7LJF | pdb_00007ljf

Cryo-EM structure of the Mpa hexamer in the presence of ATP and the Pup-FabD substrate

PDB DOI: https://doi.org/10.2210/pdb7LJF/pdb
EM Map EMD-23392: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2021-01-29 Released: 2021-05-05
Deposition Author(s): Yin, Y., Li, H.
Funding Organization(s): National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of the Mpa hexamer in the presence of ATP and the Pup-FabD substrate

Yin, Y., Li, H.

(2021) J Biological Chem

Macromolecule Content

Total Structure Weight: 400.93 kDa
Atom Count: 15,742
Modeled Residue Count: 2,007
Deposited Residue Count: 3,606
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA ATPase forming ring-shaped complexes	A, B, C, D, E A, B, C, D, E, F	601	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: arc, mpa, DSI38_15585, E5M52_17490, ERS007661_01151, ERS007665_00732, ERS007679_01634, ERS007681_02311, ERS007703_01049, ERS007720_01453... arc, mpa, DSI38_15585, E5M52_17490, ERS007661_01151, ERS007665_00732, ERS007679_01634, ERS007681_02311, ERS007703_01049, ERS007720_01453, ERS007722_00998, ERS007741_01455, ERS023446_02559, ERS024276_00114, ERS027646_02035, ERS027659_02128, ERS027661_00811, ERS075361_03050, ERS094182_01863, F6W99_00704, FRD82_11355, SAMEA2683035_00457
UniProt
Find proteins for P9WQN5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQN5 Go to UniProtKB: P9WQN5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WQN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B]	I [auth B], K [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain I [auth B] Focus chain K [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-05-05

Deposition Author(s):

Yin, Y.

Li, H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)	United States	AI070285
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	AI088075