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- PDB-7tng: Kringle domain of human Receptor Tyrosine Kinase-Like Orphan Rece... -

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Basic information

Entry
Database: PDB / ID: 7tng
TitleKringle domain of human Receptor Tyrosine Kinase-Like Orphan Receptor 1 (ROR1)
ComponentsInactive tyrosine-protein kinase transmembrane receptor ROR1
KeywordsSIGNALING PROTEIN / Receptor tyrosine kinase / Cancer / Kringle domain / Immunotherapy
Function / homology
Function and homology information


WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt receptor activity / Wnt-protein binding / astrocyte development / inner ear development / coreceptor activity / stress fiber / axon terminus / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway ...WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt receptor activity / Wnt-protein binding / astrocyte development / inner ear development / coreceptor activity / stress fiber / axon terminus / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / sensory perception of sound / : / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / receptor complex / cell population proliferation / axon / cell surface / ATP binding / plasma membrane / cytoplasm
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. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Similarity search - Domain/homology
Inactive tyrosine-protein kinase transmembrane receptor ROR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGuarino, S.R. / Di Bello, A. / Palamini, M. / Forneris, F.
Funding support United States, Switzerland, Italy, Japan, Belgium, 7items
OrganizationGrant numberCountry
The Giovanni Armenise-Harvard FoundationCDA 2013 United States
Velux Stiftung1375 Switzerland
Italian Association for Cancer ResearchMFAG 20075 Italy
Mizutani Foundation for Glycoscience200039 Japan
NATO Science for Peace and Security ProgramSPS G5701 Belgium
Ministero dell Universita e della RicercaPRIN2017RPHBCW_001 Italy
Ministero dell Universita e della RicercaDipartimento di Eccellenza 2018-2022 Italy
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structure of the kringle domain of human receptor tyrosine kinase-like orphan receptor 1 (hROR1)
Authors: Guarino, S.R. / Palamini, M. / Capillo, M.C. / Forneris, F.
History
DepositionJan 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inactive tyrosine-protein kinase transmembrane receptor ROR1


Theoretical massNumber of molelcules
Total (without water)9,6471
Polymers9,6471
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.157, 48.157, 69.021
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

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Components

#1: Protein Inactive tyrosine-protein kinase transmembrane receptor ROR1 / Neurotrophic tyrosine kinase / receptor-related 1


Mass: 9646.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROR1, NTRKR1 / Cell (production host): T7 SHuffle / Production host: Escherichia coli (E. coli) / References: UniProt: Q01973
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.4 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.8-1.2 M Sodium citrate tribasic dihydrate, 0.1 M sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.4→41.71 Å / Num. obs: 18755 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 15.82 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.063 / Net I/σ(I): 18.3
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 938 / CC1/2: 0.737 / Rpim(I) all: 0.494

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BA5,6OSN

6ba5

6osn


Resolution: 1.4→41.71 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.079 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21394 1007 5.4 %RANDOM
Rwork0.21113 ---
obs0.21127 17717 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.007 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.09 Å20 Å2
2--0.19 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 1.4→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms676 0 0 63 739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.013741
X-RAY DIFFRACTIONr_bond_other_d0.0020.018628
X-RAY DIFFRACTIONr_angle_refined_deg2.1581.6611015
X-RAY DIFFRACTIONr_angle_other_deg1.6441.5851460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.845596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.83922.27344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86615109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.029155
X-RAY DIFFRACTIONr_chiral_restr0.130.293
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02888
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02190
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0961.76360
X-RAY DIFFRACTIONr_mcbond_other3.0871.756359
X-RAY DIFFRACTIONr_mcangle_it3.3352.63452
X-RAY DIFFRACTIONr_mcangle_other3.3312.632453
X-RAY DIFFRACTIONr_scbond_it4.2861.882381
X-RAY DIFFRACTIONr_scbond_other4.2761.88381
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5122.715559
X-RAY DIFFRACTIONr_long_range_B_refined4.06720.516848
X-RAY DIFFRACTIONr_long_range_B_other4.07420.246839
X-RAY DIFFRACTIONr_rigid_bond_restr4.83931368
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.615 66 -
Rwork0.556 1291 -
obs--99.56 %

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