5YZD

Crystal structure of the prefusion form of measles virus fusion protein in complex with a fusion inhibitor peptide (FIP)

PDB DOI: https://doi.org/10.2210/pdb5YZD/pdb

Classification: VIRAL PROTEIN/INHIBITOR
Organism(s): Measles virus strain Ichinose-B95a, Measles morbillivirus, Respirovirus muris
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2017-12-14 Released: 2018-02-21
Deposition Author(s): Hashiguchi, T., Fukuda, Y., Matsuoka, R., Kuroda, D., Kubota, M., Shirogane, Y., Watanabe, S., Tsumoto, K., Kohda, D., Plemper, R.K., Yanagi, Y.
Funding Organization(s): MEXT, AMED, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.232
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 56.62 kDa
Atom Count: 3,525
Modelled Residue Count: 452
Deposited Residue Count: 517
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycoprotein F2	A	94	Measles virus strain Ichinose-B95a	Mutation(s): 0
UniProt
Find proteins for Q786F3 (Measles virus (strain Ichinose-B95a)) Explore Q786F3 Go to UniProtKB: Q786F3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q786F3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
glycoprotein F1,measles virus fusion protein	B [auth C]	419	Measles virus strain Ichinose-B95a, Measles morbillivirus This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for Q786F3 (Measles virus (strain Ichinose-B95a)) Explore Q786F3 Go to UniProtKB: Q786F3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q786F3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide CBZ-DPN-PHE-GLY	C [auth B]	4	Respirovirus muris	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	D	2		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.232
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.407	α = 90
b = 170.407	β = 90
c = 170.407	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-02-21

Deposition Author(s):

Funding Organization	Location	Grant Number
MEXT	Japan	17K19562
MEXT	Japan	24115005
AMED	Japan	17fm0208022h0001
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI071002
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HD079327

Revision History (Full details and data files)

Version 1.0: 2018-02-21
Type: Initial release
Version 1.1: 2018-03-07
Changes: Database references
Version 1.2: 2018-03-21
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2022-03-23
Changes: Author supporting evidence, Database references, Structure summary
Version 2.2: 2023-11-22
Changes: Data collection, Refinement description