[English] 日本語
Yorodumi
- PDB-4ufr: Structure of the ectodomain of LGR5 in complex with R-spondin-2 (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ufr
TitleStructure of the ectodomain of LGR5 in complex with R-spondin-2 (Fu1Fu2)
Components
  • LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
  • R-SPONDIN-2
KeywordsSIGNALING PROTEIN / WNT / LGR / RSPO
Function / homology
Function and homology information


oocyte differentiation / trachea cartilage morphogenesis / negative regulation of odontogenesis of dentin-containing tooth / lung growth / epithelial cell proliferation involved in renal tubule morphogenesis / Regulation of FZD by ubiquitination / protein-hormone receptor activity / dopaminergic neuron differentiation / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis ...oocyte differentiation / trachea cartilage morphogenesis / negative regulation of odontogenesis of dentin-containing tooth / lung growth / epithelial cell proliferation involved in renal tubule morphogenesis / Regulation of FZD by ubiquitination / protein-hormone receptor activity / dopaminergic neuron differentiation / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / epithelial tube branching involved in lung morphogenesis / bone mineralization / inner ear development / hair follicle development / canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / trans-Golgi network membrane / G protein-coupled receptor activity / osteoblast differentiation / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / regulation of cell population proliferation / heparin binding / G protein-coupled receptor signaling pathway / signaling receptor binding / cell surface / extracellular region / plasma membrane
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 / Glycoprotein hormone receptor family / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain ...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 / Glycoprotein hormone receptor family / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeats, bacterial type / Alpha-Beta Horseshoe / Leucine-rich repeat, SDS22-like subfamily / Furin-like repeat / Furin-like repeats / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Growth factor receptor cysteine-rich domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Ribbon / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Leucine-rich repeat-containing G-protein coupled receptor 5 / R-spondin-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsZebisch, M. / Jones, E.Y.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Crystal Structure of R-Spondin 2 in Complex with the Ectodomains of its Receptors Lgr5 and Znrf3.
Authors: Zebisch, M. / Jones, E.Y.
History
DepositionMar 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Structure summary
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Sep 23, 2015Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
B: R-SPONDIN-2
C: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
D: R-SPONDIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,65412
Polymers135,9984
Non-polymers6558
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-74.7 kcal/mol
Surface area49030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.148, 59.777, 112.210
Angle α, β, γ (deg.)90.00, 99.51, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5 / G-PROTEIN COUPLED RECEPTOR 49 / G-PROTEIN COUPLED RECEPTOR 6 7 / G-PROTEIN COUPLED RECEPTOR HG38 / LGR5


Mass: 54052.348 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 32-487 AND RESIDUES 538-544
Source method: isolated from a genetically manipulated source
Details: UNSTRUCTURED LOOP REPLACED WITH SHORT LINKER, A488-H537 TO NGNNGD
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: O75473
#2: Protein R-SPONDIN-2 / CYSTEINE-RICH AND SINGLE THROMBOSPONDIN DOMAIN-CONTAINING PROTEIN 2 / CRISTIN-2 / MCRISTIN-2 / ROOF ...CYSTEINE-RICH AND SINGLE THROMBOSPONDIN DOMAIN-CONTAINING PROTEIN 2 / CRISTIN-2 / MCRISTIN-2 / ROOF PLATE-SPECIFIC SPONDIN-2 / RSPO2


Mass: 13946.869 Da / Num. of mol.: 2 / Fragment: FU1-FU2, RESIDUES 39-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q8BFU0
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 5.5
Details: 25 %W/V PEG3350, 0.200 M LITHIUM SULPHATE, 0.100 M BIS-TRIS PH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.009
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.2→69 Å / Num. obs: 62167 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.8

