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- PDB-3vbc: Crystal Structure of iL-17 receptor B SEFIR domain -

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Basic information

Entry
Database: PDB / ID: 3vbc
TitleCrystal Structure of iL-17 receptor B SEFIR domain
ComponentsInterleukin-17 receptor B
KeywordsIMMUNE SYSTEM / interleukin 17 / cytokine / receptor / SEFIR / autoimmune / inflammatory
Function / homology
Function and homology information


interleukin-17 receptor activity / positive regulation of interleukin-5 production / cytokine receptor activity / positive regulation of interleukin-13 production / plasma membrane => GO:0005886 / positive regulation of inflammatory response / cell surface / extracellular region / cytoplasm
Similarity search - Function
Rossmann fold - #11530 / Interleukin-17 receptor, fibronectin-III-like domain 1 / Interleukin-17 receptor A/B, FnIII-like domain 1 superfamily / Interleukin-17 receptor A/B, FnIII-like domain 2 superfamily / Interleukin-17 receptor, fibronectin-III-like domain 1 / Interleukin-17 receptor-like / SEFIR domain / SEFIR domain / SEFIR domain profile. / Rossmann fold ...Rossmann fold - #11530 / Interleukin-17 receptor, fibronectin-III-like domain 1 / Interleukin-17 receptor A/B, FnIII-like domain 1 superfamily / Interleukin-17 receptor A/B, FnIII-like domain 2 superfamily / Interleukin-17 receptor, fibronectin-III-like domain 1 / Interleukin-17 receptor-like / SEFIR domain / SEFIR domain / SEFIR domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Interleukin-17 receptor B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhang, B. / Liu, C. / Li, X. / Deng, J.
CitationJournal: J.Immunol. / Year: 2013
Title: Crystal Structure of IL-17 Receptor B SEFIR Domain.
Authors: Zhang, B. / Liu, C. / Qian, W. / Han, Y. / Li, X. / Deng, J.
History
DepositionJan 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-17 receptor B


Theoretical massNumber of molelcules
Total (without water)18,1061
Polymers18,1061
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.971, 65.797, 89.642
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-511-

HOH

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Components

#1: Protein Interleukin-17 receptor B / IL-17 receptor B / IL-17RB / IL-17 receptor homolog 1 / IL-17ER / IL-17Rh1 / IL17Rh1 / Interleukin- ...IL-17 receptor B / IL-17RB / IL-17 receptor homolog 1 / IL-17ER / IL-17Rh1 / IL17Rh1 / Interleukin-17B receptor / IL-17B receptor


