9L2K | pdb_00009l2k

The crystal structure of SFTSV Gn and SD22 antibody complex

• PDB DOI: https://doi.org/10.2210/pdb9L2K/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe fever with thrombocytopenia syndrome virus, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-12-17 Released: 2025-06-18 
• Deposition Author(s): Shi, W.F., Quan, C.S., Qi, J.X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 
  0.312 (Depositor), 0.323 (DCC) 
• R-Value Work: 
  0.304 (Depositor), 0.309 (DCC) 
• R-Value Observed: 
  0.306 (Depositor) 

Starting Model: experimental

Literature

Molecular mechanism of potently neutralizing human monoclonal antibodies against 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 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 86.24 kDa 
• Atom Count: 4,262 
• Modeled Residue Count: 550 
• Deposited Residue Count: 781 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelopment polyprotein	A	344	Severe fever with thrombocytopenia syndrome virus	Mutation(s): 0
UniProt
Find proteins for A0A1S6K8S9 (Dabie bandavirus) Explore A0A1S6K8S9  Go to UniProtKB:  A0A1S6K8S9
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SD22 heavy chain	B [auth H]	223	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SD22 light chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
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	D [auth B]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free:  0.312 (Depositor), 0.323 (DCC) 
• R-Value Work:  0.304 (Depositor), 0.309 (DCC) 
• R-Value Observed: 0.306 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.471	α = 90
b = 70.346	β = 90.177
c = 177.469	γ = 90

Software Package:

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

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 Natural Science Foundation of China (NSFC)	China	32325003

Revision History  

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