[English] 日本語
Yorodumi
- PDB-7me4: Structure of the extracellular WNT-binding module in Drosophila R... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7me4
TitleStructure of the extracellular WNT-binding module in Drosophila Ror2/Nrk
ComponentsTyrosine-protein kinase transmembrane receptor Ror2
KeywordsSIGNALING PROTEIN / WNT signaling / receptor tyrosine kinases / acylation / growth factor signaling / co-receptor / pseudokinases / ligand / receptor / cancer
Function / homology
Function and homology information


photoreceptor cell axon guidance / rhabdomere development / Wnt-protein binding / muscle cell cellular homeostasis / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / receptor protein-tyrosine kinase / positive regulation of neuron projection development / protein tyrosine kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ...photoreceptor cell axon guidance / rhabdomere development / Wnt-protein binding / muscle cell cellular homeostasis / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / receptor protein-tyrosine kinase / positive regulation of neuron projection development / protein tyrosine kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / signal transduction / ATP binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, receptor ROR / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. ...Tyrosine-protein kinase, receptor ROR / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PALMITOLEIC ACID / Tyrosine-protein kinase transmembrane receptor Ror2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMendrola, J.M. / Shi, F. / Perry, K. / Stayrook, S.E. / Lemmon, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM122485 United States
CitationJournal: Cell Rep / Year: 2021
Title: ROR and RYK extracellular region structures suggest that receptor tyrosine kinases have distinct WNT-recognition modes.
Authors: Shi, F. / Mendrola, J.M. / Sheetz, J.B. / Wu, N. / Sommer, A. / Speer, K.F. / Noordermeer, J.N. / Kan, Z.Y. / Perry, K. / Englander, S.W. / Stayrook, S.E. / Fradkin, L.G. / Lemmon, M.A.
History
DepositionApr 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein kinase transmembrane receptor Ror2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2663
Polymers32,5881
Non-polymers6792
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.704, 74.695, 61.552
Angle α, β, γ (deg.)90.000, 106.310, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Tyrosine-protein kinase transmembrane receptor Ror2 / dRor2 / Neurospecific receptor tyrosine kinase


Mass: 32587.643 Da / Num. of mol.: 1 / Fragment: Extracellular domain, UNP residues 42-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Nrk, ROR2, CG4007 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9V6K3, receptor protein-tyrosine kinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.03 % / Description: bar
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 3 mg/ml protein, 50 mM Bis-Tris propane (pH 5.0), 21% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→59.074 Å / Num. all: 36932 / Num. obs: 36932 / % possible obs: 88.5 % / Redundancy: 2.2 % / Rpim(I) all: 0.036 / Rrim(I) all: 0.059 / Rsym value: 0.046 / Net I/av σ(I): 9.4 / Net I/σ(I): 9.1 / Num. measured all: 81880
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.75-1.841.80.7441839147470.6781.010.744178
1.84-1.962.20.5231.31178553860.4210.6750.5231.993.4
1.96-2.092.30.2532.91131250170.1970.3220.2533.692.8
2.09-2.262.20.1574.71035746080.1230.20.1575.791.4
2.26-2.472.30.0937.9976442320.0720.1180.093891.8
2.47-2.772.30.05811.8850837200.0450.0740.05811.688.2
2.77-3.22.30.04215.5775933360.0330.0540.04216.990.2
3.2-3.912.30.03516.2630226930.0270.0450.03522.886.8
3.91-5.532.40.02920487220520.0220.0370.02925.883.9
5.53-42.5012.50.02917.5283011410.0230.0370.02926.385.4

-
Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
PHENIXdev_3915refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HKL 1I71

3hkl

1i71


Resolution: 1.75→42.5 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1802 4.89 %
Rwork0.1873 35072 -
obs0.1892 36874 87.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.84 Å2 / Biso mean: 41.7807 Å2 / Biso min: 20.68 Å2
Refinement stepCycle: final / Resolution: 1.75→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 46 273 2152
Biso mean--63.49 49.07 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131933
X-RAY DIFFRACTIONf_angle_d1.2022612
X-RAY DIFFRACTIONf_chiral_restr0.07262
X-RAY DIFFRACTIONf_plane_restr0.008338
X-RAY DIFFRACTIONf_dihedral_angle_d7.749273
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.80.38321030.33922291239474
1.8-1.850.32991340.28772463259781
1.85-1.910.34311590.26612825298493
1.91-1.980.29181520.26542845299794
1.98-2.060.27141250.20972859298492
2.06-2.150.24781360.20172735287189
2.15-2.260.25221290.19222846297593
2.26-2.410.26951510.19782809296092
2.41-2.590.251300.19222699282988
2.59-2.850.21011320.18272759289190
2.85-3.270.17851510.1852717286888
3.27-4.110.19191460.15932655280186
4.11-42.50.21571540.17172569272382
Refinement TLS params.Method: refined / Origin x: 17.4457 Å / Origin y: 33.538 Å / Origin z: -17.8196 Å
111213212223313233
T0.1763 Å2-0.0106 Å20.0087 Å2-0.2 Å20.0205 Å2--0.1645 Å2
L2.2237 °2-1.0247 °20.164 °2-1.9474 °2-0.0195 °2--1.6865 °2
S0.0096 Å °-0.201 Å °-0.1161 Å °0.0946 Å °-0.0046 Å °-0.0542 Å °0.0954 Å °0.0901 Å °-0.0116 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA68 - 301
2X-RAY DIFFRACTION1allA1210
3X-RAY DIFFRACTION1allC901 - 902
4X-RAY DIFFRACTION1allW1 - 275

+
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