9C38 | pdb_00009c38

Nir1 NirD domain dimer

PDB DOI: https://doi.org/10.2210/pdb9C38/pdb

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

Deposited: 2024-05-31 Released: 2025-08-27
Deposition Author(s): Rahn, T.A., Airola, M.V.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.203 (Depositor), 0.203 (DCC)
R-Value Work:
0.172 (Depositor), 0.172 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Nir1 NirD domain dimer

Rahn, T.A., Lee, W.R., Li, W.T., Airola, M.V., Liou, J.

To be published.

Macromolecule Content

Total Structure Weight: 42.27 kDa
Atom Count: 2,698
Modeled Residue Count: 314
Deposited Residue Count: 392
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-associated phosphatidylinositol transfer protein 3	A	392	Homo sapiens	Mutation(s): 0 Gene Names: PITPNM3, NIR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZ71 (Homo sapiens) Explore Q9BZ71 Go to UniProtKB: Q9BZ71
PHAROS: Q9BZ71 GTEx: ENSG00000091622
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BZ71
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.203 (Depositor), 0.203 (DCC)
R-Value Work: 0.172 (Depositor), 0.172 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.403	α = 90
b = 69.403	β = 90
c = 150.553	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
DIALS	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM128666

Revision History (Full details and data files)

Version 1.0: 2025-08-27
Type: Initial release

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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.