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- PDB-4gt4: Structure of unliganded, inactive Ror2 kinase domain -

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Basic information

Entry
Database: PDB / ID: 4gt4
TitleStructure of unliganded, inactive Ror2 kinase domain
ComponentsTyrosine-protein kinase transmembrane receptor ROR2
KeywordsTRANSFERASE / ATP binding / phosphorylation / membrane
Function / homology
Function and homology information


regulation of synaptic signaling by nitric oxide / macrophage migration / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt-protein binding / positive regulation of macrophage differentiation / male genitalia development / astrocyte development / mitogen-activated protein kinase kinase kinase binding / PCP/CE pathway / regulation of postsynapse organization ...regulation of synaptic signaling by nitric oxide / macrophage migration / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt-protein binding / positive regulation of macrophage differentiation / male genitalia development / astrocyte development / mitogen-activated protein kinase kinase kinase binding / PCP/CE pathway / regulation of postsynapse organization / bone mineralization / coreceptor activity / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / positive regulation of synaptic transmission, glutamatergic / clathrin-coated endocytic vesicle membrane / receptor protein-tyrosine kinase / Wnt signaling pathway / positive regulation of neuron projection development / microtubule / postsynapse / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration / neuronal cell body / glutamatergic synapse / dendrite / cell surface / signal transduction / ATP binding / metal ion 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 / Immunoglobulin I-set / Immunoglobulin I-set domain / Kringle-like fold / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Tyrosine-protein kinase transmembrane receptor ROR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.406 Å
AuthorsMendrola, J.M. / Lemmon, M.A.
CitationJournal: Biochem.J. / Year: 2012
Title: Assessing the range of kinase autoinhibition mechanisms in the insulin receptor family.
Authors: Artim, S.C. / Mendrola, J.M. / Lemmon, M.A.
History
DepositionAug 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Nov 21, 2012Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: Tyrosine-protein kinase transmembrane receptor ROR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1756
Polymers70,9272
Non-polymers2484
Water4,107228
1
A: Tyrosine-protein kinase transmembrane receptor ROR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5883
Polymers35,4641
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase transmembrane receptor ROR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5883
Polymers35,4641
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.834, 112.918, 114.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Tyrosine-protein kinase transmembrane receptor ROR2 / Neurotrophic tyrosine kinase / receptor-related 2


Mass: 35463.727 Da / Num. of mol.: 2 / Fragment: tyrosine kinase domain (UNP residues 452-753)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTRKR2, ROR2 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q01974, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 0.2 M magnesium nitrate hexahydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2010 / Details: mirrors
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3993→50 Å / Num. all: 26280 / Num. obs: 26279 / % possible obs: 99.999 % / Observed criterion σ(I): 5 / Redundancy: 7.5 %
Reflection shellResolution: 2.3993→2.46 Å / Num. unique all: 1748 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_1108)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.406→45.8 Å / SU ML: 0.22 / σ(F): 1.37 / Phase error: 19.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 1329 5.06 %RANDOM
Rwork0.1773 ---
obs0.1787 26251 99.86 %-
all-26280 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.406→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4263 0 16 228 4507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024400
X-RAY DIFFRACTIONf_angle_d0.6035971
X-RAY DIFFRACTIONf_dihedral_angle_d11.9591539
X-RAY DIFFRACTIONf_chiral_restr0.044659
X-RAY DIFFRACTIONf_plane_restr0.003754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.406-2.50260.25951340.2122719X-RAY DIFFRACTION99
2.5026-2.61650.23211470.20562748X-RAY DIFFRACTION100
2.6165-2.75440.2531500.19432730X-RAY DIFFRACTION100
2.7544-2.9270.2331580.18972746X-RAY DIFFRACTION100
2.927-3.15290.23621320.18242746X-RAY DIFFRACTION100
3.1529-3.47010.17951450.17412774X-RAY DIFFRACTION100
3.4701-3.9720.19561610.16372752X-RAY DIFFRACTION100
3.972-5.00330.17471440.14952798X-RAY DIFFRACTION100
5.0033-45.80850.19341580.18652909X-RAY DIFFRACTION100
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)
15.05240.3797-1.34635.20850.31054.75150.30930.37050.9821-0.2469-0.07350.3925-0.6957-0.1941-0.27260.44530.06140.020.43590.09610.543-31.34716.4104-26.3682
23.39210.3661-0.50282.5536-0.45543.44060.05410.19510.1194-0.03240.08110.3504-0.0333-0.2393-0.12640.1722-0.0407-0.01330.1926-0.01380.1779-24.33051.0262-20.6624
33.2418-0.0682-1.13953.26420.34663.32560.10960.07750.0215-0.036-0.0817-0.0432-0.0658-0.0296-0.02740.1137-0.0222-0.00270.13770.00640.0916-9.58383.2188-14.0653
44.48560.66790.95782.26621.16534.45130.0969-0.3996-0.48490.27770.2199-0.50760.19580.6356-0.30150.39940.0709-0.1460.4979-0.03270.4653-32.2804-33.6646-2.366
53.169-0.16420.17763.66750.59613.05410.0166-0.1263-0.15860.08960.04290.0750.25070.1002-0.03870.1939-0.05230.03080.1740.03160.1704-48.6091-28.2349-7.2342
63.5550.4049-0.13383.72480.6643.111-0.0495-0.00620.36520.06180.05260.2075-0.1547-0.0342-0.00430.1687-0.0331-0.02280.1320.0160.1876-48.3071-13.0565-14.5811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 464 through 530 )
2X-RAY DIFFRACTION2chain 'A' and (resid 531 through 631 )
3X-RAY DIFFRACTION3chain 'A' and (resid 632 through 751 )
4X-RAY DIFFRACTION4chain 'B' and (resid 464 through 530 )
5X-RAY DIFFRACTION5chain 'B' and (resid 531 through 631 )
6X-RAY DIFFRACTION6chain 'B' and (resid 632 through 752 )

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