4TW0

Crystal Structure of SCARB2 in Acidic Condition (pH4.8)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 

wwPDB Validation 3D Report Full Report



Literature

Molecular mechanism of SCARB2-mediated attachment and uncoating of EV71

Dang, M.Wang, X.Wang, Q.Wang, Y.Lin, J.Sun, Y.Li, X.Zhang, L.Lou, Z.Wang, J.Rao, Z.

(2014) Protein Cell 5: 692-703

  • DOI: 10.1007/s13238-014-0087-3
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Unlike the well-established picture for the entry of enveloped viruses, the mechanism of cellular entry of non-enveloped eukaryotic viruses remains largely mysterious. Picornaviruses are representative models for such viruses, and initiate this entry ...

    Unlike the well-established picture for the entry of enveloped viruses, the mechanism of cellular entry of non-enveloped eukaryotic viruses remains largely mysterious. Picornaviruses are representative models for such viruses, and initiate this entry process by their functional receptors. Here we present the structural and functional studies of SCARB2, a functional receptor of the important human enterovirus 71 (EV71). SCARB2 is responsible for attachment as well as uncoating of EV71. Differences in the structures of SCARB2 under neutral and acidic conditions reveal that SCARB2 undergoes a pivotal pH-dependent conformational change which opens a lipid-transfer tunnel to mediate the expulsion of a hydrophobic pocket factor from the virion, a pre-requisite for uncoating. We have also identified the key residues essential for attachment to SCARB2, identifying the canyon region of EV71 as mediating the receptor interaction. Together these results provide a clear understanding of cellular attachment and initiation of uncoating for enteroviruses.


    Organizational Affiliation

    National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Scavenger receptor class B member 2A, B, C, D393Homo sapiensMutation(s): 0 
Gene Names: SCARB2CD36L2LIMP2LIMPII
Find proteins for Q14108 (Homo sapiens)
Explore Q14108 
Go to UniProtKB:  Q14108
NIH Common Fund Data Resources
PHAROS  Q14108
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
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
E, J, O, T
4 N-Glycosylation
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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
F, K, P, U
5 N-Glycosylation
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, L, M, Q, R, V, W
2 N-Glycosylation
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, N, S, X
3 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, C, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.99α = 90
b = 99.636β = 90.02
c = 125.853γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Institute of Biophysics, Chinese Academy of ScienceChina2014CB542800

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Derived calculations
  • Version 1.2: 2020-01-29
    Changes: Data collection, Derived calculations, Refinement description, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary