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- PDB-7me4: Structure of the extracellular WNT-binding module in Drosophila R... -

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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 / protein tyrosine kinase collagen receptor activity / multicellular organism development / positive regulation of kinase activity / muscle cell cellular homeostasis / plasma membrane => GO:0005886 / cell surface receptor protein tyrosine kinase signaling pathway / collagen binding / transmembrane receptor protein tyrosine kinase activity ...photoreceptor cell axon guidance / rhabdomere development / protein tyrosine kinase collagen receptor activity / multicellular organism development / positive regulation of kinase activity / muscle cell cellular homeostasis / plasma membrane => GO:0005886 / cell surface receptor protein tyrosine kinase signaling pathway / collagen binding / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / protein tyrosine kinase activity / receptor complex / protein phosphorylation / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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