9JQV | pdb_00009jqv

The crystal structure of SFTSV Gn and SD12 antibody complex

• PDB DOI: https://doi.org/10.2210/pdb9JQV/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): SFTS virus HB29, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-09-28 Released: 2025-06-18 
• Deposition Author(s): Shi, W.F., Quan, C.S., Qi, J.X.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.255 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Models: experimental

Literature

High affinity human-derived antibodies effectively rescue moribund mice with lethal severe fever with thrombocytopenia virus infection

Quan, C.S., Qi, J.X., Shi, W.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 167.98 kDa 
• Atom Count: 11,809 
• Modeled Residue Count: 1,483 
• Deposited Residue Count: 1,524 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelopment polyprotein	A, D [auth B]	325	SFTS virus HB29	Mutation(s): 0
UniProt
Find proteins for A0A0B5A886 (SFTS phlebovirus (isolate SFTSV/Human/China/HB29/2010)) Explore A0A0B5A886  Go to UniProtKB:  A0A0B5A886
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SD12 heavy chain	B [auth H], E [auth C]	223	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SD12 light chain	C [auth L], F [auth D]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

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	G [auth E]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth F], I [auth G]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.255 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.064	α = 90
b = 82.342	β = 104.31
c = 125.293	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Shi, W.F., Quan, C.S., Qi, J.X.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	32325003

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release