[English] 日本語
Yorodumi
- PDB-5bq8: Crystal structure of Norrin, a Wnt signalling activator, Crystal ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bq8
TitleCrystal structure of Norrin, a Wnt signalling activator, Crystal Form II
Components(Norrin) x 3
KeywordsSIGNALING PROTEIN / Wnt signalling pathway / Norrie disease protein / cystine-knot like growth factor / ligand for Frizzled 4 receptor
Function / homology
Function and homology information


retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / retinal rod cell differentiation / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / glycine metabolic process / retina layer formation / retinal pigment epithelium development ...retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / retinal rod cell differentiation / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / glycine metabolic process / retina layer formation / retinal pigment epithelium development / microglial cell proliferation / endothelial cell differentiation / dendritic spine development / establishment of blood-retinal barrier / vacuole organization / protein targeting to lysosome / microglia differentiation / establishment of blood-brain barrier / frizzled binding / optic nerve development / retinal ganglion cell axon guidance / lens development in camera-type eye / ubiquitin-dependent endocytosis / smoothened signaling pathway / exploration behavior / decidualization / action potential / blood vessel remodeling / canonical Wnt signaling pathway / response to axon injury / tricarboxylic acid cycle / glutathione metabolic process / visual perception / transforming growth factor beta receptor signaling pathway / cytokine activity / : / nervous system development / mitotic cell cycle / neuron apoptotic process / angiogenesis / cellular response to hypoxia / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / inflammatory response / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space
Similarity search - Function
Norrie disease protein / Glycoprotein hormone subunit beta / Cystine-knot domain / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine ...Norrie disease protein / Glycoprotein hormone subunit beta / Cystine-knot domain / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Norrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChang, T.-H. / Hsieh, F.-L. / Harlos, K. / Jones, E.Y.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0900084 United Kingdom
Cancer Research UKC375/A10976 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: Elife / Year: 2015
Title: Structure and functional properties of Norrin mimic Wnt for signalling with Frizzled4, Lrp5/6, and proteoglycan.
Authors: Chang, T.H. / Hsieh, F.L. / Zebisch, M. / Harlos, K. / Elegheert, J. / Jones, E.Y.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Norrin
B: Norrin
C: Norrin
D: Norrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9698
Polymers54,7564
Non-polymers2124
Water2,198122
1
A: Norrin
B: Norrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4003
Polymers27,3652
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-29 kcal/mol
Surface area11900 Å2
MethodPISA
2
C: Norrin
D: Norrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5695
Polymers27,3922
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-33 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.667, 53.059, 96.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 3 types, 4 molecules ACBD

#1: Protein Norrin / Norrie disease protein / X-linked exudative vitreoretinopathy 2 protein


Mass: 13668.798 Da / Num. of mol.: 2 / Fragment: UNP residues 25-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDP, EVR2 / Plasmid: Plasmid / Details (production host): pHLIgK-STR-8H-SUMO-1D4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q00604
#2: Protein Norrin / Norrie disease protein / X-linked exudative vitreoretinopathy 2 protein


Mass: 13695.845 Da / Num. of mol.: 1 / Fragment: UNP residues 25-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDP, EVR2 / Plasmid: Plasmid / Details (production host): pHLIgK-STR-8H-SUMO-1D4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q00604
#3: Protein Norrin / Norrie disease protein / X-linked exudative vitreoretinopathy 2 protein


Mass: 13722.891 Da / Num. of mol.: 1 / Fragment: UNP residues 25-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDP, EVR2 / Plasmid: Plasmid / Details (production host): pHLIgK-STR-8H-SUMO-1D4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q00604

-
Non-polymers , 3 types, 126 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 sodium acetate, pH 5.0, 5% PGA-LM, 4% PEG2000MME, 24% PEG550MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→33.65 Å / Num. obs: 36272 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.289 / Mean I/σ(I) obs: 1.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIX1.8.4_1496refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BPU

5bpu


Resolution: 2→33.65 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1801 4.98 %Random selection
Rwork0.233 ---
obs0.2338 36194 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→33.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 10 122 3319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053278
X-RAY DIFFRACTIONf_angle_d1.0764365
X-RAY DIFFRACTIONf_dihedral_angle_d13.9231265
X-RAY DIFFRACTIONf_chiral_restr0.042472
X-RAY DIFFRACTIONf_plane_restr0.004548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05411332598X-RAY DIFFRACTION100
2.0541-2.11451502589X-RAY DIFFRACTION100
2.1145-2.18270.35721180.33912611X-RAY DIFFRACTION100
2.1827-2.26071522589X-RAY DIFFRACTION100
2.2607-2.35120.31451270.28182644X-RAY DIFFRACTION100
2.3512-2.45820.30291380.28692595X-RAY DIFFRACTION100
2.4582-2.58780.28061450.26492631X-RAY DIFFRACTION100
2.5878-2.74980.26511330.25312633X-RAY DIFFRACTION100
2.7498-2.9620.28521420.25512632X-RAY DIFFRACTION100
2.962-3.25990.221510.222644X-RAY DIFFRACTION100
3.2599-3.73110.24741400.20522665X-RAY DIFFRACTION100
3.7311-4.69870.21051420.17682699X-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)
10.95640.584-0.09170.14830.2990.59840.1515-0.3081-0.05940.0552-0.13080.03490.1659-0.0361-0.00170.3922-0.02590.04310.50660.08520.387-15.948914.4495-10.6795
20.6933-0.30990.09490.6512-0.08090.60860.0461-0.43120.01210.04870.031-0.0940.06560.04910.01890.38680.024-0.01820.44780.05020.30747.830314.4056-10.2958
30.7336-0.45440.10170.46360.10590.9024-0.08550.40550.1289-0.11290.04340.02840.09-0.1298-0.00040.3549-0.0422-0.03090.40610.04030.3429-10.741616.5304-38.0973
41.0902-0.4482-0.46940.67910.1390.7916-0.03330.2548-0.1566-0.10090.0826-0.10740.12980.02580.01570.3527-0.00780.04010.337-0.02140.326812.653612.0767-37.5307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 35 through 138)
2X-RAY DIFFRACTION2(chain 'B' and resid 36 through 132)
3X-RAY DIFFRACTION3(chain 'C' and resid 35 through 133)
4X-RAY DIFFRACTION4(chain 'D' and resid 37 through 138)

+
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