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- PDB-3zzw: Crystal structure of the kinase domain of ROR2 -

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Basic information

Entry
Database: PDB / ID: 3zzw
TitleCrystal structure of the kinase domain of ROR2
ComponentsTYROSINE-PROTEIN KINASE TRANSMEMBRANE RECEPTOR ROR2
KeywordsTRANSFERASE / NEUROTROPHIC TYROSINE KINASE / RECEPTOR-RELATED 2 / ROR2 / NTRKR2 / KINASE / STRUCTURAL GENOMICS CONSORTIUM / SGC
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 / transmembrane receptor protein tyrosine kinase activity / positive regulation of synaptic transmission, glutamatergic / clathrin-coated endocytic vesicle membrane / positive regulation of neuron projection development / receptor protein-tyrosine kinase / Wnt signaling pathway / cell surface receptor protein tyrosine kinase signaling pathway / postsynapse / microtubule / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration / phosphorylation / dendrite / neuronal cell body / glutamatergic synapse / 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. / Immunoglobulin I-set / Kringle domain / Immunoglobulin I-set domain / Kringle / Kringle, conserved site ...Tyrosine-protein kinase, receptor ROR / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Immunoglobulin I-set / Kringle domain / Immunoglobulin I-set domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / 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
Tyrosine-protein kinase transmembrane receptor ROR2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Graslund, S. / Karlberg, T. / Nyman, T. ...Tresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Graslund, S. / Karlberg, T. / Nyman, T. / Schuler, H. / Thorsell, A.G. / Weigelt, J. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the Kinase Domain of Ror2
Authors: Tresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Graslund, S. / Karlberg, T. / Nyman, T. / Schuler, H. / Thorsell, A.G. / Weigelt, J. / Nordlund, P.
History
DepositionSep 5, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)66,5567
Polymers66,1362
Non-polymers4205
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-77.2 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.613, 61.301, 79.936
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, 0.0063, -0.0142), (0.0007, 0.9314, 0.364), (0.0155, 0.3639, -0.9313)
Vector: 20.4936, -6.7889, 35.5104)

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Components

#1: Protein TYROSINE-PROTEIN KINASE TRANSMEMBRANE RECEPTOR ROR2


Mass: 33067.961 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 463-751
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: MAMMALIAN GENE COLLECTION, OPEN BIOSYSTEMS (MGC)
Plasmid: PFBOH-MHL / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q01974, receptor protein-tyrosine kinase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 40.7 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2M AMMONIUM ACETATE, 2.2M AMMONIUM SULFATE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.9→3.06 Å / Num. obs: 12094 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 64.07 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.4
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 0.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JIV

2jiv


Resolution: 2.9→46.77 Å / Cor.coef. Fo:Fc: 0.8831 / Cor.coef. Fo:Fc free: 0.84 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.416
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 578 4.79 %RANDOM
Rwork0.1874 ---
obs0.1903 12075 99.7 %-
Displacement parametersBiso mean: 56.14 Å2
Baniso -1Baniso -2Baniso -3
1-21.0494 Å20 Å2-1.6921 Å2
2---19.6934 Å20 Å2
3----1.356 Å2
Refine analyzeLuzzati coordinate error obs: 0.355 Å
Refinement stepCycle: LAST / Resolution: 2.9→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4250 0 21 36 4307
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094388HARMONIC2
X-RAY DIFFRACTIONt_angle_deg15962HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1971SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes643HARMONIC5
X-RAY DIFFRACTIONt_it4388HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion3.11
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion533SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5124SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.18 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2937 134 4.68 %
Rwork0.2121 2729 -
all0.216 2863 -
obs--99.7 %
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)
14.6395-4.42633.255604.13353.3343-0.20750.83280.2048-0.12030.3713-0.3037-0.345-0.3382-0.16380.4183-0.25530.0684-0.21510.152-0.257211.9999-4.0306-14.4285
26.7642-1.08214.027510.7177-0.57837.9886-0.07630.54970.04720.03490.1357-0.9548-0.02560.9518-0.05950.0489-0.1040.2327-0.25030.0152-0.058618.8173-10.6818-4.3958
30.8931.77980.13052.4888-0.50784.6914-0.2990.075-0.2364-0.54370.24360.47080.0396-0.11780.05550.0256-0.0332-0.0043-0.365-0.0221-0.0806-1.0389-8.1443-3.7913
43.12080.30570.56341.459-0.28422.68720.0361-0.24940.1343-0.0314-0.0516-0.0315-0.0399-0.2510.01550.04190.02340.1008-0.1795-0.010.057-5.0607-4.050312.9946
53.6697-1.93010.23676.9321-2.46630.0451-0.225-0.53640.0377-0.0349-0.05620.0689-0.0367-0.08550.2812-0.04880.03670.1663-0.07880.1176-0.06324.7387-16.484242.5934
60.18191.8329-1.76281.7087-0.2372.5025-0.2315-1.1371-0.29210.2923-0.08240.00540.41380.54190.3138-0.03290.14280.04960.2560.20390.065518.0865-16.018239.6199
74.2047-0.4984-0.99311.6804-0.17661.8971-0.1655-0.7259-0.11320.12240.01810.0170.00550.26020.1474-0.2186-0.02780.0477-0.1469-0.0069-0.139120.9493-7.017326.7867
82.0231-0.0356-1.31355.16041.8103-0.1467-0.289-0.0953-0.0791-0.04410.17990.114-0.16030.35530.1091-0.0999-0.040.050.1060.03-0.07432.9207-11.499619.8127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 466:501
2X-RAY DIFFRACTION2CHAIN A AND RESID 502:530
3X-RAY DIFFRACTION3CHAIN A AND RESID 531:632
4X-RAY DIFFRACTION4CHAIN A AND RESID 633:750
5X-RAY DIFFRACTION5CHAIN B AND RESID 466:528
6X-RAY DIFFRACTION6CHAIN B AND RESID 529:594
7X-RAY DIFFRACTION7CHAIN B AND RESID 595:706
8X-RAY DIFFRACTION8CHAIN B AND RESID 707:750

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