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- PDB-5wno: Crystal structure of C. elegans LET-23 kinase domain complexed wi... -

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Basic information

Entry
Database: PDB / ID: 5wno
TitleCrystal structure of C. elegans LET-23 kinase domain complexed with AMP-PNP
ComponentsReceptor tyrosine-protein kinase let-23
KeywordsTRANSFERASE / Receptor tyrosine-protein kinase / dimerization / inactive conformation / cell signaling / Let-23 / C. elegans
Function / homology
Function and homology information


vulval cell fate specification / SHC1 events in ERBB2 signaling / Nuclear signaling by ERBB4 / Downregulation of ERBB4 signaling / GAB1 signalosome / : / Sema4D induced cell migration and growth-cone collapse / Signal transduction by L1 / ERBB2 Regulates Cell Motility / ERBB2 Activates PTK6 Signaling ...vulval cell fate specification / SHC1 events in ERBB2 signaling / Nuclear signaling by ERBB4 / Downregulation of ERBB4 signaling / GAB1 signalosome / : / Sema4D induced cell migration and growth-cone collapse / Signal transduction by L1 / ERBB2 Regulates Cell Motility / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / Signaling by ERBB2 / Downregulation of ERBB2 signaling / Extra-nuclear estrogen signaling / positive regulation of vulval development / PIP3 activates AKT signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR downregulation / PI3K events in ERBB2 signaling / EGFR Transactivation by Gastrin / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / nematode larval development / ovulation / multicellular organism development / male genitalia development / sleep / positive regulation of kinase activity / epidermal growth factor receptor activity / plasma membrane => GO:0005886 / lateral plasma membrane / transmembrane receptor protein tyrosine kinase activity / basal plasma membrane / determination of adult lifespan / cell surface receptor protein tyrosine kinase signaling pathway / epidermal growth factor receptor signaling pathway / receptor protein-tyrosine kinase / cell-cell junction / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / basolateral plasma membrane / receptor complex / apical plasma membrane / positive regulation of cell population proliferation / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily ...Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Receptor tyrosine-protein kinase let-23
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.386 Å
AuthorsLiu, L. / Thaker, T.M. / Jura, N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM109176 United States
Susan G. Komen FoundationCCR14299947 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F32CA216928 United States
CitationJournal: Structure / Year: 2018
Title: Regulation of Kinase Activity in the Caenorhabditis elegans EGF Receptor, LET-23.
Authors: Liu, L. / Thaker, T.M. / Freed, D.M. / Frazier, N. / Malhotra, K. / Lemmon, M.A. / Jura, N.
History
DepositionAug 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_first ..._citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor tyrosine-protein kinase let-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4803
Polymers37,9501
Non-polymers5312
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-11 kcal/mol
Surface area14460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.097, 77.978, 106.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Receptor tyrosine-protein kinase let-23 / Lethal protein 23


Mass: 37949.613 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 866-1191)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: let-23, kin-7, ZK1067.1 / Plasmid: pFASTbac HTa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: P24348, receptor protein-tyrosine kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG5000 MME, 0.20 M sodium chloride, 0.10 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.386→63 Å / Num. obs: 16320 / % possible obs: 98.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 65.15 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.8
Reflection shellResolution: 2.386→2.46 Å / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RIX

4rix


Resolution: 2.386→40.936 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 790 4.86 %
Rwork0.2155 --
obs0.217 16260 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.386→40.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2441 0 32 11 2484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022529
X-RAY DIFFRACTIONf_angle_d0.4553417
X-RAY DIFFRACTIONf_dihedral_angle_d13.0791508
X-RAY DIFFRACTIONf_chiral_restr0.038371
X-RAY DIFFRACTIONf_plane_restr0.003433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3858-2.53530.35981100.33132505X-RAY DIFFRACTION97
2.5353-2.7310.36871430.30682489X-RAY DIFFRACTION98
2.731-3.00570.3191490.27732529X-RAY DIFFRACTION98
3.0057-3.44050.3181260.25862600X-RAY DIFFRACTION100
3.4405-4.33390.23661230.21492631X-RAY DIFFRACTION99
4.3339-40.94230.19861390.17512716X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -27.0873 Å / Origin y: 4.4576 Å / Origin z: -19.5396 Å
111213212223313233
T0.617 Å2-0.0501 Å20.024 Å2-0.3749 Å2-0.0112 Å2--0.3961 Å2
L3.8207 °2-2.4783 °2-1.0755 °2-5.9929 °21.3228 °2--4.5331 °2
S0.118 Å °-0.0713 Å °-0.1482 Å °-0.0917 Å °-0.1816 Å °0.089 Å °0.4808 Å °-0.1488 Å °0.0508 Å °
Refinement TLS groupSelection details: all

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