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  OPMPDBTMMemProtMDmpstruc


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

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Experimental Data Snapshot

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

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 151.94 kDa 
• Atom Count: 9,855 
• Modelled Residue Count: 1,234 
• Deposited Residue Count: 1,336 
• Unique protein chains: 1

Macromolecules

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
Glycosylation
Glycosylation Sites: 14		Go to GlyGen: Q6T3U3-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C, D, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR (Subject of Investigation/LOI)	P [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG	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

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

Entry History 

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Huang, C.S., Yu, X., Min, X., Wang, Z.

Revision History  

• 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