8JR0

Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with TBAJ-587

PDB DOI: https://doi.org/10.2210/pdb8JR0/pdb
EM Map EMD-36589: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Mycobacterium tuberculosis
Expression System: Mycolicibacterium smegmatis
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-06-15 Released: 2024-05-01
Deposition Author(s): Zhang, Y., Lai, Y., Liu, F., Rao, Z., Gong, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 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

Structure of Mycobacterium tuberculosis ATP synthase

Zhang, Y., Lai, Y., Liu, F., Rao, Z., Gong, H.

To be published.

Macromolecule Content

Total Structure Weight: 558.63 kDa
Atom Count: 37,460
Modelled Residue Count: 4,889
Deposited Residue Count: 5,127
Unique protein chains: 8

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	A, B, C	549	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: atpA, Rv1308, MTCY373.28 EC: 7.1.2.2 Membrane Entity: Yes
UniProt
Find proteins for P9WPU7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPU7 Go to UniProtKB: P9WPU7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPU7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	D, E, F	486	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: atpD, Rv1310, MTCY373.30 EC: 7.1.2.2 Membrane Entity: Yes
UniProt
Find proteins for P9WPU5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPU5 Go to UniProtKB: P9WPU5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPU5
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase gamma chain	G	305	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: atpG, Rv1309, MTCY373.29 Membrane Entity: Yes
UniProt
Find proteins for P9WPU9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPU9 Go to UniProtKB: P9WPU9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPU9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase epsilon chain	H	121	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: atpC, Rv1311, MTCY373.31 Membrane Entity: Yes
UniProt
Find proteins for P9WPV1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPV1 Go to UniProtKB: P9WPV1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPV1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit c	I [auth 1] J [auth 2] K [auth 3] L [auth 4] M [auth 5] I [auth 1], J [auth 2], K [auth 3], L [auth 4], M [auth 5], N [auth 6], O [auth 7], P [auth 8], Q [auth 9]	81	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: atpE Membrane Entity: Yes
UniProt
Find proteins for A0A045H4W8 (Mycobacterium tuberculosis) Explore A0A045H4W8 Go to UniProtKB: A0A045H4W8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A045H4W8
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit a	R [auth a]	250	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: atpB, ERS007657_00358, ERS007661_00092, ERS007663_00105, ERS007665_00910, ERS007670_00031, ERS007679_03316, ERS007681_03471, ERS007688_02939, ERS007703_00159... atpB, ERS007657_00358, ERS007661_00092, ERS007663_00105, ERS007665_00910, ERS007670_00031, ERS007679_03316, ERS007681_03471, ERS007688_02939, ERS007703_00159, ERS007720_03212, ERS007722_00190, ERS007739_02359, ERS007741_03568, ERS024276_02583, ERS027646_02991, ERS027659_00329, ERS027661_00021, SAMEA2683035_01568 Membrane Entity: Yes
UniProt
Find proteins for A0A045J1C5 (Mycobacterium tuberculosis) Explore A0A045J1C5 Go to UniProtKB: A0A045J1C5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A045J1C5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit b	S [auth b]	171	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: atpF Membrane Entity: Yes
UniProt
Find proteins for A0A045H294 (Mycobacterium tuberculosis) Explore A0A045H294 Go to UniProtKB: A0A045H294
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A045H294
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Multifunctional fusion protein	T [auth d]	446	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: atpH Membrane Entity: Yes
UniProt
Find proteins for A0A045JVE3 (Mycobacterium tuberculosis) Explore A0A045JVE3 Go to UniProtKB: A0A045JVE3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A045JVE3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UTI Query on UTI Download Ideal Coordinates CCD File SDF format, chain EA [auth 1] SDF format, chain FA [auth 4] SDF format, chain GA [auth 5] SDF format, chain HA [auth 6] SDF format, chain IA [auth 7] SDF format, chain JA [auth 8] SDF format, chain KA [auth 9] MOL2 format, chain EA [auth 1] MOL2 format, chain FA [auth 4] MOL2 format, chain GA [auth 5] MOL2 format, chain HA [auth 6] MOL2 format, chain IA [auth 7] MOL2 format, chain JA [auth 8] MOL2 format, chain KA [auth 9]	EA [auth 1] FA [auth 4] GA [auth 5] HA [auth 6] IA [auth 7] EA [auth 1], FA [auth 4], GA [auth 5], HA [auth 6], IA [auth 7], JA [auth 8], KA [auth 9]	(1~{S},2~{S})-1-(6-bromanyl-2-methoxy-quinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2-fluoranyl-3-methoxy-phenyl)butan-2-ol C₃₀ H₃₃ Br F N₃ O₅ JJEGOJPMKLRSPJ-POURPWNDSA-N		Interactions Focus chain EA [auth 1] Focus chain FA [auth 4] Focus chain GA [auth 5] Focus chain HA [auth 6] Focus chain IA [auth 7] Focus chain JA [auth 8] Focus chain KA [auth 9] Interactions & Density Focus chain EA [auth 1] Focus chain FA [auth 4] Focus chain GA [auth 5] Focus chain HA [auth 6] Focus chain IA [auth 7] Focus chain JA [auth 8] Focus chain KA [auth 9]
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain W [auth B] SDF format, chain Y [auth C] MOL2 format, chain U [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth C]	U [auth A], W [auth B], Y [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain U [auth A] Focus chain W [auth B] Focus chain Y [auth C] Interactions & Density Focus chain U [auth A] Focus chain W [auth B] Focus chain Y [auth C]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain CA [auth F] MOL2 format, chain AA [auth D] MOL2 format, chain CA [auth F]	AA [auth D], CA [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth F] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth F] SDF format, chain V [auth A] SDF format, chain X [auth B] SDF format, chain Z [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth F] MOL2 format, chain V [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth C]	BA [auth D], DA [auth F], V [auth A], X [auth B], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DA [auth F] Focus chain V [auth A] Focus chain X [auth B] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth F] Focus chain V [auth A] Focus chain X [auth B] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81520108019
National Natural Science Foundation of China (NSFC)	China	32100976
National Natural Science Foundation of China (NSFC)	China	82222042

Revision History (Full details and data files)

Version 1.0: 2024-05-01
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

8JR0

Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with TBAJ-587

Structure of Mycobacterium tuberculosis ATP synthase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

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Sequence Annotations

Entity ID: 3

UniProt

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Sequence Annotations

Entity ID: 4

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Sequence Annotations

Entity ID: 5

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Entity ID: 6

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Entity ID: 7

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Entity ID: 8

UniProt

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Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)