6V3F | pdb_00006v3f

Structure of NPC1-like intracellular cholesterol transporter 1 (NPC1L1)

PDB DOI: https://doi.org/10.2210/pdb6V3F/pdb
EM Map EMD-21035: EMDB EMDataResource

Classification: LIPID TRANSPORT
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: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 6V3F

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: 151.94 kDa
Atom Count: 9,855
Modeled Residue Count: 1,234
Deposited Residue Count: 1,336
Unique protein chains: 1

Macromolecules

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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: 14	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	2		N-Glycosylation	Interactions Focus chain B Focus chain C Focus chain D Focus chain E Interactions & Density Focus chain B Focus chain C Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR (Subject of Investigation/LOI) Query on CLR 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]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File 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] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [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] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [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] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] 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] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] 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] Focus chain N [auth A] Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3

Structure Validation

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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: 2024-10-23
Changes: Data collection, Database references, Structure summary