6OUS

Structure of fusion glycoprotein from human respiratory syncytial virus

• PDB DOI: https://doi.org/10.2210/pdb6OUS/pdb

• Classification: VIRAL PROTEIN/Immune system
• Organism(s): Human respiratory syncytial virus A2, Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2019-05-05 Released: 2019-10-30 
• Deposition Author(s): Su, H.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.275 
• R-Value Work: 0.245 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 623.85 kDa 
• Atom Count: 41,597 
• Modelled Residue Count: 5,451 
• Deposited Residue Count: 5,658 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F2	A, C, E, G, I, K	84	Human respiratory syncytial virus A2	Mutation(s): 0
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420  Go to UniProtKB:  P03420

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F1 fused with Fibritin trimerization domain	B, D, F, H, J, L	414	Human respiratory syncytial virus A2, Human immunodeficiency virus 1 This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for M1E1E4 (Human immunodeficiency virus 1) Explore M1E1E4  Go to UniProtKB:  M1E1E4
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420  Go to UniProtKB:  P03420
UniProt Groups	M1E1E4P03420

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RB1 Fab Heavy Chain	M, O, Q, S, U, W	231	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RB1 Fab Light chain	N, P, R, T, V, X	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	AA [auth a], BA [auth b], CA [auth c], DA [auth d], Y, Z	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	EA [auth B], FA [auth F], GA [auth J], HA [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, C, E, G, I, K	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.275 
• R-Value Work: 0.245 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.153	α = 87.24
b = 126.595	β = 79.15
c = 148.165	γ = 86.29

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Su, H.P.

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 2.0: 2019-12-25
  Changes: Database references, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary