6H3T

Schmallenberg Virus Glycoprotein Gc Head Domain in Complex with scFv 1C11

PDB DOI: https://doi.org/10.2210/pdb6H3T/pdb

Classification: VIRAL PROTEIN
Organism(s): Mus musculus, Bovine Schmallenberg virus BH80/Germany/2011
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2018-07-19 Released: 2019-02-27
Deposition Author(s): Hellert, J., Aebischer, A., Wernike, K., Haouz, A., Brocchi, E., Reiche, S., Guardado-Calvo, P., Beer, M., Rey, F.A.
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free: 0.262
R-Value Work: 0.213
R-Value Observed: 0.218

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 116.54 kDa
Atom Count: 7,524
Modelled Residue Count: 924
Deposited Residue Count: 1,022
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv 1C11 VH	A [auth H], D [auth I]	140	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv 1C11 VL	B [auth L], E [auth M]	123	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelopment polyprotein	C [auth A], F [auth B]	248	Bovine Schmallenberg virus BH80/Germany/2011	Mutation(s): 0 Gene Names: GP
UniProt
Find proteins for H2AM12 (Bovine Schmallenberg virus (isolate Bovine/BH80/Germany/2011)) Explore H2AM12 Go to UniProtKB: H2AM12
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	H2AM12
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C], I [auth E]	7		N-Glycosylation	Interactions Focus chain G [auth C] Focus chain I [auth E] Interactions & Density Focus chain G [auth C] Focus chain I [auth E]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth D], J [auth F]	3		N-Glycosylation	Interactions Focus chain H [auth D] Focus chain J [auth F] Interactions & Density Focus chain H [auth D] Focus chain J [auth F]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free: 0.262
R-Value Work: 0.213
R-Value Observed: 0.218
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 262.789	α = 90
b = 44.397	β = 91.81
c = 93.593	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
STARANISO	data scaling
PHENIX	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2019-02-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Innovative Medicines Initiative		115760

Revision History (Full details and data files)

Version 1.0: 2019-02-27
Type: Initial release
Version 1.1: 2019-03-06
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary