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.

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

Biochemistry Department, University of Oxford, Oxford, OX1 3QU, England, United Kingdom. pietro.roversi@bioch.ox.ac.uk.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M1MR49
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

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	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G47477HI GlyCosmos: G47477HI GlyGen: G47477HI

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], H [auth A], I [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], J [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A]

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-05-28

Deposition Author(s):

Revision History (Full details and data files)

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