7BWU

Restructuring hemagglutinin-neuraminidase (HN) of Newcastle disease virus produced from Oryza sativa

PDB DOI: https://doi.org/10.2210/pdb7BWU/pdb

Classification: VIRAL PROTEIN
Organism(s): avian paramyxovirus 1
Expression System: Oryza sativa
Mutation(s): Yes

Deposited: 2020-04-16 Released: 2021-04-21
Deposition Author(s): Ma, F.S., Zhang, G.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.195
R-Value Work: 0.167
R-Value Observed: 0.168

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Restructuring a dimer antigen in transgenic rice system for high efficient B cell activation: Development of a super effective vaccine against Newcastle Disease Virus

Ma, F.S., Zhang, E.Q., Xu, Q.R., Guo, J.Q., Zhang, G.P.

To be published.

Macromolecule Content

Total Structure Weight: 233.93 kDa
Atom Count: 14,942
Modelled Residue Count: 1,779
Deposited Residue Count: 2,144
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin-neuraminidase	A [auth B], B [auth D], C [auth A], D [auth C]	536	avian paramyxovirus 1	Mutation(s): 1 Gene Names: HN EC: 3.2.1.18
UniProt
Find proteins for I7EFR1 (avian paramyxovirus 1) Explore I7EFR1 Go to UniProtKB: I7EFR1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I7EFR1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth B] Focus chain B [auth D] Focus chain C [auth A] Focus chain D [auth C]
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain H [auth D] SDF format, chain K [auth A] SDF format, chain N [auth C] MOL2 format, chain E [auth B] MOL2 format, chain H [auth D] MOL2 format, chain K [auth A] MOL2 format, chain N [auth C] mmCIF format, chain E [auth B] mmCIF format, chain H [auth D] mmCIF format, chain K [auth A] mmCIF format, chain N [auth C]	E [auth B], H [auth D], K [auth A], N [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth B] Focus chain H [auth D] Focus chain K [auth A] Focus chain N [auth C] Interactions & Density Focus chain E [auth B] Focus chain H [auth D] Focus chain K [auth A] Focus chain N [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain I [auth D] SDF format, chain L [auth A] SDF format, chain O [auth C] MOL2 format, chain F [auth B] MOL2 format, chain I [auth D] MOL2 format, chain L [auth A] MOL2 format, chain O [auth C] mmCIF format, chain F [auth B] mmCIF format, chain I [auth D] mmCIF format, chain L [auth A] mmCIF format, chain O [auth C]	F [auth B], I [auth D], L [auth A], O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain I [auth D] Focus chain L [auth A] Focus chain O [auth C] Interactions & Density Focus chain F [auth B] Focus chain I [auth D] Focus chain L [auth A] Focus chain O [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth D] SDF format, chain M [auth A] SDF format, chain P [auth C] MOL2 format, chain G [auth B] MOL2 format, chain J [auth D] MOL2 format, chain M [auth A] MOL2 format, chain P [auth C] mmCIF format, chain G [auth B] mmCIF format, chain J [auth D] mmCIF format, chain M [auth A] mmCIF format, chain P [auth C]	G [auth B], J [auth D], M [auth A], P [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain J [auth D] Focus chain M [auth A] Focus chain P [auth C] Interactions & Density Focus chain G [auth B] Focus chain J [auth D] Focus chain M [auth A] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.195
R-Value Work: 0.167
R-Value Observed: 0.168
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.88	α = 90
b = 142.07	β = 90
c = 191.21	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data processing
xia2	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-04-21

Deposition Author(s):

Ma, F.S.

Zhang, G.P.

Revision History (Full details and data files)

Version 1.0: 2021-04-21
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-09
Changes: Structure summary