4BQU

Japanin from Rhipicephalus appendiculatus bound to cholesterol: Orthorhombic crystal form

• PDB DOI: https://doi.org/10.2210/pdb4BQU/pdb

• Classification: CHOLESTEROL-BINDING PROTEIN
• Organism(s): Rhipicephalus appendiculatus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-06-02 Released: 2014-06-18 
• Deposition Author(s): Roversi, P., Johnson, S., Preston, S., Austyn, J.M., Nuttall, P., Lea, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.253 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Literature

Structural basis of cholesterol binding by a novel clade of dendritic cell modulators from ticks.

Roversi, P., Johnson, S., Preston, S.G., Nunn, M.A., Paesen, G.C., Austyn, J.M., Nuttall, P.A., Lea, S.M.

(2017) Sci Rep 7: 16057-16057

• PubMed: 29167574 
• DOI: https://doi.org/10.1038/s41598-017-16413-2
• Primary Citation of Related Structures:  
  4BOE, 4BQU


• PubMed Abstract: 
  

  Two crystal structures of Japanin, an 18 kDa immune-modulatory lipocalin from the Brown Ear Tick (Rhipicephalus appendiculatus), have been determined at 2.2 and 2.4 Å resolution. In both crystal forms the protein is in complex with cholesterol, which sits in a closed pocket at the centre of the lipocalin barrel. Both crystal forms are dimers, which are also observed in solution. Molecular modelling suggests that previously-described members of a tick protein family bearing high sequence homology to Japanin are also likely to bind cholesterol or cholesterol derivatives.

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Organizational Affiliation: 

Biochemistry Department, University of Oxford, Oxford, OX1 3QU, England, United Kingdom. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.28 kDa 
• Atom Count: 2,768 
• Modelled Residue Count: 301 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
JAPANIN	A, B	160	Rhipicephalus appendiculatus	Mutation(s): 0
UniProt
Find proteins for M1MR49 (Rhipicephalus appendiculatus) Explore M1MR49  Go to UniProtKB:  M1MR49

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47477HI GlyCosmos:  G47477HI GlyGen:  G47477HI

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	F [auth A], M [auth B]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG	J [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	K [auth A], L [auth A], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.253 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.18	α = 90
b = 133.6	β = 90
c = 71.28	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-18 
Deposition Author(s): Roversi, P., Johnson, S., Preston, S., Austyn, J.M., Nuttall, P., Lea, S.M.

Revision History  

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2014-06-25
  Changes: Atomic model, Derived calculations, Non-polymer description, Other
• Version 2.0: 2017-12-13
  Changes: Atomic model, Database references
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 3.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary