5JNX

The 6.6 A cryo-EM structure of the full-length human NPC1 in complex with the cleaved glycoprotein of Ebola virus

PDB DOI: https://doi.org/10.2210/pdb5JNX/pdb
EM Map EMD-8169: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Ebola virus - Zaire (1995)
Expression System: Homo sapiens, Insect cell expression vector pTIE1
Mutation(s): Yes
Membrane Protein: Yes PDBTMmpstruc

Deposited: 2016-05-01 Released: 2016-06-15
Deposition Author(s): Gong, X., Qian, H.W., Zhou, X.H., Wu, J.P., Wan, T., Shi, Y., Gao, F., Zhou, Q., Yan, N.
Funding Organization(s): Ministry of Science and Technology of China, National Natural Science Foundation of China, President Foundation of Chinese Academy of Sciences and Strategic Priority Research Program of the Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.56 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 244.8 kDa
Atom Count: 13,749
Modelled Residue Count: 1,868
Deposited Residue Count: 2,142
Unique protein chains: 3

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	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15118
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein	B [auth C], D [auth E], F [auth G]	158	Ebola virus - Zaire (1995)	Mutation(s): 1 Gene Names: GP Membrane Entity: Yes
UniProt
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95)) Explore P87666 Go to UniProtKB: P87666
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P87666
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein	C [auth D], E [auth F], G [auth H]	130	Ebola virus - Zaire (1995)	Mutation(s): 0 Gene Names: GP Membrane Entity: Yes
UniProt
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95)) Explore P87666 Go to UniProtKB: P87666
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P87666
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth B], I, K, M, N, H [auth B], I, K, M, N, O, P	2		N-Glycosylation	Interactions Focus chain H [auth B] Focus chain I Focus chain K Focus chain M Focus chain N Focus chain O Focus chain P Interactions & Density Focus chain H [auth B] Focus chain I Focus chain K Focus chain M Focus chain N Focus chain O Focus chain P
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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

Entity ID: 6
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	L	4		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A]	Q [auth A] R [auth A] S [auth A] T [auth A] U [auth A] Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 6.56 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	1.4

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-06-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology of China	China	2015CB9101012014, ZX09507003006
National Natural Science Foundation of China	China	project 31321062 and 81590761
President Foundation of Chinese Academy of Sciences and Strategic Priority Research Program of the Chinese Academy of Sciences	China	XDB08020100

Revision History (Full details and data files)

Version 1.0: 2016-06-15
Type: Initial release
Version 1.1: 2017-12-13
Changes: Data processing, Database references
Version 1.2: 2019-10-23
Changes: Advisory, Data collection, Database references, Derived calculations
Version 1.3: 2019-12-04
Changes: Data collection
Version 1.4: 2019-12-11
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: 2020-08-05
Changes: Derived calculations, Source and taxonomy, Structure summary