[English] 日本語
Yorodumi
- PDB-4c59: Structure of GAK kinase in complex with nanobody (NbGAK_4) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c59
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 / 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 / Clathrin-mediated endocytosis / presynapse / 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 / 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein Cyclin-G-associated kinase


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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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


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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more