Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 93.73 kDa 
• Atom Count: 6717 
• Modelled Residue Count: 789 
• Deposited Residue Count: 802 
• Unique protein chains: 2

3KAS

Machupo virus GP1 bound to human transferrin receptor 1

• PDB DOI: 10.2210/pdb3KAS/pdb

• Classification: VIRAL PROTEIN/ENDOCYTOSIS
• Organism(s): Homo sapiens, Machupo mammarenavirus
• Expression System: Cricetulus griseus, Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2009-10-19 Released: 2010-03-09 
• Deposition Author(s): Abraham, J., Corbett, K.D., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.238 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Literature

Structural basis for receptor recognition by New World hemorrhagic fever arenaviruses.

Abraham, J., Corbett, K.D., Farzan, M., Choe, H., Harrison, S.C.

(2010) Nat Struct Mol Biol 17: 438-444

• PubMed: 20208545 
• DOI: 10.1038/nsmb.1772
• Primary Citation of Related Structures:  
  3KAS


• PubMed Abstract: 
  

New World hemorrhagic fever arenaviruses are rodent-borne agents that cause severe human disease. The GP1 subunit of the surface glycoprotein mediates cell attachment through transferrin receptor 1 (TfR1). We report the structure of Machupo virus (MACV) GP1 bound with human TfR1. Atomic details of the GP1-TfR1 interface clarify the importance of TfR1 residues implicated in New World arenavirus host specificity. Analysis of sequence variation among New World arenavirus GP1s and their host-species receptors, in light of the molecular structure, indicates determinants of viral zoonotic transmission. Infectivities of pseudoviruses in cells expressing mutated TfR1 confirm that contacts at the tip of the TfR1 apical domain determine the capacity of human TfR1 to mediate infection by particular New World arenaviruses. We propose that New World arenaviruses that are pathogenic to humans fortuitously acquired affinity for human TfR1 during adaptation to TfR1 of their natural hosts.

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Organizational Affiliation: 

Laboratory of Molecular Medicine, Harvard Medical School, Boston, Massachusetts, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transferrin receptor protein 1	A	640	Homo sapiens	Mutation(s): 1  Gene Names: TFRC
UniProt & NIH Common Fund Data Resources
Find proteins for P02786 (Homo sapiens) Explore P02786  Go to UniProtKB:  P02786
PHAROS:  P02786 GTEx:  ENSG00000072274

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein	B	162	Machupo mammarenavirus	Mutation(s): 0  Gene Names: GPC
UniProt
Find proteins for Q8AZ57 (Machupo virus) Explore Q8AZ57  Go to UniProtKB:  Q8AZ57

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G55220VL GlyCosmos:  G55220VL GlyGen:  G55220VL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], L [auth B], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	G [auth A], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	K [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.238 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.951	α = 90
b = 170.228	β = 90
c = 98.471	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-19 
• Released Date: 2010-03-09 
Deposition Author(s): Abraham, J., Corbett, K.D., Harrison, S.C.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary