9ZAK | pdb_00009zak

Cryo-EM structure of Leishmania tarentolae respiratory complex IV (cytochrome c oxidase dimer)

PDB DOI: https://doi.org/10.2210/pdb9ZAK/pdb
EM Map EMD-73966: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Leishmania tarentolae
Mutation(s): No

Deposited: 2025-11-19 Released: 2026-10-07
Deposition Author(s): Liao, Y.T., Chao, L.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.21 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Conserved and divergent mitochondrial assemblies in kinetoplastid parasites

Solayman, M., Liao, Y.T., Calvo, S.E., Vacas, A.F., Papanastasiou, M., Rivera, K.D., Mani, D., Boyle, B.W., Deng, F.G., Betsinger, C.N., Carr, S.A., Chen, M.Z., Duraisingh, M.T., Fry, M.Y., Goyal, M., Issa, T.M., Kim, M., Lian, C.G., Luce, B.E., Mian, S.Y., Nguyen, K., Paul, A.S., Samuelson, J., Stefely, J.A., Udeshi, N.D., Mootha, V.K., Aphasizheva, I., Chao, L.H., Aphasizhev, R.

(2026) Mol Cell 86: 4043

DOI: https://doi.org/10.1016/j.molcel.2026.08.031

Macromolecule Content

Total Structure Weight: 756.02 kDa
Atom Count: 53,313
Modeled Residue Count: 6,448
Deposited Residue Count: 6,450
Unique protein chains: 17

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P27 protein	A, R [auth a]	223	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KL16 (Leishmania tarentolae) Explore A0A640KL16 Go to UniProtKB: A0A640KL16
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KL16
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit V, putative	B, S [auth b]	179	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KIZ0 (Leishmania tarentolae) Explore A0A640KIZ0 Go to UniProtKB: A0A640KIZ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KIZ0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	C, T [auth c]	210	Leishmania tarentolae	Mutation(s): 0 EC: 7.1.1.9
UniProt
Find proteins for P14545 (Leishmania tarentolae) Explore P14545 Go to UniProtKB: P14545
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14545
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome C oxidase subunit VI, putative	D, U [auth d]	157	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KLX8 (Leishmania tarentolae) Explore A0A640KLX8 Go to UniProtKB: A0A640KLX8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KLX8
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein, conserved, LtaP04.0630	E, V [auth e]	200	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640K7Y4 (Leishmania tarentolae) Explore A0A640K7Y4 Go to UniProtKB: A0A640K7Y4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640K7Y4
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase VIII, putative	F, W [auth f]	127	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KN71 (Leishmania tarentolae) Explore A0A640KN71 Go to UniProtKB: A0A640KN71
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KN71
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein, conserved, LtaP09.0030	G, X [auth g]	107	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640K9E6 (Leishmania tarentolae) Explore A0A640K9E6 Go to UniProtKB: A0A640K9E6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640K9E6
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase VII, putative	H, Y [auth h]	165	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KP32 (Leishmania tarentolae) Explore A0A640KP32 Go to UniProtKB: A0A640KP32
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KP32
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome-c oxidase	I [auth K], Z [auth k]	202	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KV26 (Leishmania tarentolae) Explore A0A640KV26 Go to UniProtKB: A0A640KV26
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KV26
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 10	AA [auth l], J [auth L]	95	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KG51 (Leishmania tarentolae) Explore A0A640KG51 Go to UniProtKB: A0A640KG51
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KG51
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit I	BA [auth m], K [auth M]	110	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KXE6 (Leishmania tarentolae) Explore A0A640KXE6 Go to UniProtKB: A0A640KXE6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KXE6
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	CA [auth n], L [auth N]	549	Leishmania tarentolae	Mutation(s): 0 EC: 7.1.1.9
UniProt
Find proteins for P14544 (Leishmania tarentolae) Explore P14544 Go to UniProtKB: P14544
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14544
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	DA [auth o], M [auth O]	287	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for Q34935 (Leishmania tarentolae) Explore Q34935 Go to UniProtKB: Q34935
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q34935
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein, conserved, LtaP33.2260	EA [auth p], N [auth P]	93	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KQD4 (Leishmania tarentolae) Explore A0A640KQD4 Go to UniProtKB: A0A640KQD4
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UniProt Group	A0A640KQD4
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein, conserved, LtaP36.1760	FA [auth q], O [auth Q]	82	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KUH3 (Leishmania tarentolae) Explore A0A640KUH3 Go to UniProtKB: A0A640KUH3
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UniProt Group	A0A640KUH3
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit iv	GA [auth r], P [auth R]	311	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KB61 (Leishmania tarentolae) Explore A0A640KB61 Go to UniProtKB: A0A640KB61
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KB61
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase assembly factor like protein	HA [auth s], Q [auth S]	128	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640K8B8 (Leishmania tarentolae) Explore A0A640K8B8 Go to UniProtKB: A0A640K8B8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640K8B8
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEA Query on HEA Download:Ideal Coordinates CCD File SDF format, chain JA [auth N] SDF format, chain KA [auth N] SDF format, chain MA [auth n] SDF format, chain NA [auth n] MOL2 format, chain JA [auth N] MOL2 format, chain KA [auth N] MOL2 format, chain MA [auth n] MOL2 format, chain NA [auth n] mmCIF format, chain JA [auth N] mmCIF format, chain KA [auth N] mmCIF format, chain MA [auth n] mmCIF format, chain NA [auth n]	JA [auth N], KA [auth N], MA [auth n], NA [auth n]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain JA [auth N] Focus chain KA [auth N] Focus chain MA [auth n] Focus chain NA [auth n] Interactions & Density Focus chain JA [auth N] Focus chain KA [auth N] Focus chain MA [auth n] Focus chain NA [auth n]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain IA [auth N] SDF format, chain LA [auth n] MOL2 format, chain IA [auth N] MOL2 format, chain LA [auth n] mmCIF format, chain IA [auth N] mmCIF format, chain LA [auth n]	IA [auth N], LA [auth n]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain IA [auth N] Focus chain LA [auth n] Interactions & Density Focus chain IA [auth N] Focus chain LA [auth n]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.21 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-07

Deposition Author(s):

Liao, Y.T.

Chao, L.

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-10-07
Type: Initial release

9ZAK | pdb_00009zak

Cryo-EM structure of Leishmania tarentolae respiratory complex IV (cytochrome c oxidase dimer)

Literature

Conserved and divergent mitochondrial assemblies in kinetoplastid parasites

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

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Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

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Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data