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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bqc
TitleCrystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 and sucrose octasulfate
Components
  • Frizzled-4
  • Norrin
KeywordsSIGNALING PROTEIN / Wnt signalling pathway / Norrie disease protein / Glycoprotein / G protein coupled receptor
Function / homology
Function and homology information


retina blood vessel maintenance / cone retinal bipolar cell differentiation / cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / Norrin signaling pathway / extracellular matrix-cell signaling / re-entry into mitotic cell cycle / progesterone secretion / retinal blood vessel morphogenesis / retinal rod cell differentiation ...retina blood vessel maintenance / cone retinal bipolar cell differentiation / cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / Norrin signaling pathway / extracellular matrix-cell signaling / re-entry into mitotic cell cycle / progesterone secretion / retinal blood vessel morphogenesis / retinal rod cell differentiation / locomotion involved in locomotory behavior / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / ubiquitin-dependent endocytosis / Signaling by RNF43 mutants / WNT5A-dependent internalization of FZD4 / retina layer formation / retinal pigment epithelium development / Wnt receptor activity / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / establishment of blood-retinal barrier / microglial cell proliferation / glycine metabolic process / Wnt-protein binding / endothelial cell differentiation / dendritic spine development / establishment of blood-brain barrier / protein targeting to lysosome / vacuole organization / microglia differentiation / frizzled binding / optic nerve development / retinal ganglion cell axon guidance / Class B/2 (Secretin family receptors) / negative regulation of cell-substrate adhesion / cytokine receptor activity / positive regulation of dendrite morphogenesis / lens development in camera-type eye / exploration behavior / action potential / smoothened signaling pathway / cytokine binding / decidualization / canonical Wnt signaling pathway / response to axon injury / blood vessel remodeling / vasculogenesis / glutathione metabolic process / cellular response to retinoic acid / Regulation of FZD by ubiquitination / tricarboxylic acid cycle / visual perception / cellular response to leukemia inhibitory factor / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Asymmetric localization of PCP proteins / cytokine activity / PDZ domain binding / G protein-coupled receptor activity / sensory perception of sound / clathrin-coated endocytic vesicle membrane / neuron differentiation / Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / cell-cell junction / Cargo recognition for clathrin-mediated endocytosis / mitotic cell cycle / signaling receptor activity / Clathrin-mediated endocytosis / Ca2+ pathway / nervous system development / amyloid-beta binding / cellular response to hypoxia / angiogenesis / neuron apoptotic process / collagen-containing extracellular matrix / cell population proliferation / transcription by RNA polymerase II / response to hypoxia / protein ubiquitination / positive regulation of cell migration / inflammatory response / protein heterodimerization activity / dendrite / glutamatergic synapse / ubiquitin protein ligase binding / protein-containing complex binding / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / extracellular space / plasma membrane
Similarity search - Function
Norrie disease protein / Frizzled-4 / Frizzled 4, cysteine-rich domain / 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 ...Norrie disease protein / Frizzled-4 / Frizzled 4, cysteine-rich domain / 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
sucrose octasulfate / Norrin / Frizzled-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsChang, T.-H. / Hsieh, F.-L. / Zebisch, M. / 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _struct_asym.entity_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 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
B: Frizzled-4
A: Norrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7455
Polymers30,3202
Non-polymers1,4253
Water0
1
B: Frizzled-4
A: Norrin
hetero molecules

B: Frizzled-4
A: Norrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,49010
Polymers60,6404
Non-polymers2,8506
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area8290 Å2
ΔGint-33 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.136, 119.136, 119.151
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Frizzled-4 / / hFz4 / FzE4


Mass: 16705.232 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
#2: 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
#3: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / sucrose octasulfate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE
#4: 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 / N-Acetylglucosamine


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, pH 8.0, 0.15 M NaCl, 8% PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→47.34 Å / Num. obs: 10503 / % possible obs: 100 % / Redundancy: 19.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.031 / Net I/σ(I): 14.6 / Num. measured all: 205532 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3-3.1820.62.461.63402616480.1490.548100
9-47.3416.80.04950.278344650.9990.01399.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.57 Å42.12 Å
Translation5.57 Å42.12 Å

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.2.17data scaling
PHASER2.5.6phasing
REFMAC5.8.0069refinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BPB,5BPU

5bpb

5bpu


Resolution: 3→47.34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 571 5.5 %RANDOM
Rwork0.2147 ---
obs0.2175 9904 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 190.16 Å2 / Biso mean: 113.96 Å2 / Biso min: 65.73 Å2
Baniso -1Baniso -2Baniso -3
1--3 Å2-1.5 Å20 Å2
2---3 Å20 Å2
3---9.74 Å2
Refinement stepCycle: final / Resolution: 3→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1759 0 83 0 1842
Biso mean--112.7 --
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191894
X-RAY DIFFRACTIONr_bond_other_d0.0030.021720
X-RAY DIFFRACTIONr_angle_refined_deg1.1812.022577
X-RAY DIFFRACTIONr_angle_other_deg0.9353.0063984
X-RAY DIFFRACTIONr_chiral_restr0.050.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212026
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02416
X-RAY DIFFRACTIONr_mcbond_it5.2837.828894
X-RAY DIFFRACTIONr_mcbond_other5.287.826893
X-RAY DIFFRACTIONr_mcangle_it7.39711.7221114
X-RAY DIFFRACTIONr_rigid_bond_restr1.0833612
X-RAY DIFFRACTIONr_sphericity_free39.74852
X-RAY DIFFRACTIONr_sphericity_bonded22.40653562
LS refinement shellResolution: 3→3.078 Å
RfactorNum. reflection% reflection
Rfree0.45 48 -
Rwork0.35 685 -
obs--100 %
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)
14.7769-0.86360.96527.8459-3.77665.92650.12830.43080.3069-0.4207-0.06820.258-0.072-0.0085-0.06020.12840.0824-0.02930.3001-0.03840.0495-6.707-35.229-8.174
23.2197-1.4125-3.68880.91832.07235.8745-0.20740.3353-0.15550.23170.10130.14840.4087-0.29560.10610.18090.14770.01670.46220.04370.1049-18.824-48.94510.44
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 166
2X-RAY DIFFRACTION2A34 - 133

+
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