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- PDB-6rpx: Cytokine receptor-like factor 3 C-terminus residues 174-442: native -

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Basic information

Entry
Database: PDB / ID: 6rpx
TitleCytokine receptor-like factor 3 C-terminus residues 174-442: native
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 / SAD / Resolution: 1.61 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

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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
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.030, 40.380, 76.530
Angle α, β, γ (deg.)90.00, 99.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

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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
Details: C-terminal domain of murine CRLF3 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25 % PEG 3,350, 0.2 M ammonium acetate, 0.1 M Bis-Tris. Cryoprotected in perfluoropolyether oil.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.61→37.691 Å / Num. obs: 33326 / % possible obs: 96.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.063 / Net I/σ(I): 13.3
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2356 / CC1/2: 0.504 / Rrim(I) all: 1.053 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.61→37.691 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6
RfactorNum. reflection% reflection
Rfree0.2012 1613 4.84 %
Rwork0.1774 --
obs0.1785 33325 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.14 Å2
Refinement stepCycle: LAST / Resolution: 1.61→37.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 0 108 2113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092053
X-RAY DIFFRACTIONf_angle_d1.0662800
X-RAY DIFFRACTIONf_dihedral_angle_d16.0791201
X-RAY DIFFRACTIONf_chiral_restr0.159304
X-RAY DIFFRACTIONf_plane_restr0.007369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.65740.29741390.27782525X-RAY DIFFRACTION95
1.6574-1.71090.29161110.26312615X-RAY DIFFRACTION95
1.7109-1.77210.29811310.24612605X-RAY DIFFRACTION96
1.7721-1.8430.28591540.22552604X-RAY DIFFRACTION96
1.843-1.92690.21821370.1942610X-RAY DIFFRACTION96
1.9269-2.02850.20121410.17892634X-RAY DIFFRACTION96
2.0285-2.15550.23761280.17162622X-RAY DIFFRACTION97
2.1555-2.3220.20571240.17352661X-RAY DIFFRACTION97
2.322-2.55560.20631350.18152687X-RAY DIFFRACTION97
2.5556-2.92530.22751460.1912657X-RAY DIFFRACTION97
2.9253-3.6850.19431310.16962728X-RAY DIFFRACTION98
3.685-37.70090.14531360.14652764X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4942-0.29961.5170.9836-0.50362.3149-0.0059-0.1614-0.14720.08740.05040.0696-0.1044-0.0354-0.03180.155-0.00650.02770.1377-0.00970.183162.829230.528980.3534
22.8837-0.21940.34141.709-0.33924.5129-0.0234-0.3340.06470.1826-0.0697-0.0027-0.2843-0.26380.08990.1892-0.0229-0.00630.1656-0.00170.135590.021338.48100.167
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 181 through 273 )
2X-RAY DIFFRACTION2chain 'A' and (resid 274 through 442 )

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