Aa]	480	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CZ13 (Mus musculus) Explore Q9CZ13 Go to UniProtKB: Q9CZ13
IMPC: MGI:107876
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CZ13
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 2, mitochondrial	B [auth AB], M [auth Ab]	453	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9DB77 (Mus musculus) Explore Q9DB77 Go to UniProtKB: Q9DB77
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9DB77
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	C [auth AC], N [auth Ac]	381	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P00158 (Mus musculus) Explore P00158 Go to UniProtKB: P00158
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00158
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1, heme protein, mitochondrial	D [auth AD], O [auth Ad]	325	Mus musculus	Mutation(s): 0 EC: 7.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D0M3 (Mus musculus) Explore Q9D0M3 Go to UniProtKB: Q9D0M3
IMPC: MGI:1913695
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9D0M3
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	E [auth AE], I [auth AI], P [auth Ae]	274	Mus musculus	Mutation(s): 0 EC: 7.1.1.8
UniProt
Find proteins for Q9CR68 (Mus musculus) Explore Q9CR68 Go to UniProtKB: Q9CR68
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CR68
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 7	F [auth AF], Q [auth Af]	111	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CQB4 (Mus musculus) Explore Q9CQB4 Go to UniProtKB: Q9CQB4
IMPC: MGI:1914780
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CQB4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 8	G [auth AG], R [auth Ag]	82	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CQ69 (Mus musculus) Explore Q9CQ69 Go to UniProtKB: Q9CQ69
IMPC: MGI:107807
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CQ69
Sequence Annotations Expand
Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 6, mitochondrial	H [auth AH], S [auth Ah]	89	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P99028 (Mus musculus) Explore P99028 Go to UniProtKB: P99028
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P99028
Sequence Annotations Expand
Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 9	J [auth AJ], T [auth Aj]	64	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8R1I1 (Mus musculus) Explore Q8R1I1 Go to UniProtKB: Q8R1I1
IMPC: MGI:1913402
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8R1I1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 10	K [auth AK], U [auth Ak]	56	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9CPX8 (Mus musculus) Explore Q9CPX8 Go to UniProtKB: Q9CPX8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CPX8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download Ideal Coordinates CCD File SDF format, chain BA [auth Aa] SDF format, chain HA [auth Ac] SDF format, chain JA [auth Ag] MOL2 format, chain BA [auth Aa] MOL2 format, chain HA [auth Ac] MOL2 format, chain JA [auth Ag] mmCIF format, chain BA [auth Aa] mmCIF format, chain HA [auth Ac] mmCIF format, chain JA [auth Ag]	BA [auth Aa], HA [auth Ac], JA [auth Ag]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain BA [auth Aa] Focus chain HA [auth Ac] Focus chain JA [auth Ag] Interactions & Density Focus chain BA [auth Aa] Focus chain HA [auth Ac] Focus chain JA [auth Ag]
U10 (Subject of Investigation/LOI) Query on U10 Download Ideal Coordinates CCD File SDF format, chain FA [auth Ac] SDF format, chain Y [auth AC] MOL2 format, chain FA [auth Ac] MOL2 format, chain Y [auth AC] mmCIF format, chain FA [auth Ac] mmCIF format, chain Y [auth AC]	FA [auth Ac], Y [auth AC]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain FA [auth Ac] Focus chain Y [auth AC] Interactions & Density Focus chain FA [auth Ac] Focus chain Y [auth AC]
3PE (Subject of Investigation/LOI) Query on 3PE Download Ideal Coordinates CCD File SDF format, chain EA [auth Ac] SDF format, chain X [auth AC] MOL2 format, chain EA [auth Ac] MOL2 format, chain X [auth AC] mmCIF format, chain EA [auth Ac] mmCIF format, chain X [auth AC]	EA [auth Ac], X [auth AC]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain EA [auth Ac] Focus chain X [auth AC] Interactions & Density Focus chain EA [auth Ac] Focus chain X [auth AC]
HEC (Subject of Investigation/LOI) Query on HEC Download Ideal Coordinates CCD File SDF format, chain AA [auth AD] SDF format, chain IA [auth Ad] MOL2 format, chain AA [auth AD] MOL2 format, chain IA [auth Ad] mmCIF format, chain AA [auth AD] mmCIF format, chain IA [auth Ad]	AA [auth AD], IA [auth Ad]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain AA [auth AD] Focus chain IA [auth Ad] Interactions & Density Focus chain AA [auth AD] Focus chain IA [auth Ad]
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain CA [auth Ac] SDF format, chain DA [auth Ac] SDF format, chain V [auth AC] SDF format, chain W [auth AC] MOL2 format, chain CA [auth Ac] MOL2 format, chain DA [auth Ac] MOL2 format, chain V [auth AC] MOL2 format, chain W [auth AC] mmCIF format, chain CA [auth Ac] mmCIF format, chain DA [auth Ac] mmCIF format, chain V [auth AC] mmCIF format, chain W [auth AC]	CA [auth Ac], DA [auth Ac], V [auth AC], W [auth AC]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain CA [auth Ac] Focus chain DA [auth Ac] Focus chain V [auth AC] Focus chain W [auth AC] Interactions & Density Focus chain CA [auth Ac] Focus chain DA [auth Ac] Focus chain V [auth AC] Focus chain W [auth AC]
UQ6 (Subject of Investigation/LOI) Query on UQ6 Download Ideal Coordinates CCD File SDF format, chain GA [auth Ac] SDF format, chain Z [auth AC] MOL2 format, chain GA [auth Ac] MOL2 format, chain Z [auth AC] mmCIF format, chain GA [auth Ac] mmCIF format, chain Z [auth AC]	GA [auth Ac], Z [auth AC]	5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL C₃₉ H₆₀ O₄ DYOSCPIQEYRQEO-XQCASOQKSA-N		Interactions Focus chain GA [auth Ac] Focus chain Z [auth AC] Interactions & Density Focus chain GA [auth Ac] Focus chain Z [auth AC]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-18

Deposition Author(s):

Shin, Y.-C.

Liao, M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	RO1 DK081418
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	RO1 DK089883

Revision History (Full details and data files)

Version 1.0: 2024-09-18
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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8IBC

Respiratory complex CIII2, focus-refined of type IB, Wild type mouse under cold temperature

Respiratory complex CIII2, focus-refined of type IB, Wild type mouse under cold temperature

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)