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- PDB-8fe9: Crystal structure of Ack1 kinase K161Q mutant in complex with the... -

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Basic information

Entry
Database: PDB / ID: 8fe9
TitleCrystal structure of Ack1 kinase K161Q mutant in complex with the selective inhibitor (R)-9b
ComponentsActivated CDC42 kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / tyrosine kinase / inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / cytoophidium / GTPase inhibitor activity / Signaling by LTK / clathrin-coated vesicle / epidermal growth factor receptor binding / positive regulation of peptidyl-tyrosine phosphorylation / WW domain binding / phosphorylation ...regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / cytoophidium / GTPase inhibitor activity / Signaling by LTK / clathrin-coated vesicle / epidermal growth factor receptor binding / positive regulation of peptidyl-tyrosine phosphorylation / WW domain binding / phosphorylation / small GTPase-mediated signal transduction / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity / cytoplasmic vesicle membrane / adherens junction / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / endocytosis / protein tyrosine kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / endosome / protein serine kinase activity / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / : / : / SAM domain-like ...Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / : / : / SAM domain-like / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-WTP / Activated CDC42 kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPaung, Y. / Kan, Y. / Seeliger, M.S. / Miller, W.T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119437 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI164424 United States
Department of Veterans Affairs (VA, United States)BX002292 United States
CitationJournal: Biochemistry / Year: 2023
Title: Biochemical Studies of Systemic Lupus Erythematosus-Associated Mutations in Nonreceptor Tyrosine Kinases Ack1 and Brk.
Authors: Kan, Y. / Paung, Y. / Kim, Y. / Seeliger, M.A. / Miller, W.T.
History
DepositionDec 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 20, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entry_details.has_protein_modification / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Description: Ligand identity
Details: We were made aware that the previous model accidentally contained the wrong ligand. We don't know how the wrong ligand entered the previous structure. The ligand built now is the correct one ...Details: We were made aware that the previous model accidentally contained the wrong ligand. We don't know how the wrong ligand entered the previous structure. The ligand built now is the correct one that was used in the experiment.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8972
Polymers32,4941
Non-polymers4031
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.690, 91.690, 190.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Activated CDC42 kinase 1 / ACK-1 / Tyrosine kinase non-receptor protein 2


Mass: 32494.395 Da / Num. of mol.: 1 / Mutation: K161Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNK2, ACK1 / Plasmid: pFASTBAC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary
References: UniProt: Q07912, non-specific protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-WTP / 5-chloro-N~2~-[4-(4-methylpiperazin-1-yl)phenyl]-N~4~-{[(2R)-oxolan-2-yl]methyl}pyrimidine-2,4-diamine


Mass: 402.921 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27ClN6O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.05 M Bis-Tris (pH 5.8), 19% PEG3350, 0.3 M MgCl2, 2.5% glycerol
PH range: 6.0-6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.19→28.99 Å / Num. obs: 7020 / % possible obs: 99 % / Redundancy: 19.3 % / Biso Wilson estimate: 91.22 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 19.6
Reflection shellResolution: 3.2→3.28 Å / Rmerge(I) obs: 1.088 / Num. unique obs: 624 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
autoPROCdata processing
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→28.99 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5564
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2283 698 10.02 %
Rwork0.188 6266 -
obs0.1922 6964 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 106.1 Å2
Refinement stepCycle: LAST / Resolution: 3.2→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 28 0 2226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322283
X-RAY DIFFRACTIONf_angle_d0.6253092
X-RAY DIFFRACTIONf_chiral_restr0.0409333
X-RAY DIFFRACTIONf_plane_restr0.0041398
X-RAY DIFFRACTIONf_dihedral_angle_d14.4443858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.30561300.24551173X-RAY DIFFRACTION95.6
3.45-3.790.29051380.21161229X-RAY DIFFRACTION99.64
3.79-4.340.22771390.1841249X-RAY DIFFRACTION99.71
4.34-5.460.22221410.17891268X-RAY DIFFRACTION99.86
5.47-28.990.19711500.17651347X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 33.9464180607 Å / Origin y: 18.4997766693 Å / Origin z: 24.7594459404 Å
111213212223313233
T0.610259384937 Å2-0.0371372452538 Å20.0529394916041 Å2-0.5219681385 Å2-0.106391047872 Å2--0.621347367972 Å2
L2.76058997518 °20.171269087324 °2-1.81340361875 °2-5.07248759568 °2-3.45150484493 °2--8.25489601983 °2
S-0.111827737252 Å °0.0657118521988 Å °-0.464068791721 Å °-0.175508279064 Å °-0.0621514047368 Å °0.00216920962855 Å °0.848491419458 Å °0.0634947237596 Å °0.151306551499 Å °
Refinement TLS groupSelection details: ALL

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