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- PDB-4c59: Structure of GAK kinase in complex with nanobody (NbGAK_4) -

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Basic information

Entry
Database: PDB / ID: 4c59
TitleStructure of GAK kinase in complex with nanobody (NbGAK_4)
Components
  • Cyclin-G-associated kinaseGAK (protein)
  • NANOBODYSingle-domain antibody
KeywordsTRANSFERASE / KINASE / CONFORMATIONAL PLASTICITY / ACTIVATION
Function / homology
Function and homology information


regulation of clathrin coat assembly / synaptic vesicle uncoating / Golgi to lysosome transport / protein localization to Golgi apparatus / clathrin coat assembly / clathrin coat disassembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding ...regulation of clathrin coat assembly / synaptic vesicle uncoating / Golgi to lysosome transport / protein localization to Golgi apparatus / clathrin coat assembly / clathrin coat disassembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding / Golgi Associated Vesicle Biogenesis / Golgi organization / chaperone cofactor-dependent protein refolding / intracellular transport / receptor-mediated endocytosis / cyclin binding / 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 / cell cycle / phosphorylation / focal adhesion / protein serine kinase activity / intracellular membrane-bounded organelle / 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 / C2 domain superfamily / Protein-tyrosine phosphatase-like / 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 / Immunoglobulins / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-FEF / Cyclin-G-associated kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
LAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChaikuad, A. / Keates, T. / Allerston, C.K. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Muller-Knapp, S.
CitationJournal: Biochem. J. / Year: 2014
Title: Structure of cyclin G-associated kinase (GAK) trapped in different conformations using nanobodies.
Authors: Chaikuad, A. / Keates, T. / Vincke, C. / Kaufholz, M. / Zenn, M. / Zimmermann, B. / Gutierrez, C. / Zhang, R.G. / Hatzos-Skintges, C. / Joachimiak, A. / Muyldermans, S. / Herberg, F.W. / Knapp, S. / Muller, S.
History
DepositionSep 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Feb 20, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / diffrn_source / entity / entity_name_com / entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_entity_src_syn / struct_biol / struct_ref / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity.src_method / _pdbx_database_status.recvd_author_approval / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6343
Polymers53,2692
Non-polymers3651
Water1,13563
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-3.6 kcal/mol
Surface area22740 Å2
MethodPQS
Unit cell
Length a, b, c (Å)174.268, 37.753, 75.546
Angle α, β, γ (deg.)90.00, 111.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cyclin-G-associated kinase / GAK (protein)


Mass: 38183.551 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 14-351
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(DE3) / Variant (production host): R3
References: UniProt: O14976, non-specific serine/threonine protein kinase
#2: Protein NANOBODY / Single-domain antibody


Mass: 15085.511 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-FEF / (2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME}


Mass: 365.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N3O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSYNTHETIC, NON-BIOLOGICAL SEQUENCE

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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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7.5 / Details: 9% PEG 3350, 0.06 M MAGNESIUM FORMATE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0121
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2012 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0121 Å / Relative weight: 1
ReflectionResolution: 2.8→19.75 Å / Num. obs: 11580 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3LL6 AND 1OP9

3ll6
PDB Unreleased entry

1op9


Resolution: 2.8→19.75 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.877 / SU B: 32.781 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26163 549 4.7 %RANDOM
Rwork0.20238 ---
obs0.20516 11028 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.577 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å20 Å22.81 Å2
2---0.39 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2957 0 27 63 3047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193065
X-RAY DIFFRACTIONr_bond_other_d0.0010.022892
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.9554155
X-RAY DIFFRACTIONr_angle_other_deg0.653.0016634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1915391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51124.015132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16615512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.831519
X-RAY DIFFRACTIONr_chiral_restr0.0610.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023635
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02716
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_it1.2563.4671552
X-RAY DIFFRACTIONr_mcbond_other1.2563.4671551
X-RAY DIFFRACTIONr_mcangle_it2.1455.1931935
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4293.651513
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 38 -
Rwork0.284 805 -
obs--99.41 %
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)
17.60950.61212.61259.68671.2779.43810.01781.1998-0.14070.10160.30820.82060.4936-0.6995-0.3260.20450.08110.05440.96750.00930.272317.522522.6278-63.1537
27.15990.008-0.51191.0963-0.49341.59620.07391.0909-0.1634-0.2974-0.0853-0.01960.0746-0.13060.01140.17640.0434-0.00520.26230.04650.099525.508823.3375-49.438
36.08270.714-2.00133.0148-0.90166.535-0.14990.3474-0.41140.0022-0.0902-0.20680.57540.17780.240.08150.0262-0.02820.06740.00680.159840.163117.5156-36.1982
44.22982.6604-0.66715.80241.76172.56610.2774-0.34490.4330.3068-0.10310.1409-0.23940.2496-0.17430.0965-0.0497-0.00940.0457-0.03570.131947.284331.2258-16.5329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 55
2X-RAY DIFFRACTION2A56 - 200
3X-RAY DIFFRACTION3A201 - 333
4X-RAY DIFFRACTION4B1 - 128

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