Mass: 18105.744 Da / Num. of mol.: 1 / Mutation: K364A, K367A, K368A, K369A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il17rb, Evi27, Il17br / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JIP3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 45.05 %
Crystal growTemperature: 293 K / pH: 6
Details: 0.2 M NaAc, pH 5.0, 1.6 M Ammonium citrate dibasic, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 15902 / % possible obs: 99.4 % / Observed criterion σ(I): 2.3 / Redundancy: 6.6 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 19.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→32.9 Å / SU ML: 0.23 / Isotropic thermal model: isotropic / σ(F): 1.34 / Phase error: 25.4 / Stereochemistry target values: ML / Details: ISOTROPIC PLUS TLS REFINEMENT
RfactorNum. reflection% reflection
Rfree0.223 771 5.01 %
Rwork0.181 --
obs0.183 15387 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.26 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6921 Å20 Å2-0 Å2
2--2.01 Å20 Å2
3----1.3179 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 0 73 1159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071122
X-RAY DIFFRACTIONf_angle_d1.0031531
X-RAY DIFFRACTIONf_dihedral_angle_d17.699388
X-RAY DIFFRACTIONf_chiral_restr0.071176
X-RAY DIFFRACTIONf_plane_restr0.004192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.91280.39561500.32472351X-RAY DIFFRACTION98
1.9128-2.06050.27591190.2322416X-RAY DIFFRACTION100
2.0605-2.26780.22761220.18242398X-RAY DIFFRACTION100
2.2678-2.59580.18441130.16682449X-RAY DIFFRACTION100
2.5958-3.270.20991350.162453X-RAY DIFFRACTION100
3.27-32.9040.21320.16642549X-RAY DIFFRACTION100
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)
17.59211.3049-0.90884.01485.56569.61820.0166-0.58190.45481.7198-0.48640.73710.00510.15270.28580.3503-0.0218-0.02850.2138-0.06710.181418.623539.574626.7226
27.0404-2.17770.99255.82380.19580.19380.0371.0891-0.6448-0.9401-0.35130.10040.72160.37970.18220.33560.04640.06750.2754-0.05720.186717.584223.9649.7585
36.2955-4.47442.14784.1455-3.30925.79460.47490.94390.9883-1.4969-0.2129-0.79130.05391.0308-0.1870.32130.04020.06540.32920.02580.296918.641733.53087.8941
49.49611.61841.44730.28380.35665.1404-0.01580.21041.1251-0.32820.0683-0.0073-0.57610.08930.01530.23320.01760.01220.19260.0030.293216.484541.457215.2058
54.35950.44920.1678.0197-1.39242.392-0.2113-0.2136-0.22270.4574-0.01040.089-0.02220.45230.16140.1408-0.0154-0.04320.1773-0.0070.171222.110131.290318.584
64.9424-1.33750.61975.7112-3.54262.05240.3150.0672-0.4793-0.0695-0.00341.01730.09860.2584-0.31840.16780.0061-0.00220.1688-0.0240.374627.913722.003421.2569
77.4733-0.3704-3.95412.042-1.58093.8725-0.154-1.3061-0.8330.5838-0.1085-0.1798-0.66940.7220.32990.18990.032-0.0150.31920.09640.336720.92722.520726.1222
84.1802-0.4552-1.4392.7926-1.11411.07860.23020.01490.0006-0.0929-0.0939-0.0856-0.1306-0.23020.04180.15870.00640.00430.14530.0020.172112.794127.128818.4729
92.22290.7840.01150.4401-0.11790.9802-0.04330.2704-0.594-0.1983-0.055-0.2153-0.1923-0.05880.15460.2397-0.02610.03250.19440.01410.395313.392117.761619.8816
104.4808-3.81312.60884.8021-5.3777.9898-1.1281-2.5535-0.07591.48790.43981.1649-0.3646-0.49430.64030.51630.0940.07890.7113-0.13940.2955.405325.003929.8972
112.54150.63781.61972.87552.31526.73990.0743-0.35760.20940.08270.18540.2596-0.868-1.3776-0.13860.17970.04030.02330.2184-0.01710.20087.246229.385118.6055
125.5432-1.06581.52718.62093.44872.11870.85541.1711-0.5508-0.9488-0.7551-0.22990.11690.3844-0.21770.5190.0665-0.08120.4872-0.16670.42799.417217.40226.3206
132.0489-1.13840.76334.3091-2.14951.01060.02760.1059-0.3101-0.61260.0990.18660.22430.007-0.09920.197-0.0307-0.00020.170.00410.18843.955727.2315.0798
145.99732.07344.59691.78262.60816.09420.18820.1650.963-0.0706-0.20410.44010.401-0.20630.08730.1520.03180.00530.1470.04370.3785.855739.988814.6855
150.223-1.11570.03686.6561.30011.95990.1212-0.5702-0.20110.5979-0.33731.45250.1686-0.18710.25490.21080.01610.07310.3632-0.03380.50858.862540.687525.6329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 325:331)
2X-RAY DIFFRACTION2(chain A and resid 332:341)
3X-RAY DIFFRACTION3(chain A and resid 342:350)
4X-RAY DIFFRACTION4(chain A and resid 351:357)
5X-RAY DIFFRACTION5(chain A and resid 358:364)
6X-RAY DIFFRACTION6(chain A and resid 365:376)
7X-RAY DIFFRACTION7(chain A and resid 377:383)
8X-RAY DIFFRACTION8(chain A and resid 384:417)
9X-RAY DIFFRACTION9(chain A and resid 418:429)
10X-RAY DIFFRACTION10(chain A and resid 430:436)
11X-RAY DIFFRACTION11(chain A and resid 437:446)
12X-RAY DIFFRACTION12(chain A and resid 447:453)
13X-RAY DIFFRACTION13(chain A and resid 454:466)
14X-RAY DIFFRACTION14(chain A and resid 467:474)
15X-RAY DIFFRACTION15(chain A and resid 475:481)

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