8DH6 | pdb_00008dh6

Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs

PDB DOI: https://doi.org/10.2210/pdb8DH6/pdb
EM Map EMD-27430: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2022-06-25 Released: 2022-07-20
Deposition Author(s): Godoy, A.S., Song, Y., Cheruvara, H., Quigley, A., Oliva, G.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.94 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs

Godoy, A.S., Song, Y., Cheruvara, H., Quigley, A., Oliva, G.

To be published.

Macromolecule Content

Total Structure Weight: 185.62 kDa
Atom Count: 12,901
Modeled Residue Count: 1,560
Deposited Residue Count: 1,575
Unique protein chains: 9

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A [auth a]	534	Saccharomyces cerevisiae	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P00401 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00401 Go to UniProtKB: P00401
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00401
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B [auth b]	236	Saccharomyces cerevisiae	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P00410 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00410 Go to UniProtKB: P00410
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00410
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	C [auth c]	269	Saccharomyces cerevisiae	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P00420 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00420 Go to UniProtKB: P00420
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00420
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 4, mitochondrial	D [auth d]	130	Saccharomyces cerevisiae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P04037 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04037 Go to UniProtKB: P04037
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04037
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5A, mitochondrial	E [auth e]	133	Saccharomyces cerevisiae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00424 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00424 Go to UniProtKB: P00424
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00424
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6, mitochondrial	F [auth f]	108	Saccharomyces cerevisiae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00427 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00427 Go to UniProtKB: P00427
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00427
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7, mitochondrial	G [auth g]	59	Saccharomyces cerevisiae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P10174 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P10174 Go to UniProtKB: P10174
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10174
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 8, mitochondrial	H [auth h]	51	Saccharomyces cerevisiae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P04039 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04039 Go to UniProtKB: P04039
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04039
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 9, mitochondrial	I [auth i]	55	Saccharomyces cerevisiae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07255 Go to UniProtKB: P07255
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07255
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEA Query on HEA Download:Ideal Coordinates CCD File SDF format, chain N [auth a] SDF format, chain M [auth a] MOL2 format, chain N [auth a] MOL2 format, chain M [auth a] mmCIF format, chain N [auth a] mmCIF format, chain M [auth a]	M [auth a], N [auth a]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain M [auth a] Focus chain N [auth a] Interactions & Density Focus chain M [auth a] Focus chain N [auth a]
PEF Query on PEF Download:Ideal Coordinates CCD File SDF format, chain Z [auth h] SDF format, chain Y [auth g] SDF format, chain X [auth e] SDF format, chain V [auth c] SDF format, chain U [auth c] SDF format, chain T [auth b] SDF format, chain R [auth b] SDF format, chain Q [auth b] SDF format, chain P [auth a] SDF format, chain O [auth a] MOL2 format, chain Z [auth h] MOL2 format, chain Y [auth g] MOL2 format, chain X [auth e] MOL2 format, chain V [auth c] MOL2 format, chain U [auth c] MOL2 format, chain T [auth b] MOL2 format, chain R [auth b] MOL2 format, chain Q [auth b] MOL2 format, chain P [auth a] MOL2 format, chain O [auth a] mmCIF format, chain Z [auth h] mmCIF format, chain Y [auth g] mmCIF format, chain X [auth e] mmCIF format, chain V [auth c] mmCIF format, chain U [auth c] mmCIF format, chain T [auth b] mmCIF format, chain R [auth b] mmCIF format, chain Q [auth b] mmCIF format, chain P [auth a] mmCIF format, chain O [auth a]	O [auth a] P [auth a] Q [auth b] R [auth b] T [auth b] O [auth a], P [auth a], Q [auth b], R [auth b], T [auth b], U [auth c], V [auth c], X [auth e], Y [auth g], Z [auth h]	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C₃₇ H₇₄ N O₈ P SLKDGVPOSSLUAI-PGUFJCEWSA-N		Interactions Focus chain O [auth a] Focus chain P [auth a] Focus chain Q [auth b] Focus chain R [auth b] Focus chain T [auth b] Focus chain U [auth c] Focus chain V [auth c] Focus chain X [auth e] Focus chain Y [auth g] Focus chain Z [auth h] Interactions & Density Focus chain O [auth a] Focus chain P [auth a] Focus chain Q [auth b] Focus chain R [auth b] Focus chain T [auth b] Focus chain U [auth c] Focus chain V [auth c] Focus chain X [auth e] Focus chain Y [auth g] Focus chain Z [auth h]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain W [auth d] MOL2 format, chain W [auth d] mmCIF format, chain W [auth d]	W [auth d]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain W [auth d] Interactions & Density Focus chain W [auth d]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain S [auth b] SDF format, chain L [auth a] MOL2 format, chain S [auth b] MOL2 format, chain L [auth a] mmCIF format, chain S [auth b] mmCIF format, chain L [auth a]	L [auth a], S [auth b]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain L [auth a] Focus chain S [auth b] Interactions & Density Focus chain L [auth a] Focus chain S [auth b]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain J [auth a] MOL2 format, chain J [auth a] mmCIF format, chain J [auth a]	J [auth a]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth a] Interactions & Density Focus chain J [auth a]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth a] MOL2 format, chain K [auth a] mmCIF format, chain K [auth a]	K [auth a]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth a] Interactions & Density Focus chain K [auth a]