5HNS

Structure of glycosylated NPC1 luminal domain C

PDB DOI: https://doi.org/10.2210/pdb5HNS/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2016-01-18 Released: 2016-02-10
Deposition Author(s): Zhao, Y., Ren, J., Harlos, K., Stuart, D.I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.238
R-Value Work: 0.224
R-Value Observed: 0.225

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Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Structure of glycosylated NPC1 luminal domain C reveals insights into NPC2 and Ebola virus interactions.

Zhao, Y., Ren, J., Harlos, K., Stuart, D.I.

(2016) FEBS Lett 590: 605-612

PubMed: 26846330 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/1873-3468.12089
Primary Citation of Related Structures:
5HNS

PubMed Abstract:
Niemann-pick type C1 (NPC1) is an endo/lysosomal membrane protein involved in intracellular cholesterol trafficking, and its luminal domain C is an essential endosomal receptor for Ebola and Marburg viruses. We have determined the crystal structure of glycosylated NPC1 luminal domain C and find all seven possible sites are glycosylated. Mapping the disease mutations onto the glycosylated structure reveals a potential binding face for NPC2. Knowledge-based docking of NPC1 onto Ebola viral glycoprotein and sequence analysis of filovirus susceptible and refractory species reveals four critical residues, H418, Q421, F502 and F504, some or all of which are likely responsible for the species-specific susceptibility to the virus infection.

Organizational Affiliation

Division of Structural Biology, University of Oxford, Headington, Oxford, UK.

Macromolecule Content

Total Structure Weight: 60.73 kDa
Atom Count: 3,943
Modelled Residue Count: 431
Deposited Residue Count: 488
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Niemann-Pick C1 protein	A, B	244	Homo sapiens	Mutation(s): 0 Gene Names: NPC1
UniProt & NIH Common Fund Data Resources
Find proteins for O15118 (Homo sapiens) Explore O15118 Go to UniProtKB: O15118
PHAROS: O15118 GTEx: ENSG00000141458
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15118
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Entity ID: 3
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	D	4		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[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	I	5		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 5
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	J	3		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	L [auth A], M [auth A], N [auth B], O [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.238
R-Value Work: 0.224
R-Value Observed: 0.225
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.89	α = 90
b = 115.91	β = 90
c = 147.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Coot	model building
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-02-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-02-10
Type: Initial release
Version 1.1: 2016-03-02
Changes: Database references
Version 1.2: 2016-03-16
Changes: Database references
Version 1.3: 2019-10-16
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary