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- PDB-4wzx: ULK3 regulates cytokinetic abscission by phosphorylating ESCRT-II... -

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Basic information

Entry
Database: PDB / ID: 4wzx
TitleULK3 regulates cytokinetic abscission by phosphorylating ESCRT-III proteins
Components
  • IST1 homolog
  • Serine/threonine-protein kinase ULK3
KeywordsCELL CYCLE / MIT domain / ULK3 / MIM / IST1 / ESCRT
Function / homology
Function and homology information


MIT domain binding / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / ciliary tip / collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / positive regulation of collateral sprouting / fibroblast activation / phagophore assembly site membrane / midbody abscission ...MIT domain binding / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / ciliary tip / collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / positive regulation of collateral sprouting / fibroblast activation / phagophore assembly site membrane / midbody abscission / piecemeal microautophagy of the nucleus / multivesicular body assembly / positive regulation of smoothened signaling pathway / Flemming body / phagophore assembly site / reticulophagy / smoothened signaling pathway / response to starvation / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of proteolysis / autophagosome assembly / mitophagy / autophagosome / negative regulation of smoothened signaling pathway / establishment of protein localization / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H2AS121 kinase activity / histone H3S57 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / histone H2BS36 kinase activity / Rho-dependent protein serine/threonine kinase activity / Hedgehog 'on' state / histone H3S10 kinase activity / AMP-activated protein kinase activity / 3-phosphoinositide-dependent protein kinase activity / histone H3T11 kinase activity / histone H3T3 kinase activity / histone H3T45 kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / autophagy / azurophil granule lumen / cellular senescence / intracellular protein localization / nuclear envelope / protein transport / protein autophosphorylation / midbody / non-specific serine/threonine protein kinase / regulation of autophagy / cadherin binding / protein domain specific binding / cell division / protein serine kinase activity / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / protein-containing complex binding / chromatin / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase Atg1-like / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Vacuolar protein sorting-associated protein Ist1 / Vacuolar protein sorting-associated protein IST1-like / Regulator of Vps4 activity in the MVB pathway / MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Serine/threonine-protein kinase Atg1-like / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Vacuolar protein sorting-associated protein Ist1 / Vacuolar protein sorting-associated protein IST1-like / Regulator of Vps4 activity in the MVB pathway / MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / Methane Monooxygenase Hydroxylase; Chain G, 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, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / IST1 homolog / Serine/threonine-protein kinase ULK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3859 Å
AuthorsCaballe, A. / Wenzel, D.M. / Agromayor, M. / Alam, S.L. / Skalicky, J.J. / Kloc, M. / Carlton, J.G. / Labrador, L. / Sundquist, W.I. / Martin-Serrano, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM112080 United States
American Cancer SocietyPF-14-102-01-CSM United States
CitationJournal: Elife / Year: 2015
Title: ULK3 regulates cytokinetic abscission by phosphorylating ESCRT-III proteins.
Authors: Caballe, A. / Wenzel, D.M. / Agromayor, M. / Alam, S.L. / Skalicky, J.J. / Kloc, M. / Carlton, J.G. / Labrador, L. / Sundquist, W.I. / Martin-Serrano, J.
History
DepositionNov 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase ULK3
E: IST1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4424
Polymers13,2872
Non-polymers1552
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-25 kcal/mol
Surface area6410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.117, 79.117, 96.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

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Components

#1: Protein Serine/threonine-protein kinase ULK3 / Unc-51-like kinase 3


Mass: 10551.107 Da / Num. of mol.: 1 / Fragment: MIT 2 domain (UNP residues 359-449)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ULK3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL
References: UniProt: Q6PHR2, non-specific serine/threonine protein kinase
#2: Protein/peptide IST1 homolog / hIST1 / Putative MAPK-activating protein PM28


Mass: 2735.975 Da / Num. of mol.: 1 / Fragment: MIT-interacting motif (UNP residues 342-364) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P53990
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50mM MES pH 6.5, 5mM Cobalt chloride, 800mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→40.5 Å / Num. obs: 23604 / % possible obs: 99.2 % / Redundancy: 28.4 % / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.013 / Net I/σ(I): 66
Reflection shellResolution: 1.38→1.41 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.124 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.842 / Rpim(I) all: 0.638 / % possible all: 85.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3859→39.558 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.18 1993 8.49 %
Rwork0.1513 --
obs0.1537 23479 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3859→39.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 6 69 893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009837
X-RAY DIFFRACTIONf_angle_d1.1281117
X-RAY DIFFRACTIONf_dihedral_angle_d16.012331
X-RAY DIFFRACTIONf_chiral_restr0.047125
X-RAY DIFFRACTIONf_plane_restr0.005147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3859-1.42060.37641270.3251333X-RAY DIFFRACTION88
1.4206-1.4590.29951490.25671521X-RAY DIFFRACTION99
1.459-1.50190.26941400.2021511X-RAY DIFFRACTION99
1.5019-1.55040.22541360.19091558X-RAY DIFFRACTION99
1.5504-1.60580.24011380.17741513X-RAY DIFFRACTION99
1.6058-1.67010.20981520.16531534X-RAY DIFFRACTION99
1.6701-1.74610.2521340.161542X-RAY DIFFRACTION100
1.7461-1.83820.20641410.15291544X-RAY DIFFRACTION100
1.8382-1.95340.22791380.15621549X-RAY DIFFRACTION99
1.9534-2.10420.20161400.15661544X-RAY DIFFRACTION100
2.1042-2.31590.1711460.14081569X-RAY DIFFRACTION100
2.3159-2.6510.20651450.14761573X-RAY DIFFRACTION100
2.651-3.33970.17941530.15291570X-RAY DIFFRACTION100
3.3397-39.57450.14031540.13921625X-RAY DIFFRACTION99

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