3JD8 | pdb_00003jd8

cryo-EM structure of the full-length human NPC1 at 4.4 angstrom

• PDB DOI: https://doi.org/10.2210/pdb3JD8/pdb
• EM Map EMD-6640: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2016-05-01 Released: 2016-06-01 
• Deposition Author(s): Gong, X., Qian, H.W., Zhou, X.H., Wu, J.P., Zhou, Q., Yan, N.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.43 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

The structure of Niemann-Pick C1 protein

Gong, X., Qiang, H.W., Zhou, X.H., Wu, J.P., Zhou, Q., Yan, N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 147.7 kDa 
• Atom Count: 8,050 
• Modeled Residue Count: 1,133 
• Deposited Residue Count: 1,278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Niemann-Pick C1 protein	A	1,278	Homo sapiens	Mutation(s): 0  Gene Names: NPC1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O15118 (Homo sapiens) Explore O15118  Go to UniProtKB:  O15118
PHAROS:  O15118 GTEx:  ENSG00000141458
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: O15118-1

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, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N/A
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	4		N/A
Glycosylation Resources
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	R [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG	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], P [auth A], Q [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: 4.43 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	1.4

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-01 
Deposition Author(s): Gong, X., Qian, H.W., Zhou, X.H., Wu, J.P., Zhou, Q., Yan, N.

Revision History  

• Version 1.0: 2016-06-01
  Type: Initial release
  
• Version 1.1: 2016-06-08
  Changes: Other
• Version 1.2: 2018-06-13
  Changes: Advisory, Data collection, Database references, Source and taxonomy
• Version 1.3: 2019-10-09
  Changes: Data collection, Derived calculations, Other
• Version 1.4: 2019-12-18
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary