9JCW | pdb_00009jcw

Crystal structure of human MIGA1 LD targeting domain

• PDB DOI: https://doi.org/10.2210/pdb9JCW/pdb

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


• Deposited: 2024-08-30 Released: 2026-03-11 
• Deposition Author(s): Yang, K.L., Zhang, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.244 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: in silico

Literature

Structural basis for mitoguardin-1 mediated lipid transport at ER-mitochondrial membrane contact sites.

Yang, K.L., Zhang, L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 184.14 kDa 
• Atom Count: 12,482 
• Modeled Residue Count: 1,526 
• Deposited Residue Count: 1,548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitoguardin 1	A [auth C], B [auth F], C [auth A], D [auth E], E [auth B], F [auth D]	258	Homo sapiens	Mutation(s): 0  Gene Names: MIGA1, FAM73A
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NAN2 (Homo sapiens) Explore Q8NAN2  Go to UniProtKB:  Q8NAN2
PHAROS:  Q8NAN2 GTEx:  ENSG00000180488

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEF (Subject of Investigation/LOI)	G [auth C], H [auth A], I [auth E], J [auth B], K [auth D]	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C37 H74 N O8 P SLKDGVPOSSLUAI-PGUFJCEWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.244 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.645	α = 90
b = 157.782	β = 90
c = 163.907	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-11 
Deposition Author(s): Yang, K.L., Zhang, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-03-11
  Type: Initial release