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- PDB-4bso: Crystal structure of R-spondin 1 (Fu1Fu2) - Native -

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Basic information

Entry
Database: PDB / ID: 4bso
TitleCrystal structure of R-spondin 1 (Fu1Fu2) - Native
ComponentsR-SPONDIN-1
KeywordsSIGNALING PROTEIN / ADULT STEM CELL / LEUCINE-RICH REPEAT G-PROTEIN COUPLED RECEPTOR / FURIN DOMAIN / WNT SIGNALING / CONGENITAL ANONYCHIA
Function / homology
Function and homology information


regulation of receptor internalization / positive regulation of Wnt signaling pathway / Regulation of FZD by ubiquitination / G protein-coupled receptor binding / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / heparin binding / positive regulation of protein phosphorylation / signaling receptor binding / extracellular region / nucleus
Similarity search - Function
R-spondin, Fu-CRD domain / Furin-like repeat, cysteine-rich / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Furin-like repeat / Furin-like repeats ...R-spondin, Fu-CRD domain / Furin-like repeat, cysteine-rich / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsPeng, W.C. / de Lau, W. / Forneris, F. / Granneman, J.C.M. / Huch, M. / Clevers, H. / Gros, P.
CitationJournal: Cell Rep. / Year: 2013
Title: Structure of Stem Cell Growth Factor R-Spondin 1 in Complex with the Ectodomain of its Receptor Lgr5.
Authors: Peng, W.C. / De Lau, W. / Forneris, F. / Granneman, J.C.M. / Huch, M. / Clevers, H. / Gros, P.
History
DepositionJun 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: R-SPONDIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0888
Polymers13,7071
Non-polymers3817
Water36020
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.160, 63.900, 92.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein R-SPONDIN-1


Mass: 13706.780 Da / Num. of mol.: 1 / Fragment: FU1FU2, RESIDUES 31-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q2MKA7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL GS AND C-TERMINAL AAA ADDED BY CLONING PLASMID, PLUS C-TERMINAL 6XHIS TAG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.57 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.88
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2.2→34.4 Å / Num. obs: 5873 / % possible obs: 100 % / Observed criterion σ(I): 2.4 / Redundancy: 7.3 % / Biso Wilson estimate: 37.94 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.1

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.2→34.48 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 266 4.5 %
Rwork0.2121 --
obs0.2139 5872 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms729 0 22 20 771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021817
X-RAY DIFFRACTIONf_angle_d2.1241080
X-RAY DIFFRACTIONf_dihedral_angle_d18.333310
X-RAY DIFFRACTIONf_chiral_restr0.133112
X-RAY DIFFRACTIONf_plane_restr0.009143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.77170.29291260.22542734X-RAY DIFFRACTION100
2.7717-34.48370.23911400.20822872X-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)
12.0391-0.75050.74334.9522-2.6513.1672-0.2089-0.1863-0.06230.3595-0.6407-0.4571.49730.2226-0.64050.7249-0.0507-0.02230.3048-0.01070.1908-0.7602-17.6447-4.7945
20.04990.10480.04890.1950.1020.14110.26370.1732-0.3675-0.3536-0.24590.0758-0.31870.3507-0.00070.3368-0.0525-0.02990.33370.04190.2565-0.3339-14.005-14.5979
30.02130.01240.00230.07730.07720.0788-0.5954-0.2130.155-0.5331-0.045-0.493-0.03440.03330.00060.88390.02120.01172.30620.07721.2628-16.552-11.3377-6.9056
4-0.00120.02860.00413.5616-1.21890.4169-0.2124-0.24850.5941-0.8617-0.07080.30770.1457-0.0036-0.15850.32850.0007-0.09850.3935-0.00480.2731-5.4447-16.0191-17.2416
51.83620.52361.43991.62682.67494.62080.4980.518-0.1646-0.48450.53910.19310.24060.28040.69270.227-0.0012-0.06440.14940.05750.24412.1485-7.7531-16.8424
61.2283-0.3439-0.12390.8142-0.2821.35340.2723-0.2292-0.262-0.67060.1790.78220.5683-0.15370.40010.29690.0279-0.23340.1430.10030.3937-9.041-1.9962-22.836
70.24260.05760.10410.3585-0.16770.2449-0.085-0.0390.0499-0.41590.033-0.12560.6564-0.0620.00330.5027-0.0178-0.11990.26620.02270.2685-7.95236.519-28.5517
84.6589-2.06171.02450.9654-0.56680.45030.28450.84090.4107-0.3361-0.331-1.0706-0.08460.212-0.2310.7529-0.0174-0.09570.4912-0.26660.9001-7.862210.1537-41.9493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 8 THROUGH 27 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 28 THROUGH 35 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 36 THROUGH 41 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 42 THROUGH 52 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 53 THROUGH 62 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 63 THROUGH 81 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 82 THROUGH 96 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 97 THROUGH 113 )

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