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- PDB-4c8v: Xenopus RSPO2 Fu1-Fu2 crystal form I -

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Basic information

Entry
Database: PDB / ID: 4c8v
TitleXenopus RSPO2 Fu1-Fu2 crystal form I
ComponentsR-SPONDIN-2
KeywordsSIGNALING PROTEIN / WNT / ZNRF3 / RNF43 / LGR4 / LGR5 / LGR6 / RSPO / R-SPO / RSPO1 / RSPO3 / RSPO4 / RECEPTOR / MEMBRANE / SIGNALLING
Function / homology
Function and homology information


anal fin development / caudal fin development / dorsal fin development / pectoral fin development / pelvic fin development / Regulation of FZD by ubiquitination / dorsal/ventral axis specification / lysosomal protein catabolic process / BMP receptor binding / negative regulation of BMP signaling pathway ...anal fin development / caudal fin development / dorsal fin development / pectoral fin development / pelvic fin development / Regulation of FZD by ubiquitination / dorsal/ventral axis specification / lysosomal protein catabolic process / BMP receptor binding / negative regulation of BMP signaling pathway / BMP signaling pathway / skeletal system development / Wnt signaling pathway / heparin binding / lysosome / extracellular space
Similarity search - Function
Spondin-like TSP1 domain / Spondin-like TSP1 domain / 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 ...Spondin-like TSP1 domain / Spondin-like TSP1 domain / 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 speciesXENOPUS TROPICALIS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsZebisch, M. / Jones, E.Y.
CitationJournal: Nat.Commun. / Year: 2013
Title: Structural and Molecular Basis of Znrf3/Rnf43 Transmembrane Ubiquitin Ligase Inhibition by the Wnt Agonist R-Spondin.
Authors: Zebisch, M. / Xu, Y. / Krastev, C. / Macdonald, B.T. / Chen, M. / Gilbert, R.J.C. / He, X. / Jones, E.Y.
History
DepositionOct 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Other / Source and taxonomy / Category: entity_src_gen / pdbx_database_status
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _pdbx_database_status.status_code_sf
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: R-SPONDIN-2
B: R-SPONDIN-2
C: R-SPONDIN-2
D: R-SPONDIN-2
E: R-SPONDIN-2
F: R-SPONDIN-2
G: R-SPONDIN-2
H: R-SPONDIN-2


Theoretical massNumber of molelcules
Total (without water)110,2548
Polymers110,2548
Non-polymers00
Water5,224290
1
A: R-SPONDIN-2


Theoretical massNumber of molelcules
Total (without water)13,7821
Polymers13,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: R-SPONDIN-2


Theoretical massNumber of molelcules
Total (without water)13,7821
Polymers13,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: R-SPONDIN-2


Theoretical massNumber of molelcules
Total (without water)13,7821
Polymers13,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: R-SPONDIN-2


Theoretical massNumber of molelcules
Total (without water)13,7821
Polymers13,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: R-SPONDIN-2


Theoretical massNumber of molelcules
Total (without water)13,7821
Polymers13,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: R-SPONDIN-2


Theoretical massNumber of molelcules
Total (without water)13,7821
Polymers13,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: R-SPONDIN-2


Theoretical massNumber of molelcules
Total (without water)13,7821
Polymers13,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
H: R-SPONDIN-2


Theoretical massNumber of molelcules
Total (without water)13,7821
Polymers13,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)97.138, 97.138, 292.916
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
R-SPONDIN-2 / ROOF PLATE-SPECIFIC SPONDIN-2 / RSPO2


Mass: 13781.749 Da / Num. of mol.: 8 / Fragment: FU1-FU2, RESIDUES 35-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS (SILURANA) TROPICALIS (tropical clawed frog)
Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q5M7L6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.75 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Aug 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 71285 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.3

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.2→39.72 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.659 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27035 3589 5 %RANDOM
Rwork0.22318 ---
obs0.22558 67674 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.153 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6791 0 0 290 7081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197032
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9629447
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7455867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57422.434341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.823151203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8661571
X-RAY DIFFRACTIONr_chiral_restr0.0990.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215459
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 269 -
Rwork0.36 4996 -
obs--99.87 %

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