9UBG | pdb_00009ubg

Cryo-EM structure of Pyruvate carboxylase from Mycobacterium tuberculosis in complex with Acetyl-CoA and ADP

PDB DOI: https://doi.org/10.2210/pdb9UBG/pdb
EM Map EMD-63875: EMDB EMDataResource

Classification: LIGASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-04-03 Released: 2025-05-07
Deposition Author(s): Singh, A., Sharma, D., Raza, M., Singh, S., Das, U.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Cryo-EM structure of Pyruvate carboxylase from Mycobacterium tuberculosis in complex with Acetyl-CoA and ADP

Singh, A., Sharma, D., Raza, M., Singh, S., Das, U.

To be published.

Macromolecule Content

Total Structure Weight: 455.32 kDa
Atom Count: 31,829
Modeled Residue Count: 4,180
Deposited Residue Count: 4,180
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate carboxylase	A, B [auth C], C [auth D], D [auth B]	1,045	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: pca, Rv2967c EC: 6.4.1.1
UniProt
Find proteins for I6YEU0 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6YEU0 Go to UniProtKB: I6YEU0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I6YEU0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO (Subject of Investigation/LOI) Query on ACO Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth A]	G [auth A], J [auth C], K [auth D], N [auth B]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain G [auth A] Focus chain J [auth C] Focus chain K [auth D] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth C] Focus chain K [auth D] Focus chain N [auth B]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain L [auth D] SDF format, chain H [auth C] SDF format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain L [auth D] MOL2 format, chain H [auth C] MOL2 format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain L [auth D] mmCIF format, chain H [auth C] mmCIF format, chain E [auth A]	E [auth A], H [auth C], L [auth D], O [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Focus chain L [auth D] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth C] Focus chain L [auth D] Focus chain O [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain M [auth D] SDF format, chain I [auth C] SDF format, chain F [auth A] MOL2 format, chain P [auth B] MOL2 format, chain M [auth D] MOL2 format, chain I [auth C] MOL2 format, chain F [auth A] mmCIF format, chain P [auth B] mmCIF format, chain M [auth D] mmCIF format, chain I [auth C] mmCIF format, chain F [auth A]	F [auth A], I [auth C], M [auth D], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Focus chain M [auth D] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth C] Focus chain M [auth D] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.2
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	India	--

Revision History (Full details and data files)

Version 1.0: 2025-05-07
Type: Initial release
Version 2.0: 2025-07-23
Type: Coordinate replacement
Reason: Polymer geometry
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Structure summary