9NPT | pdb_00009npt

RAVV GP in complex with Nanosota-MB1

• PDB DOI: https://doi.org/10.2210/pdb9NPT/pdb
• EM Map EMD-49632: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Vicugna pacos, Ravn virus - Ravn, Kenya, 1987
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2025-03-11 Released: 2025-12-31 
• Deposition Author(s): Ye, G., Bu, F., Liu, B., Li, F.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.98 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of receptor recognition and nanobody neutralization of marburgvirus

Ye, G., Bu, F., Liu, B., Li, F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 227.58 kDa 
• Atom Count: 9,372 
• Modeled Residue Count: 1,152 
• Deposited Residue Count: 1,989 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanosota-MB1	A [auth G], H, I	158	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein GP1	B [auth A], D [auth C], F [auth E]	258	Ravn virus - Ravn, Kenya, 1987	Mutation(s): 0  Gene Names: GP
UniProt
Find proteins for Q1PDC7 (Lake Victoria marburgvirus (strain Ravn-87)) Explore Q1PDC7  Go to UniProtKB:  Q1PDC7
Glycosylation
Glycosylation Sites: 1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein GP2	C [auth B], E [auth D], G [auth F]	247	Ravn virus - Ravn, Kenya, 1987	Mutation(s): 0  Gene Names: GP
UniProt
Find proteins for Q1PDC7 (Lake Victoria marburgvirus (strain Ravn-87)) Explore Q1PDC7  Go to UniProtKB:  Q1PDC7
Glycosylation
Glycosylation Sites: 1

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	J [auth R], K [auth S], L [auth T]	3		N-Glycosylation

Entity ID: 5
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	M [auth X], N [auth Y], O [auth Z]	5		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.98 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Ye, G., Bu, F., Liu, B., Li, F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI089728
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI171954

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release