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- PDB-4c57: Structure of GAK kinase in complex with a nanobody -

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Basic information

Entry
Database: PDB / ID: 4c57
TitleStructure of GAK kinase in complex with a nanobody
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 disassembly / clathrin coat assembly / 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 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 / 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 / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
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: 2.55 Å
AuthorsChaikuad, A. / Keates, T. / Krojer, T. / Allerston, C.K. / 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. / 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: diffrn_source / entity ...diffrn_source / entity / entity_name_com / entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_entity_src_syn / struct_ref / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description ..._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: Cyclin-G-associated kinase
C: NANOBODY
D: NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,00314
Polymers107,7084
Non-polymers1,29510
Water3,333185
1
A: Cyclin-G-associated kinase
C: NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5648
Polymers53,8542
Non-polymers7106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint2.9 kcal/mol
Surface area24260 Å2
MethodPQS
2
B: Cyclin-G-associated kinase
D: NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4396
Polymers53,8542
Non-polymers5864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint2.6 kcal/mol
Surface area23400 Å2
MethodPQS
Unit cell
Length a, b, c (Å)75.160, 86.660, 83.910
Angle α, β, γ (deg.)90.00, 96.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Antibody , 2 types, 4 molecules ABCD

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


Mass: 38183.551 Da / Num. of mol.: 2 / 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: Antibody NANOBODY / Single-domain antibody


Mass: 15670.259 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 195 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: 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.: 2 / Source method: obtained synthetically / Formula: C20H19N3O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSYNTHETIC, NON-BIOLOGICAL PROTEIN

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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 7
Details: 14% PEG 3350, 0.2 M SODIUM SULFATE, 0.1 M BIS-TRIS PROPANE, PH 7.0, 10% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2012 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→83.39 Å / Num. obs: 34717 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 64.92 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.5
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / % possible all: 95.1

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LL6 AND 1OP9

3ll6
PDB Unreleased entry

1op9


Resolution: 2.55→74.68 Å / Cor.coef. Fo:Fc: 0.9439 / Cor.coef. Fo:Fc free: 0.9224 / SU R Cruickshank DPI: 0.455 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.432 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.261
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 1738 5.01 %RANDOM
Rwork0.1776 ---
obs0.1802 34695 99.02 %-
Displacement parametersBiso mean: 79.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.5385 Å20 Å20.8531 Å2
2--12.7107 Å20 Å2
3----11.1722 Å2
Refine analyzeLuzzati coordinate error obs: 0.422 Å
Refinement stepCycle: LAST / Resolution: 2.55→74.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 88 185 6923
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016904HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.099354HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3189SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes168HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1076HARMONIC5
X-RAY DIFFRACTIONt_it6904HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion2.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion893SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7761SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.63 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2623 140 4.95 %
Rwork0.2271 2689 -
all0.2288 2829 -
obs--99.02 %
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)
13.94592.20930.06963.64120.60051.09110.1093-0.31760.09820.1647-0.0819-0.10590.0511-0.0577-0.0274-0.2087-0.0028-0.0367-0.3285-0.0240.013-39.92519.149438.2198
23.0025-2.09510.25054.5040.65431.90180.23850.47610.0672-0.8896-0.0303-0.3491-0.26930.1211-0.20820.1642-0.02410.0513-0.2926-0.0413-0.2298-36.2954-3.13793.8978
35.2684-0.1252-0.55388.367-0.14951.9216-0.0061-0.2606-0.05270.54260.025-0.5732-0.1740.0108-0.0189-0.2748-0.024-0.1587-0.30920.00130.2937-9.232228.2444.287
410.98670.82111.21499.56990.70694.67330.4182-0.0710.5511-0.29850.0595-0.81420.41430.6577-0.4777-0.2124-0.01380.0099-0.1806-0.2207-0.1449-4.9575-21.60775.7779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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