7LIW | pdb_00007liw

Local refinement of human ATP citrate lyase E599Q mutant ASH domain

PDB DOI: https://doi.org/10.2210/pdb7LIW/pdb
EM Map EMD-23387: EMDB EMDataResource

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-01-28 Released: 2021-05-19
Deposition Author(s): Wei, X., Marmorstein, R.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.85 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7LIW

This is version 1.4 of the entry. See complete history.

Literature

Reply to: Acetyl-CoA is produced by the citrate synthase homology module of ATP-citrate lyase.

Wei, X., Marmorstein, R.

(2021) Nat Struct Mol Biol 28: 639-641

PubMed: 34294921 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-021-00625-2
Primary Citation Related Structures:
7LIW, 7LJ9, 7LLA

Organizational Affiliation

Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

Macromolecule Content

Total Structure Weight: 485.4 kDa
Atom Count: 14,598
Modeled Residue Count: 1,871
Deposited Residue Count: 4,404
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-citrate synthase	A, B, C, D	1,101	Homo sapiens	Mutation(s): 1 Gene Names: ACLY EC: 2.3.3.8
UniProt & NIH Common Fund Data Resources
Find proteins for P53396 (Homo sapiens) Explore P53396 Go to UniProtKB: P53396
PHAROS: P53396 GTEx: ENSG00000131473
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53396
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
Y2A (Subject of Investigation/LOI) Query on Y2A Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	(2S)-2-hydroxy-2-[2-oxo-2-(phosphonooxy)ethyl]butanedioic acid C₆ H₉ O₁₀ P RAAPFOXFYNTKEB-LURJTMIESA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.85 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-05-19

Deposition Author(s):

Marmorstein, R.

Revision History (Full details and data files)

Version 1.0: 2021-05-19
Type: Initial release
Version 1.1: 2021-07-28
Changes: Database references
Version 1.2: 2021-08-25
Changes: Database references
Version 1.3: 2024-05-29
Changes: Data collection
Version 1.4: 2025-06-04
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.