6V3H | pdb_00006v3h

Structure of NPC1-like intracellular cholesterol transporter 1 (NPC1L1) in complex with an ezetimibe analog

PDB DOI: https://doi.org/10.2210/pdb6V3H/pdb
EM Map EMD-21037: EMDB EMDataResource

Classification: LIPID TRANSPORT/INHIBITOR
Organism(s): Rattus norvegicus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2019-11-25 Released: 2020-07-01
Deposition Author(s): Huang, C.S., Yu, X., Min, X., Wang, Z.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 6V3H

This is version 2.1 of the entry. See complete history.

Literature

Cryo-EM structures of NPC1L1 reveal mechanisms of cholesterol transport and ezetimibe inhibition

Huang, C.S., Yu, X., Fordstrom, P., Choi, K., Chung, B.C., Roh, S.H., Chiu, W., Zhou, M., Min, X., Wang, Z.

(2020) Sci Adv 6: eabb1989

DOI: https://doi.org/10.1126/sciadv.abb1989

Macromolecule Content

Total Structure Weight: 153.19 kDa
Atom Count: 9,926
Modeled Residue Count: 1,232
Deposited Residue Count: 1,336
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NPC1-like intracellular cholesterol transporter 1	A	1,336	Rattus norvegicus	Mutation(s): 0 Gene Names: Npc1l1 Membrane Entity: Yes
UniProt
Find proteins for Q6T3U3 (Rattus norvegicus) Explore Q6T3U3 Go to UniProtKB: Q6T3U3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6T3U3
Glycosylation
Glycosylation Sites: 12	Glycosylation Focus chain A	Go to GlyGen: Q6T3U3-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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	B, C, D, E, F B, C, D, E, F, G	2		N-Glycosylation	Interactions Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Interactions & Density Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QO1 (Subject of Investigation/LOI) Query on QO1 Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	4-[(2S,3R)-3-[(3S)-3-(4-fluorophenyl)-3-hydroxypropyl]-1-(4-{3-[(methylsulfonyl)amino]prop-1-yn-1-yl}phenyl)-4-oxoazetidin-2-yl]phenyl beta-D-glucopyranosiduronic acid C₃₄ H₃₅ F N₂ O₁₁ S DWURZHBEXYXPMW-WHTAKPIKSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	N [auth A], O [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [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] MOL2 format, chain I [auth A] MOL2 format, chain H [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] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
QO1	BindingDB: 6V3H	IC50: min: 4, max: 44 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-07-01
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-11-20
Changes: Data collection, Database references, Structure summary

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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.