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- PDB-6bhc: Crystal structure of pseduokinase PEAK1 (Sugen Kinase 269) -

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Basic information

Entry
Database: PDB / ID: 6bhc
TitleCrystal structure of pseduokinase PEAK1 (Sugen Kinase 269)
ComponentsPseudopodium-enriched atypical kinase 1
KeywordsTRANSFERASE / Pseudokinase
Function / homology
Function and homology information


focal adhesion assembly / regulation of focal adhesion assembly / substrate adhesion-dependent cell spreading / non-membrane spanning protein tyrosine kinase activity / cell migration / actin cytoskeleton / protein autophosphorylation / protein kinase activity / protein phosphorylation / focal adhesion ...focal adhesion assembly / regulation of focal adhesion assembly / substrate adhesion-dependent cell spreading / non-membrane spanning protein tyrosine kinase activity / cell migration / actin cytoskeleton / protein autophosphorylation / protein kinase activity / protein phosphorylation / focal adhesion / identical protein binding / cytoplasm
Similarity search - Function
Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Inactive tyrosine-protein kinase PEAK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHa, B.H. / Boggon, T.J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS085078 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM109487 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM114621 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102262 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The crystal structure of pseudokinase PEAK1 (Sugen kinase 269) reveals an unusual catalytic cleft and a novel mode of kinase fold dimerization.
Authors: Ha, B.H. / Boggon, T.J.
History
DepositionOct 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: 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
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: Pseudopodium-enriched atypical kinase 1


Theoretical massNumber of molelcules
Total (without water)50,1481
Polymers50,1481
Non-polymers00
Water1,838102
1
A: Pseudopodium-enriched atypical kinase 1

A: Pseudopodium-enriched atypical kinase 1


Theoretical massNumber of molelcules
Total (without water)100,2972
Polymers100,2972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area2360 Å2
ΔGint-30 kcal/mol
Surface area35580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.923, 72.724, 103.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Pseudopodium-enriched atypical kinase 1 / Sugen kinase 269 / Tyrosine-protein kinase SgK269


Mass: 50148.320 Da / Num. of mol.: 1 / Mutation: S1542T and deletion from 1409 to 1451
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEAK1, KIAA2002 / Plasmid: pET22b / Details (production host): Uncleavable C-terminal 6xHis tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q9H792, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100 mM N-(2-Acetamido) iminodiacetic acid (ADA) pH 6.8, 11 % (v/v) PEG 3350
PH range: 6.5 - 7.5

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 31, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20320 / % possible obs: 98.7 % / Redundancy: 6.6 % / Rpim(I) all: 0.087 / Rrim(I) all: 0.228 / Net I/σ(I): 10.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1919 / CC1/2: 0.823 / Rpim(I) all: 0.443 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000v712data reduction
HKL-2000v712data scaling
BALBESccp4 onlinephasing
ARP/wARPARP/wARP onlinemodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WQM

2wqm


Resolution: 2.3→42.081 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.88
RfactorNum. reflection% reflection
Rfree0.234 955 4.77 %
Rwork0.1938 --
obs0.1958 20019 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 0 102 3081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023041
X-RAY DIFFRACTIONf_angle_d0.4184115
X-RAY DIFFRACTIONf_dihedral_angle_d14.121864
X-RAY DIFFRACTIONf_chiral_restr0.037471
X-RAY DIFFRACTIONf_plane_restr0.003523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.42140.28911360.21452611X-RAY DIFFRACTION97
2.4214-2.57310.26051340.21412728X-RAY DIFFRACTION99
2.5731-2.77170.27061040.20742725X-RAY DIFFRACTION99
2.7717-3.05060.26581430.21042714X-RAY DIFFRACTION99
3.0506-3.49190.20891270.1922682X-RAY DIFFRACTION97
3.4919-4.39860.18931580.16682749X-RAY DIFFRACTION100
4.3986-42.08790.25091530.19662855X-RAY DIFFRACTION98
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)
13.52580.4917-1.84160.46730.10523.05380.1632-0.13310.21920.0286-0.10220.3085-0.2897-0.3953-0.08670.33310.087-0.00540.3188-0.0170.3981-22.69922.487726.9616
22.2644-0.3633-1.0222.46690.33211.50740.1108-0.0902-0.06430.3009-0.09120.1578-0.0133-0.17350.02450.1827-0.0213-0.01490.17430.00710.1424-13.1932-6.596531.0978
32.4719-0.25860.00462.70260.33893.1852-0.0244-0.5089-0.09350.6691-0.0632-0.19060.09360.08840.05360.3236-0.0149-0.03420.23720.09890.23620.9066-14.732337.925
40.83690.1876-0.84441.5225-0.35993.87460.0395-0.1313-0.1169-0.044-0.0846-0.22750.18970.27260.03770.19320.0032-0.00710.16270.00810.20116.0828-5.931316.7193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1285 through 1455 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1456 through 1578 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1579 through 1645 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1646 through 1744 )

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