9UB6 | pdb_00009ub6

Crystal structure of SFTSV Gn head with nanobody VHH261

• PDB DOI: https://doi.org/10.2210/pdb9UB6/pdb

• Classification: VIRAL PROTEIN
• Organism(s): SFTS virus HB29, Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM, Mammalian expression vector pCAGGS
• Mutation(s): No 


• Deposited: 2025-04-02 Released: 2025-10-22 
• Deposition Author(s): Wu, Y., Chang, Z., Wu, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of SFTSV Gn head with nanobody VHH261

Wu, Y., Chang, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.81 kDa 
• Atom Count: 3,350 
• Modeled Residue Count: 425 
• Deposited Residue Count: 433 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein N	A	318	SFTS virus HB29	Mutation(s): 0
UniProt
Find proteins for R4V2Q5 (Dabie bandavirus) Explore R4V2Q5  Go to UniProtKB:  R4V2Q5
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody VHH261	B	115	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	C	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.71	α = 90
b = 172.71	β = 90
c = 136.03	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Wu, Y., Chang, Z., Wu, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32090014

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release