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- PDB-7me5: Structure of the extracellular WNT-binding module in Drl-2 -

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Basic information

Entry
Database: PDB / ID: 7me5
TitleStructure of the extracellular WNT-binding module in Drl-2
ComponentsTyrosine-protein kinase transmembrane receptor DRL-2
KeywordsSIGNALING PROTEIN / WNT signaling / receptor tyrosine kinases / acylation / growth factor signaling / co-receptor / pseudokinases / ligand / receptor / cancer
Function / homology
Function and homology information


synaptic target inhibition / chemorepulsion of axon / : / multicellular organism development / Wnt-protein binding / positive regulation of kinase activity / motor neuron axon guidance / plasma membrane => GO:0005886 / salivary gland morphogenesis / cell surface receptor protein tyrosine kinase signaling pathway ...synaptic target inhibition / chemorepulsion of axon / : / multicellular organism development / Wnt-protein binding / positive regulation of kinase activity / motor neuron axon guidance / plasma membrane => GO:0005886 / salivary gland morphogenesis / cell surface receptor protein tyrosine kinase signaling pathway / axonogenesis / peptidyl-tyrosine phosphorylation / receptor complex / protein kinase activity / protein heterodimerization activity / ATP binding
Similarity search - Function
WIF domain / WIF domain superfamily / WIF domain / WIF domain profile. / Wnt-inhibitory factor-1 like 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 domain profile. ...WIF domain / WIF domain superfamily / WIF domain / WIF domain profile. / Wnt-inhibitory factor-1 like 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Derailed 2, isoform B
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShi, F. / Mendrola, J.M. / 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

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Assembly

Deposited unit
A: Tyrosine-protein kinase transmembrane receptor DRL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2872
Polymers18,0661
Non-polymers2211
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.978, 91.583, 76.362
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Tyrosine-protein kinase transmembrane receptor DRL-2 / Derailed 2


Mass: 18065.623 Da / Num. of mol.: 1 / Fragment: Extracellular domain, UNP residues 26-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Drl-2, CG12463, Dmel\CG3915, dnl, DNT-like, DRL-2, drl-2, drl2, CG3915, Dmel_CG3915
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7JQT0
#2: 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: obtained synthetically / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.93 Å3/Da / Density % sol: 58 % / Description: bar
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12 mg/ml protein, 100mM Tris (ph 8.5), 100 mM sodium acetate, 25% PEG 6000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 24, 2012 / Details: Osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→45.79 Å / Num. obs: 13786 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Net I/σ(I): 19.1 / Num. measured all: 90856 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.053.60.89833669290.5970.5241.0481.594.2
8.94-45.795.70.0210601860.9990.0090.02275.698.8

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Processing

Software
NameVersionClassification
PHENIXdev_3915refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YGN

2ygn


Resolution: 2→29.97 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 636 4.63 %
Rwork0.2303 13112 -
obs0.2315 13748 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.08 Å2 / Biso mean: 46.0118 Å2 / Biso min: 21.26 Å2
Refinement stepCycle: final / Resolution: 2→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 14 84 1307
Biso mean--79.6 47.49 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031262
X-RAY DIFFRACTIONf_angle_d0.6251727
X-RAY DIFFRACTIONf_chiral_restr0.063193
X-RAY DIFFRACTIONf_plane_restr0.005225
X-RAY DIFFRACTIONf_dihedral_angle_d6.526169
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.150.3651900.35362554264497
2.15-2.370.34451060.291326082714100
2.37-2.710.34691270.287226232750100
2.71-3.420.27961580.248426002758100
3.42-29.970.20461550.182627272882100

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