8IAY

Crystal structure of canine distemper virus hemagglutinin

PDB DOI: https://doi.org/10.2210/pdb8IAY/pdb

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

Deposited: 2023-02-09 Released: 2024-02-07
Deposition Author(s): Fukuhara, H., Yumoto, K., Sako, M., Kajikawa, M., Ose, T., Hashiguchi, T., Kamishikiryo, J., Maita, N., Kuroki, K., Maenaka, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.03 Å
R-Value Free: 0.336
R-Value Work: 0.284
R-Value Observed: 0.286

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Glycan-shielded homodimer structure and dynamical features of the canine distemper virus hemagglutinin relevant for viral entry and efficient vaccination

Fukuhara, H., Yumoto, K., Sako, M., Kajikawa, M., Ose, T., Kawamura, M., Yoda, M., Chen, S., Ito, Y., Takeda, S., Mwaba, M.H., Wang, J., Hashiguchi, T., Kamishikiryo, J., Maita, N., Kitatsuji, C., Takeda, M., Kuroki, K., Maenaka, K.

(2024) Elife

DOI: https://doi.org/10.7554/eLife.88929.1

Macromolecule Content

Total Structure Weight: 105.15 kDa
Atom Count: 6,563
Modelled Residue Count: 841
Deposited Residue Count: 936
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 glycoprotein	A, B	468	Morbillivirus canis	Mutation(s): 0
UniProt
Find proteins for C0LEZ2 (Morbillivirus canis) Explore C0LEZ2 Go to UniProtKB: C0LEZ2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C0LEZ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.03 Å
R-Value Free: 0.336
R-Value Work: 0.284
R-Value Observed: 0.286
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.156	α = 90
b = 86.156	β = 90
c = 302.936	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-07

Deposition Author(s):

Kamishikiryo, J.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	15H02384
Japan Society for the Promotion of Science (JSPS)	Japan	22121007

Revision History (Full details and data files)

Version 1.0: 2024-02-07
Type: Initial release

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 R01GM133198.