8Z03

Lactate bound to human GTP-specific succinyl-CoA synthetase

• PDB DOI: https://doi.org/10.2210/pdb8Z03/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-04-08 Released: 2024-12-11 
• Deposition Author(s): Liu, R.L., Ren, X.L., Li, L.T., Zhang, Y., Huang, H., Zhao, Y.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.244 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

Nuclear GTPSCS functions as a lactyl-CoA ligase to promote histone lactylation and glioma progression

Liu, R.L., Ren, X.L., Feng, H.X., Sheng, X.L., Li, L.T., Zhang, Y., Huang, H., Zhao, Y.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 77.85 kDa 
• Atom Count: 5,493 
• Modelled Residue Count: 704 
• Deposited Residue Count: 716 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial	A	321	Homo sapiens	Mutation(s): 0  Gene Names: SUCLG1 EC: 6.2.1.4 (PDB Primary Data), 6.2.1.5 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P53597 (Homo sapiens) Explore P53597  Go to UniProtKB:  P53597
PHAROS:  P53597 GTEx:  ENSG00000163541

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial	B	395	Homo sapiens	Mutation(s): 0  Gene Names: SUCLG2 EC: 6.2.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96I99 (Homo sapiens) Explore Q96I99  Go to UniProtKB:  Q96I99
PHAROS:  Q96I99 GTEx:  ENSG00000172340

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA (Subject of Investigation/LOI)	C [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
PO4 (Subject of Investigation/LOI)	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
2OP (Subject of Investigation/LOI)	E [auth B]	(2S)-2-HYDROXYPROPANOIC ACID C3 H6 O3 JVTAAEKCZFNVCJ-REOHCLBHSA-N
MG (Subject of Investigation/LOI)	F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.244 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.12	α = 90
b = 134.37	β = 92.13
c = 57.83	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Liu, R.L., Ren, X.L., Li, L.T., Zhang, Y., Huang, H., Zhao, Y.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM135504
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA251677
National Natural Science Foundation of China (NSFC)	China	81973164

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release