37LU | pdb_000037lu

NPC1-NPC2 complex with bis-sterol molecule JM046, pH 5.5

PDB DOI: https://doi.org/10.2210/pdb37LU/pdb
EM Map EMD-78289: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2026-07-25 Released: 2026-09-30
Deposition Author(s): Wu, X., Yan, N.
Funding Organization(s): Other private, National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 37LU

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

Literature

Conformation switch of NPC1 epitomizes a lumen-to-membrane alternating access for nonpolar substrates

Wu, X., Dehghani-Ghahnaviyeh, S., Rasouli, A., Malona, J., Antalek, M., Jones, L.H., Fan, X., Peng, A., Tajkhorshid, E., Qian, H., Yan, N.

To be published.

Macromolecule Content

Total Structure Weight: 164.98 kDa
Atom Count: 10,768
Modeled Residue Count: 1,325
Deposited Residue Count: 1,429
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NPC intracellular cholesterol transporter 1	A	1,278	Homo sapiens	Mutation(s): 0 Gene Names: NPC1
UniProt & NIH Common Fund Data Resources
Find proteins for O15118 (Homo sapiens) Explore O15118 Go to UniProtKB: O15118
PHAROS: O15118 GTEx: ENSG00000141458
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15118
Glycosylation
Glycosylation Sites: 15	Glycosylation Focus chain A	Go to GlyGen: O15118-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NPC intracellular cholesterol transporter 2	B [auth D]	151	Homo sapiens	Mutation(s): 0 Gene Names: NPC2, HE1
UniProt & NIH Common Fund Data Resources
Find proteins for P61916 (Homo sapiens) Explore P61916 Go to UniProtKB: P61916
PHAROS: P61916 GTEx: ENSG00000119655
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61916
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth D]	Go to GlyGen: P61916-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B], E, F [auth G], G [auth H], H [auth I], D [auth B], E, F [auth G], G [auth H], H [auth I], I [auth F]	2		N-Glycosylation	Interactions Focus chain D [auth B] Focus chain E Focus chain F [auth G] Focus chain G [auth H] Focus chain H [auth I] Focus chain I [auth F] Interactions & Density Focus chain D [auth B] Focus chain E Focus chain F [auth G] Focus chain G [auth H] Focus chain H [auth I] Focus chain I [auth F]

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain S [auth A] MOL2 format, chain U [auth D] MOL2 format, chain S [auth A] mmCIF format, chain U [auth D] mmCIF format, chain S [auth A]	S [auth A], U [auth D]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain S [auth A] Focus chain U [auth D] Interactions & Density Focus chain S [auth A] Focus chain U [auth D]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain T [auth D] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain T [auth D] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] L [auth A] M [auth A] N [auth A] J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], T [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	United States	--
National Science Foundation (NSF, United States)	United States	DMR-2011750

Revision History (Full details and data files)

Version 1.0: 2026-09-30
Type: Initial release