4BOE | pdb_00004boe

Japanin from Rhipicephalus appendiculatus bound to cholesterol: Tetragonal crystal form

• PDB DOI: https://doi.org/10.2210/pdb4BOE/pdb

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


• Deposited: 2013-05-19 Released: 2014-05-28 
• 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: 2.24 Å
• R-Value Free: 
  0.198 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

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 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].
Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7RH, England, United Kingdom. [e-mail].
Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, England, United Kingdom.
Department of Zoology, University of Oxford, Oxford, OX1 3PS, England, United Kingdom.
Akari Therapeutics, Plc, 75/76 Wimpole Street, London, W1G 9RT, England, United Kingdom.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom.
Nuffield Department of Surgical Sciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, England, United Kingdom.
Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, 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)

Macromolecule Content 

• Total Structure Weight: 20.66 kDa 
• Atom Count: 1,498 
• Modeled Residue Count: 154 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
JAPANIN	A	160	Rhipicephalus appendiculatus	Mutation(s): 0
UniProt
Find proteins for M1MR49 (Rhipicephalus appendiculatus) Explore M1MR49  Go to UniProtKB:  M1MR49
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	B	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G47477HI GlyCosmos: G47477HI GlyGen: G47477HI

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	C [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG	K [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MPD	D [auth A], E [auth A], H [auth A], I [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
IMD	F [auth A], G [auth A], J [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.198 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.33	α = 90
b = 84.33	β = 90
c = 90.52	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: 2014-05-28 
Deposition Author(s): Roversi, P., Johnson, S., Preston, S., Austyn, J.M., Nuttall, P., Lea, S.M.

Revision History  

• Version 1.0: 2014-05-28
  Type: Initial release
  
• 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
• Version 3.2: 2024-11-06
  Changes: Structure summary