9Z9K | pdb_00009z9k

Cryo-EM structure of Leishmania tarentolae respiratory complex III (cytochrome bc1 complex)

PDB DOI: https://doi.org/10.2210/pdb9Z9K/pdb
EM Map EMD-73948: EMDB EMDataResource

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

Deposited: 2025-11-18 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: 3.02 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: 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: 587.07 kDa
Atom Count: 41,308
Modeled Residue Count: 5,116
Deposited Residue Count: 5,116
Unique protein chains: 12

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial processing peptidase alpha subunit, putative	A, L [auth a]	479	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KGT7 (Leishmania tarentolae) Explore A0A640KGT7 Go to UniProtKB: A0A640KGT7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KGT7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial processing peptide beta subunit, putative	B, M [auth b]	490	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KTP0 (Leishmania tarentolae) Explore A0A640KTP0 Go to UniProtKB: A0A640KTP0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KTP0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome c reductase complex 14 kDa protein	C, N [auth c]	191	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KSC9 (Leishmania tarentolae) Explore A0A640KSC9 Go to UniProtKB: A0A640KSC9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KSC9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	D, O [auth d]	371	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for P14548 (Leishmania tarentolae) Explore P14548 Go to UniProtKB: P14548
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14548
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1, heme protein, mitochondrial, putative	E, P [auth e]	258	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KA58 (Leishmania tarentolae) Explore A0A640KA58 Go to UniProtKB: A0A640KA58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KA58
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
LtaP17.1410, Hypothetical protein, conserved	F, Q [auth f]	67	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KF59 (Leishmania tarentolae) Explore A0A640KF59 Go to UniProtKB: A0A640KF59
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KF59
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
LtaP32.3800, Hypothetical protein, conserved	G, R [auth g]	147	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KPN1 (Leishmania tarentolae) Explore A0A640KPN1 Go to UniProtKB: A0A640KPN1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KPN1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Rieske iron-sulfur protein, putative	H, S [auth h]	279	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KYQ2 (Leishmania tarentolae) Explore A0A640KYQ2 Go to UniProtKB: A0A640KYQ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KYQ2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
LtaP35.0250, Hypothetical protein, conserved	I, T [auth i]	107	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KRZ1 (Leishmania tarentolae) Explore A0A640KRZ1 Go to UniProtKB: A0A640KRZ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KRZ1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome-c reductase-like protein	J, U [auth j]	70	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KNT3 (Leishmania tarentolae) Explore A0A640KNT3 Go to UniProtKB: A0A640KNT3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KNT3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
LtaP27.0110, Hypothetical protein, conserved	K, V [auth k]	75	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KKU7 (Leishmania tarentolae) Explore A0A640KKU7 Go to UniProtKB: A0A640KKU7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A640KKU7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
unassigned helix	W [auth L], X [auth l]	24	Leishmania tarentolae	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain BA [auth d] SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain AA [auth d] MOL2 format, chain BA [auth d] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain AA [auth d] mmCIF format, chain BA [auth d] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain AA [auth d]	AA [auth d], BA [auth d], Y [auth D], Z [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth d] Focus chain BA [auth d] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth d] Focus chain BA [auth d] Focus chain Y [auth D] Focus chain Z [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK Query on UNK	W [auth L], X [auth l]	L-PEPTIDE LINKING	C₄ H₉ N O₂		--

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.02 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4.7.0

Structure Validation

View Full Validation Report

View more in-depth experimental data

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

9Z9K | pdb_00009z9k

Cryo-EM structure of Leishmania tarentolae respiratory complex III (cytochrome bc1 complex)

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

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

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

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)