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- PDB-5z55: NMR Solution Structure of the Kringle domain of human receptor ty... -

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Basic information

Entry
Database: PDB / ID: 5z55
TitleNMR Solution Structure of the Kringle domain of human receptor tyrosine kinase-like orphan receptor 1 (ROR1)
ComponentsInactive tyrosine-protein kinase transmembrane receptor ROR1
KeywordsONCOPROTEIN / ROR1 / Kringle
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 / axon terminus / stress fiber / transmembrane receptor protein tyrosine kinase activity / sensory perception of sound ...WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt receptor activity / Wnt-protein binding / astrocyte development / inner ear development / coreceptor activity / axon terminus / stress fiber / transmembrane receptor protein tyrosine kinase activity / sensory perception of sound / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of neuron projection development / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / receptor complex / phosphorylation / cell surface / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Tyrosine-protein kinase, receptor ROR / Plasminogen Kringle 4 / Plasminogen Kringle 4 / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Kringle domain / Kringle / Immunoglobulin I-set ...Tyrosine-protein kinase, receptor ROR / Plasminogen Kringle 4 / Plasminogen Kringle 4 / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Kringle domain / Kringle / Immunoglobulin I-set / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Inactive tyrosine-protein kinase transmembrane receptor ROR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMa, X. / Hu, K.F.
Funding support China, 5items
OrganizationGrant numberCountry
National Key Research and Development Program of China2017YFC0906900 China
National Natural Science Foundation of China21573258 China
National Natural Science Foundation of China81401904 China
Yunnan Provincial Science and Technology Department2015FA028 China
Yunnan Provincial Science and Technology Department2015FB170 China
CitationJournal: Biomol NMR Assign / Year: 2018
Title: Backbone and side-chain chemical shift assignments of the kringle domain of human receptor tyrosine kinase-like orphan receptor 1 (ROR1).
Authors: Ma, X. / Zhang, Y. / Liu, B. / Yang, J. / Hu, K.
History
DepositionJan 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,5631
Polymers9,5631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5220 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 96structures with the lowest energy
RepresentativeModel #1medoid

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Components

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


Mass: 9562.522 Da / Num. of mol.: 1 / Fragment: Kringle domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROR1, NTRKR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01973

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1HBHA(CO)NH
121isotropic1H(CCO)NH
131isotropic1C(CO)NH
141isotropic1CBCA (CO) NH
151isotropic1(Hali)CaliCaroHaro-TOCSY
161isotropic2HNCA
1151isotropic23D HN(CA)CB
1141isotropic23D HNCO
1131isotropic23D (H)CCH-TOCSY
1121isotropic23D CCH-TOCSY
1111isotropic22D 1H-15N HSQC
1101isotropic22D 1H-13C CT-HSQC
191isotropic23D 1H-15N NOESY
181isotropic23D 1H-13C NOESY aliphatic
171isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution / Contents: 0.8 mM 99%U-13C, U-15N ROR1Kr, 94% H2O/6% D2O
Details: Kringle domain of human receptor tyrosine kinase-like orphan receptor 1 (ROR1)
Label: 13C_15N_ROR1Kr / Solvent system: 94% H2O/6% D2O
SampleConc.: 0.8 mM / Component: ROR1Kr / Isotopic labeling: 99%U-13C, U-15N
Sample conditionsDetails: buffer: 25 mM Tris, 150 mM NaCl, 6% D2O and 0.02% NaN3 (w/v) at pH 8.0 and 298 K
Ionic strength: 150 mM / Label: conditions_1 / pH: 8.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 6
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 96 / Conformers submitted total number: 10

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