5NFF

Crystal structure of GP1 receptor binding domain from Morogoro virus

• PDB DOI: https://doi.org/10.2210/pdb5NFF/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Morogoro mammarenavirus
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2017-03-14 Released: 2017-04-19 
• Deposition Author(s): Israeli, H., Cohen-Dvashi, H., Shulman, A., Shimon, A., Diskin, R.
• Funding Organization(s): ISF - ICORE

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.207 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 7 assigned by authors.

Biological Assembly 8  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 8 assigned by authors.

Biological Assembly 9  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 9 assigned by authors.

Biological Assembly 10  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 10 assigned by authors.

Biological Assembly 11  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 11 assigned by authors.

Biological Assembly 12  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 12 assigned by authors.

Biological Assembly 13  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 13 assigned by authors.

Biological Assembly 14  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 14 assigned by authors.

Biological Assembly 15  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 15 assigned by authors.

Biological Assembly 16  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 16 assigned by authors.

Macromolecule Content

• Total Structure Weight: 317.55 kDa 
• Atom Count: 20,391 
• Modelled Residue Count: 2,496 
• Deposited Residue Count: 2,736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein	A [auth B], B [auth A], C, D, E, F, G, H, I, J, K, L, M, N, O, P	171	Morogoro mammarenavirus	Mutation(s): 0  Gene Names: GPC
UniProt
Find proteins for C6ZK00 (Morogoro mammarenavirus) Explore C6ZK00  Go to UniProtKB:  C6ZK00

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Q, R	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	S	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G04854NQ GlyCosmos:  G04854NQ GlyGen:  G04854NQ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	T	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G75436UI GlyCosmos:  G75436UI GlyGen:  G75436UI

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	CA [auth D], DA [auth E], EA [auth E], HA [auth G], IA [auth G], JA [auth H], KA [auth I], MA [auth J], NA [auth K], OA [auth L], U [auth B], V [auth B], X [auth A], Y [auth A], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CIT	AA [auth C], BA [auth C], FA [auth E], GA [auth F], LA [auth I], W [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.207 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.769	α = 90
b = 127.769	β = 90
c = 251.704	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Israeli, H., Cohen-Dvashi, H., Shulman, A., Shimon, A., Diskin, R.

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Funding Organization	Location	Grant Number
ISF - ICORE	Israel	1775/12

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-05-10
  Changes: Database references
• Version 1.2: 2019-08-14
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary