[English] 日本語
Yorodumi
- PDB-5bqe: Crystal structure of Norrin in complex with the cysteine-rich dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bqe
TitleCrystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 -Methylated form
Components
  • (Norrin) x 2
  • Frizzled-4
KeywordsSIGNALING PROTEIN / Wnt signalling pathway / Norrie disease protein / Glycoprotein / G protein coupled receptor
Function / homology
Function and homology information


cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / progesterone secretion / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / retinal rod cell differentiation ...cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / progesterone secretion / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / retinal rod cell differentiation / retina vasculature morphogenesis in camera-type eye / locomotion involved in locomotory behavior / Signaling by RNF43 mutants / ubiquitin-dependent endocytosis / WNT5A-dependent internalization of FZD4 / glycine metabolic process / regulation of vascular endothelial growth factor receptor signaling pathway / retina layer formation / positive regulation of neuron projection arborization / Wnt receptor activity / retinal pigment epithelium development / non-canonical Wnt signaling pathway / endothelial cell differentiation / microglial cell proliferation / Wnt-protein binding / dendritic spine development / establishment of blood-retinal barrier / vacuole organization / protein targeting to lysosome / positive regulation of dendrite morphogenesis / microglia differentiation / establishment of blood-brain barrier / optic nerve development / frizzled binding / Class B/2 (Secretin family receptors) / retinal ganglion cell axon guidance / cytokine receptor activity / lens development in camera-type eye / smoothened signaling pathway / cytokine binding / exploration behavior / decidualization / action potential / blood vessel remodeling / negative regulation of cell-substrate adhesion / canonical Wnt signaling pathway / response to axon injury / Regulation of FZD by ubiquitination / vasculogenesis / cellular response to retinoic acid / tricarboxylic acid cycle / visual perception / glutathione metabolic process / substrate adhesion-dependent cell spreading / Asymmetric localization of PCP proteins / transforming growth factor beta receptor signaling pathway / cellular response to leukemia inhibitory factor / cytokine activity / PDZ domain binding / sensory perception of sound / clathrin-coated endocytic vesicle membrane / G protein-coupled receptor activity / Wnt signaling pathway / neuron differentiation / Cargo recognition for clathrin-mediated endocytosis / cell-cell junction / Clathrin-mediated endocytosis / nervous system development / mitotic cell cycle / signaling receptor activity / : / amyloid-beta binding / Ca2+ pathway / neuron apoptotic process / angiogenesis / cellular response to hypoxia / transcription by RNA polymerase II / response to hypoxia / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cilium / positive regulation of cell migration / inflammatory response / protein heterodimerization activity / ubiquitin protein ligase binding / dendrite / positive regulation of DNA-templated transcription / protein-containing complex binding / glutamatergic synapse / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / plasma membrane
Similarity search - Function
Frizzled-4 / Frizzled 4, cysteine-rich domain / Norrie disease protein / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Glycoprotein hormone subunit beta / Cystine-knot domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region ...Frizzled-4 / Frizzled 4, cysteine-rich domain / Norrie disease protein / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Glycoprotein hormone subunit beta / Cystine-knot domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Norrin
B: Norrin
C: Frizzled-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7148
Polymers44,0973
Non-polymers6175
Water2,072115
1
A: Norrin
B: Norrin
C: Frizzled-4
hetero molecules

C: Frizzled-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,85012
Polymers60,8564
Non-polymers9948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544x,-y-1,-z-1/21
MethodPISA
Unit cell
Length a, b, c (Å)98.920, 98.920, 120.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

-
Components

-
Protein , 3 types, 3 molecules ABC

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


Mass: 13614.706 Da / Num. of mol.: 1 / Fragment: residues 25-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDP, EVR2 / Plasmid: 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: 13722.891 Da / Num. of mol.: 1 / Fragment: residues 25-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDP, EVR2 / Plasmid: pHLIgK-STR-8H-SUMO-1D4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q00604
#3: Protein Frizzled-4 / hFz4 / FzE4


Mass: 16759.324 Da / Num. of mol.: 1 / Fragment: residues 42-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD4 / Plasmid: pHLsec-mVenus-12H / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9ULV1

-
Sugars , 1 types, 1 molecules

#5: 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.: 1
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

-
Non-polymers , 3 types, 119 molecules

#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bicine, pH 9.0, 10% PEG6000

-
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: 2.3→49.46 Å / Num. obs: 26816 / % possible obs: 98.9 % / Redundancy: 6 % / Biso Wilson estimate: 48.29 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.045 / Net I/σ(I): 10.7 / Num. measured all: 161410 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.385.61.2121.41403725140.2880.56197.2
8.91-49.465.10.03430.627735490.9990.01698.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å49.46 Å
Translation2.3 Å49.46 Å

-
Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
MOSFLMdata reduction
PHASER2.5.2phasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BPB,5BPU

5bpb

5bpu


Resolution: 2.3→49.46 Å / FOM work R set: 0.7608 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 1345 5.02 %Random selection
Rwork0.1966 25458 --
obs0.1978 26803 98.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.26 Å2 / Biso mean: 63.08 Å2 / Biso min: 30.05 Å2
Refinement stepCycle: final / Resolution: 2.3→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 39 115 2711
Biso mean--74.44 57.06 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042665
X-RAY DIFFRACTIONf_angle_d0.9273559
X-RAY DIFFRACTIONf_chiral_restr0.039383
X-RAY DIFFRACTIONf_plane_restr0.003455
X-RAY DIFFRACTIONf_dihedral_angle_d17.341028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.38230.35211400.32882416255697
2.3823-2.47770.35831390.30792498263798
2.4777-2.59040.26881220.27212492261498
2.5904-2.7270.29021300.25462511264198
2.727-2.89780.26261380.24542523266199
2.8978-3.12160.21821260.22272532265899
3.1216-3.43560.22891490.19982528267799
3.4356-3.93260.22521420.17242565270799
3.9326-4.95390.17261280.14062623275199
4.9539-49.47140.17811310.18642770290199
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)
11.3224-0.09480.03831.2739-0.3183-0.2811-0.1541-0.18510.0324-0.3046-0.00990.5456-0.0505-0.2043-0.0010.51330.0254-0.0480.3580.01420.3175-15.6448-34.7305-6.8736
21.7321-0.5548-0.43863.3845-3.04883.1797-0.2218-0.6999-0.38281.1860.6492-0.8012-0.42762.0732-0.2470.49150.1293-0.11820.914-0.0640.71791.071-69.0431-9.9434
31.7661-0.27330.05110.6978-0.345-0.7765-0.1855-0.08340.21580.04050.20370.0076-0.0227-0.05820.00710.47230.0187-0.05080.2399-0.01180.2398-6.3333-31.2301-3.2528
41.2399-0.2191-0.03020.2410.125-0.03620.2491-0.1821-0.5291-1.3584-0.1053-0.56610.05880.0503-0.00060.685-0.1163-0.02040.38080.03720.4207-7.5047-42.1372-14.0401
50.2805-0.02320.52720.90160.59480.9935-0.02290.8250.0919-0.052-0.43950.4830.0713-0.7316-0.05530.27490.004-0.05940.4136-0.01390.4746-18.5396-63.7011-18.1329
60.23510.12990.12370.69320.17540.2048-0.10870.0383-0.121-0.08530.21290.0603-0.15870.12830.00010.37380.0155-0.00530.3678-0.04970.4292-8.0004-63.3228-16.272
70.0528-0.07240.02650.1943-0.38820.5442-0.1189-0.2056-0.23210.14980.05890.0833-0.00360.0878-0.00070.48720.07650.00170.47920.00590.3429-6.8457-35.32872.1397
81.35240.26611.23972.72720.73380.7723-0.1784-0.0529-0.37530.35350.47610.24920.23780.5570.11910.47770.0990.07540.3714-0.03670.3824-5.6333-74.0643-12.3498
90.03190.1480.1990.3726-0.12631.2988-0.03920.1137-0.08260.6948-0.31750.04210.10310.1445-0.01170.42650.01390.02030.30480.07360.4133-11.1406-63.6235-8.0561
100.19280.2494-0.12480.6032-0.7861.06020.3017-0.4666-0.57880.0420.07250.13721.3028-1.06570.08090.4088-0.0685-0.03220.69670.08170.5021-29.9148-25.5259-14.8859
110.11920.18660.20650.39940.01370.36450.1848-0.1665-0.00650.3847-0.5038-0.1719-0.3401-0.7949-0.00710.46380.11860.01590.5984-0.02880.5352-30.1023-16.3512-15.6861
121.4641.3289-0.24150.90010.38220.8505-0.18870.2507-0.1657-0.01180.20970.07630.3974-0.5342-0.05510.4110.0079-0.05520.58420.01350.4272-24.3547-22.2708-29.0583
130.92350.30950.28130.304-0.2520.2636-0.0668-0.0396-0.13550.1516-0.1460.1619-0.2431-0.56130.00010.4-0.00790.00260.37250.01810.3595-22.2998-20.0691-14.132
142.4192-0.3592.96341.4811-0.56263.9498-0.05490.42740.11120.1012-0.2575-0.42640.44251.0915-0.34870.2677-0.03720.00080.30720.04670.3831-11.9793-17.8264-30.5662
151.63950.7753-0.69640.4448-0.11960.38060.2055-0.32230.37470.22870.0394-0.21690.1989-0.68670.00220.46790.0486-0.09230.415-0.00080.4604-15.3696-12.246-22.8601
163.52231.21474.66645.02862.19337.2667-0.48590.21710.0458-0.18010.2248-0.2781-0.28821.53460.98610.4306-0.0156-0.0720.51370.03440.3787-11.0928-19.8415-11.0953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 77 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 88 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 123 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 133 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 48 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 49 through 77 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 93 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 116 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 117 through 133 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 43 through 58 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 59 through 71 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 72 through 93 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 94 through 117 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 118 through 135 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 136 through 152 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 153 through 164 )C0

+
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