8V0J | pdb_00008v0j

Structure of the complex between Human LIAS and H-protein in the presence of s-adenosyl-l-methionine

• PDB DOI: https://doi.org/10.2210/pdb8V0J/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia
• Mutation(s): No 


• Deposited: 2023-11-17 Released: 2025-08-20 
• Deposition Author(s): Esakova, O.A., Warui, D.M., Neti, S.S., Alumasa, J.N., Booker, S.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the mechanism of the human lipoyl synthase (LIAS) and its complex with the H-protein

Esakova, O.A., Warui, D.M., Neti, S.S., Alumasa, J.N., Booker, S.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A3B2C1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 185.11 kDa 
• Atom Count: 9,413 
• Modeled Residue Count: 1,165 
• Deposited Residue Count: 1,623 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoyl synthase, mitochondrial	A [auth C], B [auth A], C [auth B]	368	Homo sapiens	Mutation(s): 0  Gene Names: LIAS EC: 2.8.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for O43766 (Homo sapiens) Explore O43766  Go to UniProtKB:  O43766
PHAROS:  O43766 GTEx:  ENSG00000121897

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine cleavage system H protein, mitochondrial	D [auth F], E [auth D], F [auth E]	173	Homo sapiens	Mutation(s): 0  Gene Names: GCSH
UniProt & NIH Common Fund Data Resources
Find proteins for P23434 (Homo sapiens) Explore P23434  Go to UniProtKB:  P23434
PHAROS:  P23434 GTEx:  ENSG00000140905

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	I [auth C], L [auth A], O [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SF4 (Subject of Investigation/LOI)	G [auth C], J [auth A], M [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S	H [auth C], K [auth A], N [auth B]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
YVI (Subject of Investigation/LOI)	P [auth F], Q [auth D], S [auth E]	6-THIOOCTANOIC ACID C8 H16 O2 S LABZAONVGARYLS-ZETCQYMHSA-N
PO4	R [auth D], T [auth E]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.26	α = 90
b = 171.377	β = 90
c = 196.381	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Esakova, O.A., Warui, D.M., Neti, S.S., Alumasa, J.N., Booker, S.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-122595
National Science Foundation (NSF, United States)	United States	MCB1716686
Howard Hughes Medical Institute (HHMI)	United States	SJB

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release