-
Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.2→110.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 23.344 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26172 1184 1.9 %RANDOM
Rwork0.20805 ---
obs0.20909 60900 90.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.664 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20.71 Å2
2--0.18 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→110.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8722 0 34 150 8906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198977
X-RAY DIFFRACTIONr_bond_other_d0.0010.028478
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.97312200
X-RAY DIFFRACTIONr_angle_other_deg0.847319507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.48951117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8724.141396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.511151498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.661549
X-RAY DIFFRACTIONr_chiral_restr0.0880.21392
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022090
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_it1.8693.0794480
X-RAY DIFFRACTIONr_mcbond_other1.8683.0784479
X-RAY DIFFRACTIONr_mcangle_it2.9374.6115590
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4363.3184497
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
Rfree0.344 50 -
Rwork0.362 2902 -
obs--59.03 %
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)
15.3197-0.74823.07380.66150.19954.55960.183-0.0497-0.6914-0.1047-0.01430.09990.7463-0.1314-0.16880.3914-0.00630.05630.06940.00810.116717.065-15.681819.9634
21.54540.21170.37563.32860.84792.4839-0.0154-0.0960.00440.02220.0931-0.47330.06290.287-0.07770.2310.06790.03260.0936-0.00360.074135.76961.648534.418
31.7083-1.13-1.66933.5521.63954.98920.0459-0.07320.24650.11350.0078-0.4782-0.34870.3426-0.05370.4017-0.0542-0.01620.0594-0.01670.121726.047431.758854.421
42.7159-3.1743-0.74663.99832.0788.0626-0.134-0.1704-0.32050.2576-0.05830.5994-0.1951-1.47870.19230.62160.04120.2090.3162-0.05660.47595.376735.258666.9096
57.3357-1.1795-0.11876.2619-1.38128.7004-0.0228-0.009-0.4278-0.13870.00121.37820.2455-0.93980.02160.46460.071-0.04490.3651-0.13810.379310.18-3.676439.7267
65.78311.38610.574810.9324-5.608111.9458-0.47290.81881.5264-0.7387-0.05090.1498-0.9896-0.82180.52380.51980.1642-0.11210.46630.07320.498921.525611.219920.042
78.6115-0.6118-0.60641.33370.42222.89210.00770.07380.9316-0.11580.10560.215-0.6409-0.2711-0.11330.3584-0.02580.06210.07420.02420.1838-5.148257.672899.7174
81.867-1.5735-1.48913.78471.41522.0288-0.0596-0.24930.22810.29340.2767-0.5168-0.04680.4174-0.21710.2778-0.11070.05590.1298-0.0810.107818.279239.667498.3443
91.1185-0.1157-0.75942.93191.85175.17750.1002-0.059-0.17860.26110.015-0.17990.35340.3808-0.11520.2989-0.0050.06880.0369-0.01310.096220.12189.616676.0356
104.73040.8986-2.23670.60960.92079.69860.1770.5586-0.191-0.1927-0.0990.22070.4153-1.3481-0.0780.6395-0.024-0.24760.2237-0.0760.46558.70916.14954.5563
118.07811.23252.41827.60040.43979.9979-0.05480.50990.1981-0.79470.00190.8163-0.0312-0.75650.05290.3218-0.05840.05320.2594-0.08080.1887-0.556245.437580.3934
128.9433.4268-3.300111.9907-6.459212.12230.0018-0.6288-1.50760.5230.26780.3790.8055-1.1687-0.26960.4729-0.13070.0290.42080.05360.4693-0.862430.4999102.7827
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 129
2X-RAY DIFFRACTION2A130 - 291
3X-RAY DIFFRACTION3A292 - 437
4X-RAY DIFFRACTION4A438 - 544
5X-RAY DIFFRACTION5B40 - 95
6X-RAY DIFFRACTION6B96 - 141
7X-RAY DIFFRACTION7C1 - 129
8X-RAY DIFFRACTION8C130 - 291
9X-RAY DIFFRACTION9C292 - 437
10X-RAY DIFFRACTION10C438 - 544
11X-RAY DIFFRACTION11D40 - 95
12X-RAY DIFFRACTION12D96 - 141

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more