5XBM | pdb_00005xbm

Structure of SCARB2-JL2 complex

• PDB DOI: https://doi.org/10.2210/pdb5XBM/pdb

• Classification: IMMUNE SYSTEM/PROTEIN BINDING
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): No 


• Deposited: 2017-03-20 Released: 2018-06-27 
• Deposition Author(s): Zhang, X., Yang, P., Wang, N., Zhang, J., Li, J., Guo, H., Yin, X., Rao, Z., Wang, X., Zhang, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.293 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

The binding of a monoclonal antibody to the apical region of SCARB2 blocks EV71 infection.

Zhang, X., Yang, P., Wang, N., Zhang, J., Li, J., Guo, H., Yin, X., Rao, Z., Wang, X., Zhang, L.

(2017) Protein Cell 8: 590-600

• PubMed: 28447294 
• DOI: https://doi.org/10.1007/s13238-017-0405-7
• Primary Citation Related Structures: 
  5XBM


• PubMed Abstract: 
  

  Entero virus 71 (EV71) causes hand, foot, and mouth disease (HFMD) and occasionally leads to severe neurological complications and even death. Scavenger receptor class B member 2 (SCARB2) is a functional receptor for EV71, that mediates viral attachment, internalization, and uncoating. However, the exact binding site of EV71 on SCARB2 is unknown. In this study, we generated a monoclonal antibody (mAb) that binds to human but not mouse SCARB2. It is named JL2, and it can effectively inhibit EV71 infection of target cells. Using a set of chimeras of human and mouse SCARB2, we identified that the region containing residues 77-113 of human SCARB2 contributes significantly to JL2 binding. The structure of the SCARB2-JL2 complex revealed that JL2 binds to the apical region of SCARB2 involving α-helices 2, 5, and 14. Our results provide new insights into the potential binding sites for EV71 on SCARB2 and the molecular mechanism of EV71 entry.

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Organizational Affiliation: 
• Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 193.47 kDa 
• Atom Count: 13,343 
• Modeled Residue Count: 1,646 
• Deposited Residue Count: 1,658 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of JL2	A, D	213	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of JL2	B, E	222	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysosome membrane protein 2	C, F	394	Homo sapiens	Mutation(s): 0  Gene Names: SCARB2, CD36L2, LIMP2, LIMPII
UniProt & NIH Common Fund Data Resources
Find proteins for Q14108 (Homo sapiens) Explore Q14108  Go to UniProtKB:  Q14108
PHAROS:  Q14108 GTEx:  ENSG00000138760
Glycosylation
Glycosylation Sites: 7		Go to GlyGen: Q14108-1

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	G, M, R	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, I, J, N, O, P	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	K, L, Q	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	S [auth C], T [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.293 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.863	α = 90
b = 75.646	β = 100.11
c = 164.305	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-27 
Deposition Author(s): Zhang, X., Yang, P., Wang, N., Zhang, J., Li, J., Guo, H., Yin, X., Rao, Z., Wang, X., Zhang, L.

Revision History  

• Version 1.0: 2018-06-27
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary