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- PDB-4o38: Crystal structure of the human cyclin G associated kinase (GAK) -

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Basic information

Entry
Database: PDB / ID: 4o38
TitleCrystal structure of the human cyclin G associated kinase (GAK)
ComponentsCyclin-G-associated kinase
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / protein kinase / serine/threonine kinase / cyclin G / p53 / clathrine / membrane trafficking / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding / Cell cycle / Cell junction / Golgi apparatus / Kinase / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


regulation of clathrin coat assembly / Golgi to lysosome transport / synaptic vesicle uncoating / protein localization to Golgi apparatus / clathrin coat disassembly / clathrin coat assembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding ...regulation of clathrin coat assembly / Golgi to lysosome transport / synaptic vesicle uncoating / protein localization to Golgi apparatus / clathrin coat disassembly / clathrin coat assembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding / Golgi Associated Vesicle Biogenesis / Golgi organization / chaperone cofactor-dependent protein refolding / intracellular transport / cyclin binding / receptor-mediated endocytosis / protein localization to plasma membrane / negative regulation of neuron projection development / presynapse / Clathrin-mediated endocytosis / protein-folding chaperone binding / vesicle / non-specific serine/threonine protein kinase / intracellular membrane-bounded organelle / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / perinuclear region of cytoplasm / Golgi apparatus / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain ...Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Protein-tyrosine phosphatase-like / C2 domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / 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
SUCCINIC ACID / Cyclin-G-associated kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.097 Å
AuthorsZhang, R. / Hatzos-Skintges, C. / Weger, A. / Chaikuad, A. / Eswaran, J. / Fedorov, O. / King, O. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...Zhang, R. / Hatzos-Skintges, C. / Weger, A. / Chaikuad, A. / Eswaran, J. / Fedorov, O. / King, O. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the human cyclin G associated kinase (GAK)
Authors: Zhang, R. / Hatzos-Skintges, C. / Weger, A. / Chaikuad, A. / Eswaran, J. / Fedorov, O. / King, O. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Joachimiak, A.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJan 1, 2014ID: 3LL6
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Cyclin-G-associated kinase
B: Cyclin-G-associated kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8266
Polymers76,4052
Non-polymers4204
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-21 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.425, 103.425, 131.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-589-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 26 - 334 / Label seq-ID: 17 - 325

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe dimeric form in the asymmetric unit could occur at high concentration, and represent an inactive form of the kinase. Monomeric state is the active form.

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Components

#1: Protein Cyclin-G-associated kinase


Mass: 38202.582 Da / Num. of mol.: 2 / Fragment: kinase domain (11-347)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O14976, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0M succinic acid, 0.1M Bis-Tris Propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.97912
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.979121
ReflectionResolution: 2.097→74.11 Å / Num. all: 48311 / Num. obs: 48245 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 36.6
Reflection shellResolution: 2.097→2.14 Å / Redundancy: 14 % / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2356 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.097→74.11 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.986 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.144 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19502 2442 5.1 %RANDOM
Rwork0.16469 ---
obs0.1662 45803 99.77 %-
all-48245 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.877 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.44 Å2
Refine analyzeLuzzati coordinate error obs: 0.265 Å
Refinement stepCycle: LAST / Resolution: 2.097→74.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 28 254 4550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194426
X-RAY DIFFRACTIONr_bond_other_d0.0050.024294
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9835988
X-RAY DIFFRACTIONr_angle_other_deg1.0139889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96524.412204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40215762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0661528
X-RAY DIFFRACTIONr_chiral_restr0.0910.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214989
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02999
X-RAY DIFFRACTIONr_mcbond_it3.0333.0972184
X-RAY DIFFRACTIONr_mcbond_other3.033.0952183
X-RAY DIFFRACTIONr_mcangle_it4.7394.6062724
X-RAY DIFFRACTIONr_mcangle_other4.7394.6072725
X-RAY DIFFRACTIONr_scbond_it4.1223.5842242
X-RAY DIFFRACTIONr_scbond_other4.063.5812240
X-RAY DIFFRACTIONr_scangle_other6.4075.1723255
X-RAY DIFFRACTIONr_long_range_B_refined10.41125.2674955
X-RAY DIFFRACTIONr_long_range_B_other10.4125.2764956
Refine LS restraints NCS

Ens-ID: 1 / Number: 15976 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.097→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 189 -
Rwork0.223 3286 -
obs--98.86 %
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)
17.89680.92031.71443.56360.88634.48510.0120.1789-0.1029-0.2253-0.11640.4270.0604-0.34580.10430.36450.0280.02080.2451-0.0090.146964.598677.54812.2767
22.1611-0.1049-1.2230.9016-0.71361.4020.01490.12830.17010.06570.1056-0.0569-0.0654-0.191-0.12050.30330.03260.06740.2253-0.04310.145862.636468.643421.0942
30.812-0.3337-0.87671.34020.68491.2994-0.01640.1251-0.1594-0.0114-0.14170.0780.005-0.12030.1580.26040.04030.11510.1848-0.09540.157271.74248.89268.87
44.9846-0.3629-1.621111.06873.073613.6905-0.4679-0.0243-1.41950.4437-0.11120.15441.7448-0.62370.57920.58250.01550.30310.05370.04160.475256.627331.241647.6705
51.920.4201-1.88840.4999-0.511.9222-0.3056-0.1103-0.2976-0.1957-0.0566-0.09110.37190.07210.36210.31610.0540.0740.2328-0.02920.127553.058846.780444.3326
60.6523-0.1761-0.8460.71650.08121.21040.07180.1025-0.0728-0.196-0.1265-0.06140.0216-0.05480.05480.26010.04250.010.2492-0.05320.077449.118258.686840.1171
71.5832-0.4919-0.51980.68920.19053.36930.03590.05540.0113-0.0192-0.12390.06950.0717-0.17620.0880.22910.0462-0.00680.2489-0.0680.11433963.581450.1803
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 68
2X-RAY DIFFRACTION2A69 - 128
3X-RAY DIFFRACTION3A129 - 334
4X-RAY DIFFRACTION4B26 - 64
5X-RAY DIFFRACTION5B65 - 169
6X-RAY DIFFRACTION6B170 - 262
7X-RAY DIFFRACTION7B263 - 337

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