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- PDB-6rpz: Cytokine receptor-like factor 3 C-terminus residues 174-442: nati... -

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Basic information

Entry
Database: PDB / ID: 6rpz
TitleCytokine receptor-like factor 3 C-terminus residues 174-442: native collected with 1.7A wavelength
ComponentsCytokine receptor-like factor 3
KeywordsBLOOD CLOTTING / platelet development / fibronectin domain / SPRY domain
Function / homology
Function and homology information


negative regulation of G1/S transition of mitotic cell cycle / positive regulation of receptor signaling pathway via JAK-STAT / negative regulation of cell growth / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Cytokine receptor-like factor 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.74 Å
AuthorsMifsud, R.W. / Yan, Y. / Bennett, C. / Read, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust209407/Z/17/Z United Kingdom
CitationJournal: Blood / Year: 2022
Title: CRLF3 plays a key role in the final stage of platelet genesis and is a potential therapeutic target for thrombocythemia.
Authors: Bennett, C. / Lawrence, M. / Guerrero, J.A. / Stritt, S. / Waller, A.K. / Yan, Y. / Mifsud, R.W. / Ballester-Beltran, J. / Baig, A. / Mueller, A. / Mayer, L. / Warland, J. / Penkett, C.J. / ...Authors: Bennett, C. / Lawrence, M. / Guerrero, J.A. / Stritt, S. / Waller, A.K. / Yan, Y. / Mifsud, R.W. / Ballester-Beltran, J. / Baig, A. / Mueller, A. / Mayer, L. / Warland, J. / Penkett, C.J. / Akbari, P. / Moreau, T. / Evans, A.L. / Mookerjee, S. / Hoffman, G.J. / Saeb-Parsy, K. / Adams, D.J. / Couzens, A.L. / Bender, M. / Erber, W.N. / Nieswandt, B. / Read, R.J. / Ghevaert, C.
History
DepositionMay 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytokine receptor-like factor 3


Theoretical massNumber of molelcules
Total (without water)30,0571
Polymers30,0571
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.800, 40.600, 76.660
Angle α, β, γ (deg.)90.000, 99.800, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Cytokine receptor-like factor 3 / Cytokine receptor-like molecule 9 / CREME-9 / Cytokine receptor-related factor 4


Mass: 30057.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crlf3, Creme9, Cytor4 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21-CodonPlusTM-(DE3)-RP / References: UniProt: Q9Z2L7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 12 % PEG 3,350, 0.1M sodium acetate . Cryoprotected in 25 % ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.7007 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7007 Å / Relative weight: 1
ReflectionResolution: 1.74→32.15 Å / Num. obs: 24310 / % possible obs: 88.4 % / Redundancy: 9.3 % / Biso Wilson estimate: 27.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.064 / Net I/σ(I): 20
Reflection shellResolution: 1.74→1.79 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6424 / CC1/2: 0.492 / Rrim(I) all: 0.913 / % possible all: 49.2

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6RPX

6rpx


Resolution: 1.74→32.15 Å / SU ML: 0.1819 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8743
RfactorNum. reflection% reflection
Rfree0.2054 1204 4.95 %
Rwork0.1734 --
obs0.175 24310 87.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.32 Å2
Refinement stepCycle: LAST / Resolution: 1.74→32.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 0 165 2168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01132053
X-RAY DIFFRACTIONf_angle_d1.08042792
X-RAY DIFFRACTIONf_chiral_restr0.0617301
X-RAY DIFFRACTIONf_plane_restr0.0086367
X-RAY DIFFRACTIONf_dihedral_angle_d3.49751201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.810.351780.34051484X-RAY DIFFRACTION51.52
1.81-1.890.3111150.27842162X-RAY DIFFRACTION74.7
1.89-1.990.26431260.21712561X-RAY DIFFRACTION88.39
1.99-2.120.22771510.18642645X-RAY DIFFRACTION91.28
2.12-2.280.19691440.17672741X-RAY DIFFRACTION94.37
2.28-2.510.23071490.17942773X-RAY DIFFRACTION96.12
2.51-2.870.2051330.1792857X-RAY DIFFRACTION97.08
2.87-3.620.21971620.16442888X-RAY DIFFRACTION98.26
3.62-32.150.16461460.15272995X-RAY DIFFRACTION99.24

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