8JZB | pdb_00008jzb

Langya Henipavirus attachment protein

PDB DOI: https://doi.org/10.2210/pdb8JZB/pdb
EM Map EMD-36741: EMDB EMDataResource

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

Deposited: 2023-07-05 Released: 2024-04-17
Deposition Author(s): Yan, R.H., Guo, Y.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.76 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8JZB

This is version 1.1 of the entry. See complete history.

Literature

A special homotetrameric architecture of langya virus glycoprotein

Yan, R.H., Guo, Y.Y.

To be published.

Macromolecule Content

Total Structure Weight: 278.31 kDa
Atom Count: 16,660
Modeled Residue Count: 2,120
Deposited Residue Count: 2,496
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
langya virus attachment protein G	A [auth B], B [auth D], C [auth F], D [auth H]	624	Henipavirus	Mutation(s): 0

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth D] SDF format, chain N [auth F] SDF format, chain O [auth H] SDF format, chain M [auth D] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth D] MOL2 format, chain N [auth F] MOL2 format, chain O [auth H] MOL2 format, chain M [auth D] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth D] mmCIF format, chain N [auth F] mmCIF format, chain O [auth H] mmCIF format, chain M [auth D]	J [auth B] K [auth B] L [auth D] M [auth D] N [auth F] J [auth B], K [auth B], L [auth D], M [auth D], N [auth F], O [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth F] Focus chain O [auth H] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth F] Focus chain O [auth H]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.76 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.