7N4U | pdb_00007n4u

Structure of human NPC1L1

PDB DOI: https://doi.org/10.2210/pdb7N4U/pdb
EM Map EMD-24178: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2021-06-04 Released: 2021-09-01
Deposition Author(s): Li, X., Long, T.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.34 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structures of dimeric human NPC1L1 provide insight into mechanisms for cholesterol absorption.

Long, T., Liu, Y., Qin, Y., DeBose-Boyd, R.A., Li, X.

(2021) Sci Adv 7

PubMed: 34407950 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abh3997
Primary Citation Related Structures:
7N4U, 7N4V, 7N4X

PubMed Abstract:
Polytopic Niemann-Pick C1-like 1 (NPC1L1) plays a major role in intestinal absorption of biliary cholesterol, vitamin E (VE), and vitamin K (VK). The drug ezetimibe inhibits NPC1L1-mediated absorption of cholesterol, lowering of circulating levels of low-density lipoprotein cholesterol. Here, we report cryo-electron microscopy structures of human NPC1L1 (hNPC1L1) bound to either cholesterol or a lipid resembling VE. These findings, together with functional assays, reveal that the same intramolecular channel in hNPC1L1 mediates transport of VE and cholesterol. hNPC1L1 exists primarily as a homodimer; dimerization is mediated by aromatic residues within a region of transmembrane helix 2 that exhibits a horizonal orientation in the membrane. Mutation of tryptophan-347 lies in this region disrupts dimerization and the resultant monomeric NPC1L1 exhibits reduced efficiency of cholesterol uptake. These findings identify the oligomeric state of hNPC1L1 as a target for therapies that inhibit uptake of dietary cholesterol and reduce the incidence of cardiovascular disease.

Organizational Affiliation

Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Macromolecule Content

Total Structure Weight: 300.05 kDa
Atom Count: 15,396
Modeled Residue Count: 1,906
Deposited Residue Count: 2,664
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of NPC1-like intracellular cholesterol transporter 1	A, B	1,332	Homo sapiens	Mutation(s): 0 Gene Names: NPC1L1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHC9 (Homo sapiens) Explore Q9UHC9 Go to UniProtKB: Q9UHC9
PHAROS: Q9UHC9 GTEx: ENSG00000015520
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UHC9
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q9UHC9-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F, G C, D, E, F, G, H	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth A]	P [auth A], Q [auth B]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth B] Interactions & Density Focus chain P [auth A] Focus chain Q [auth B]
VIV (Subject of Investigation/LOI) Query on VIV Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain O [auth A] MOL2 format, chain X [auth B] MOL2 format, chain O [auth A] mmCIF format, chain X [auth B] mmCIF format, chain O [auth A]	O [auth A], X [auth B]	(2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL C₂₉ H₅₀ O₂ GVJHHUAWPYXKBD-IEOSBIPESA-N		Interactions Focus chain O [auth A] Focus chain X [auth B] Interactions & Density Focus chain O [auth A] Focus chain X [auth B]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A], N [auth A], V [auth B], W [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] R [auth B] I [auth A], J [auth A], K [auth A], L [auth A], R [auth B], S [auth B], T [auth B], U [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]