9JTZ | pdb_00009jtz

Crystal structure of Nir2 C-terminal domain in complex with phosphatidic acid

• PDB DOI: https://doi.org/10.2210/pdb9JTZ/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-07 Released: 2025-10-15 
• Deposition Author(s): Kim, D., Lee, C.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.258 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Structure of Nir2 reveals a phosphatidic acid sensing mechanism at the ER-PM contact sites

Kim, D., Lee, S., Jun, Y., Lee, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.58 kDa 
• Atom Count: 6,047 
• Modeled Residue Count: 754 
• Deposited Residue Count: 852 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-associated phosphatidylinositol transfer protein 1	A, B, C	284	Mus musculus	Mutation(s): 0  Gene Names: Pitpnm1, Dres9, Mpt1, Nir2, Pitpnm
UniProt & NIH Common Fund Data Resources
Find proteins for O35954 (Mus musculus) Explore O35954  Go to UniProtKB:  O35954
IMPC:  MGI:1197524

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
44E (Subject of Investigation/LOI)	D [auth A]	(2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate C15 H29 O8 P SFZZRGHNPILUOD-CYBMUJFWSA-N
DW3	E [auth A]	2-oxidanylethanal C2 H4 O2 WGCNASOHLSPBMP-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.258 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.941	α = 90
b = 108.764	β = 90
c = 120.535	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Kim, D., Lee, C.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021M3A9G8022417
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1A2C2009550

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release