4DAG | pdb_00004dag

Structure of the Human Metapneumovirus Fusion Protein with Neutralizing Antibody Identifies a Pneumovirus Antigenic Site

PDB DOI: https://doi.org/10.2210/pdb4DAG/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): human metapneumovirus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2012-01-12 Released: 2012-02-29
Deposition Author(s): Jardetzky, T.S., Wen, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.39 Å
R-Value Free:
0.289 (Depositor), 0.281 (DCC)
R-Value Work:
0.260 (Depositor), 0.245 (DCC)
R-Value Observed:
0.261 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structure of the human metapneumovirus fusion protein with neutralizing antibody identifies a pneumovirus antigenic site.

Wen, X., Krause, J.C., Leser, G.P., Cox, R.G., Lamb, R.A., Williams, J.V., Crowe, J.E., Jardetzky, T.S.

(2012) Nat Struct Mol Biol 19: 461-463

PubMed: 22388735 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.2250
Primary Citation Related Structures:
4DAG

PubMed Abstract:
Human metapneumovirus and respiratory syncytial virus cause lower respiratory tract infections. The virus fusion (F) glycoprotein promotes membrane fusion by refolding from a metastable pre-fusion to a stable post-fusion conformation. F is also a major target of the neutralizing antibody response. Here we show that a potently neutralizing anti-human metapneumovirus antibody (DS7) binds a structurally invariant domain of F, revealing a new epitope that could be targeted in vaccine development.

Organizational Affiliation

Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA.

Macromolecule Content

Total Structure Weight: 92.41 kDa
Atom Count: 6,064
Modeled Residue Count: 816
Deposited Residue Count: 848
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A	415	human metapneumovirus	Mutation(s): 0
UniProt
Find proteins for G3KCK8 (human metapneumovirus) Explore G3KCK8 Go to UniProtKB: G3KCK8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G3KCK8
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutralizing Antibody DS7 heavy chain	B [auth H]	220	Homo sapiens	Mutation(s): 0 Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857 Go to UniProtKB: P01857
PHAROS: P01857 GTEx: ENSG00000211896
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01857
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutralizing Antibody DS7 light chain	C [auth L]	213	Homo sapiens	Mutation(s): 0 Gene Names: IGL@
UniProt
Find proteins for Q8N5F4 (Homo sapiens) Explore Q8N5F4 Go to UniProtKB: Q8N5F4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N5F4
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[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	D [auth B], E [auth C]	5		N-Glycosylation	Interactions Focus chain D [auth B] Focus chain E [auth C] Interactions & Density Focus chain D [auth B] Focus chain E [auth C]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.39 Å
R-Value Free: 0.289 (Depositor), 0.281 (DCC)
R-Value Work: 0.260 (Depositor), 0.245 (DCC)
R-Value Observed: 0.261 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 258.96	α = 90
b = 258.96	β = 90
c = 167.36	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SHARP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-02-29

Deposition Author(s):

Jardetzky, T.S.

Wen, X.

Revision History (Full details and data files)

Version 1.0: 2012-02-29
Type: Initial release
Version 1.1: 2012-04-04
Changes: Database references
Version 1.2: 2012-04-18
Changes: Database references
Version 1.3: 2017-08-02
Changes: Refinement description, Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary