8UCM | pdb_00008ucm

Komagataella pastoris Cytochrome c oxidase in complex with human VMAT2 and Reserpine

PDB DOI: https://doi.org/10.2210/pdb8UCM/pdb
EM Map EMD-42131: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Komagataella pastoris
Expression System: Komagataella pastoris
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-09-26 Released: 2024-10-09
Deposition Author(s): Ye, J., Liu, B., Li, W.
Funding Organization(s): American Heart Association

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.14 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

Komagataella pastoris Cytochrome c oxidase in complex with human VMAT2 and Reserpine

Ye, J., Liu, B., Li, W.

To be published.

Macromolecule Content

Total Structure Weight: 235.42 kDa
Atom Count: 15,430
Modeled Residue Count: 1,916
Deposited Residue Count: 2,056
Unique protein chains: 10

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptic vesicular amine transporter	A	514	Homo sapiens	Mutation(s): 0 Gene Names: SLC18A2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q05940 (Homo sapiens) Explore Q05940 Go to UniProtKB: Q05940
PHAROS: Q05940 GTEx: ENSG00000165646
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05940
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	B [auth a]	535	Komagataella pastoris	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for F2R0K8 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Explore F2R0K8 Go to UniProtKB: F2R0K8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2R0K8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	C [auth b]	236	Komagataella pastoris	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F2R0J7 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Explore F2R0J7 Go to UniProtKB: F2R0J7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2R0J7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	D [auth c]	268	Komagataella pastoris	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F2R0J6 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Explore F2R0J6 Go to UniProtKB: F2R0J6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2R0J6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 4	E [auth d]	117	Komagataella pastoris	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F2QT92 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Explore F2QT92 Go to UniProtKB: F2QT92
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2QT92
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5	F [auth e]	124	Komagataella pastoris	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F2QVW8 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Explore F2QVW8 Go to UniProtKB: F2QVW8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2QVW8
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6	G [auth f]	100	Komagataella pastoris	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F2QVA2 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Explore F2QVA2 Go to UniProtKB: F2QVA2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2QVA2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7	H [auth g]	58	Komagataella pastoris	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F2QS38 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Explore F2QS38 Go to UniProtKB: F2QS38
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2QS38
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 8	I [auth h]	48	Komagataella pastoris	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F2QRE4 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Explore F2QRE4 Go to UniProtKB: F2QRE4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2QRE4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 9	J [auth i]	56	Komagataella pastoris	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A1G4KPQ9 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Explore A0A1G4KPQ9 Go to UniProtKB: A0A1G4KPQ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1G4KPQ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEA (Subject of Investigation/LOI) Query on HEA Download:Ideal Coordinates CCD File SDF format, chain M [auth a] SDF format, chain N [auth a] MOL2 format, chain M [auth a] MOL2 format, chain N [auth a] mmCIF format, chain M [auth a] mmCIF format, chain N [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]
PTY (Subject of Investigation/LOI) Query on PTY Download:Ideal Coordinates CCD File SDF format, chain P [auth c] SDF format, chain Q [auth c] SDF format, chain S [auth e] SDF format, chain T [auth i] MOL2 format, chain P [auth c] MOL2 format, chain Q [auth c] MOL2 format, chain S [auth e] MOL2 format, chain T [auth i] mmCIF format, chain P [auth c] mmCIF format, chain Q [auth c] mmCIF format, chain S [auth e] mmCIF format, chain T [auth i]	P [auth c], Q [auth c], S [auth e], T [auth i]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain P [auth c] Focus chain Q [auth c] Focus chain S [auth e] Focus chain T [auth i] Interactions & Density Focus chain P [auth c] Focus chain Q [auth c] Focus chain S [auth e] Focus chain T [auth i]
YHR (Subject of Investigation/LOI) Query on YHR 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]	reserpine C₃₃ H₄₀ N₂ O₉ QEVHRUUCFGRFIF-MDEJGZGSSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
CUA (Subject of Investigation/LOI) Query on CUA Download:Ideal Coordinates CCD File SDF format, chain O [auth b] MOL2 format, chain O [auth b] mmCIF format, chain O [auth b]	O [auth b]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain O [auth b] Interactions & Density Focus chain O [auth b]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain R [auth d] MOL2 format, chain R [auth d] mmCIF format, chain R [auth d]	R [auth d]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain R [auth d] Interactions & Density Focus chain R [auth d]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain L [auth a] MOL2 format, chain L [auth a] mmCIF format, chain L [auth a]	L [auth a]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain L [auth a] Interactions & Density Focus chain L [auth a]

Binding Affinity Annotations
ID	Source	Binding Affinity
YHR	BindingDB: 8UCM	Ki: min: 1, max: 630 (nM) from 4 assay(s)
		Kd: 8 (nM) from 1 assay(s)
		IC50: min: 1.3, max: 100 (nM) from 12 assay(s)