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- PDB-4c58: Structure of GAK kinase in complex with nanobody (NbGAK_4) -

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Basic information

Entry
Database: PDB / ID: 4c58
TitleStructure of GAK kinase in complex with nanobody (NbGAK_4)
Components
  • Cyclin-G-associated kinase
  • nanobody
KeywordsTRANSFERASE / KINASE / CONFORMATIONAL PLASTICITY / ACTIVATION
Function / homology
Function and homology information


regulation of clathrin coat assembly / Golgi to lysosome transport / synaptic vesicle uncoating / clathrin coat disassembly / protein localization to Golgi apparatus / 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 / clathrin coat disassembly / protein localization to Golgi apparatus / clathrin coat assembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding / Golgi Associated Vesicle Biogenesis / Golgi organization / : / intracellular transport / receptor-mediated endocytosis / cyclin binding / protein localization to plasma membrane / presynapse / Clathrin-mediated endocytosis / negative regulation of neuron projection development / protein-folding chaperone binding / vesicle / non-specific serine/threonine protein kinase / protein serine kinase activity / focal adhesion / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / perinuclear region of cytoplasm / Golgi apparatus / ATP binding / membrane / cytosol
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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-824 / Cyclin-G-associated kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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 6, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / exptl_crystal_grow / pdbx_entity_src_syn / struct_ref / struct_ref_seq / 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 / _entity.pdbx_description / _entity.src_method / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg
Revision 1.3Dec 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)53,7846
Polymers53,2692
Non-polymers5154
Water3,495194
1
A: Cyclin-G-associated kinase
hetero molecules

A: Cyclin-G-associated kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2728
Polymers76,3672
Non-polymers9056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area5140 Å2
ΔGint-10.3 kcal/mol
Surface area24850 Å2
MethodPISA
2
B: nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1482
Polymers15,0861
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.866, 37.430, 76.010
Angle α, β, γ (deg.)90.00, 108.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cyclin-G-associated kinase


Mass: 38183.551 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 27-351
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


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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-824 / 9-HYDROXY-4-PHENYLPYRROLO[3,4-C]CARBAZOLE-1,3(2H,6H)-DIONE / 9-HYDROXY-4-PHENYL-6H-PYRROLO[3,4-C]CARBAZOLE-1,3-DIONE


Mass: 328.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H12N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 12% PEG 3350, 0.13 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: 2.16→45.09 Å / Num. obs: 22748 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.3
Reflection shellResolution: 2.16→2.28 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3LL6 AND 1OP9

3ll6
PDB Unreleased entry

1op9


Resolution: 2.16→38.38 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.053 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24172 1170 5.1 %RANDOM
Rwork0.17929 ---
obs0.18241 21576 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.243 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å2-1.23 Å2
2--2.15 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.16→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 37 194 3216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193120
X-RAY DIFFRACTIONr_bond_other_d0.0010.022123
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.9714229
X-RAY DIFFRACTIONr_angle_other_deg0.9213.0035170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.555400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14523.913138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26815531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1431522
X-RAY DIFFRACTIONr_chiral_restr0.0960.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02637
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 82 -
Rwork0.277 1525 -
obs--99.44 %
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)
110.5536-1.5509-1.50010.98760.60364.38630.2041.6098-0.3602-0.4354-0.232-0.11090.37270.47110.0280.37650.11770.0560.6761-0.01750.11128.38820.609-52.33
22.5798-0.01990.81541.2211-0.43723.1942-0.00110.4803-0.038-0.122-0.0277-0.0780.15830.17460.02880.0878-0.00610.00610.1032-0.00480.005732.37919.509-29.424
32.15530.53040.42432.60371.52963.86260.1497-0.05770.19990.1028-0.08210.2307-0.31930.1362-0.06760.1523-0.03540.02880.0154-0.02260.050426.71831.61-1.116
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 89
2X-RAY DIFFRACTION2A90 - 333
3X-RAY DIFFRACTION3B1 - 128

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