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- PDB-5ncn: Crystal structure Dbf2(NTR)-Mob1 complex -

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Basic information

Entry
Database: PDB / ID: 5ncn
TitleCrystal structure Dbf2(NTR)-Mob1 complex
Components
  • Cell cycle protein kinase DBF2
  • DBF2 kinase activator protein MOB1
KeywordsSIGNALING PROTEIN / kinase
Function / homology
Function and homology information


: / Sid2-Mob1 complex / protein serine/threonine kinase activity => GO:0004674 / nuclear division / mitotic spindle pole body / kinase regulator activity / serine/threonine protein kinase complex / regulation of exit from mitosis / cellular bud neck / vacuolar acidification ...: / Sid2-Mob1 complex / protein serine/threonine kinase activity => GO:0004674 / nuclear division / mitotic spindle pole body / kinase regulator activity / serine/threonine protein kinase complex / regulation of exit from mitosis / cellular bud neck / vacuolar acidification / exit from mitosis / spindle pole body / protein kinase activator activity / mitotic cytokinesis / chromosome, centromeric region / nuclear periphery / regulation of cytokinesis / regulation of protein localization / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of protein phosphorylation / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / RNA binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / Protein kinase, C-terminal / Protein kinase C terminal domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal ...MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / Protein kinase, C-terminal / Protein kinase C terminal domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
PHOSPHATE ION / Cell cycle protein kinase DBF2 / DBF2 kinase activator protein MOB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.501 Å
AuthorsGogl, G. / Remenyi, A. / Parker, B. / Weiss, E.
CitationJournal: Biochemistry / Year: 2020
Title: Ndr/Lats Kinases Bind Specific Mob-Family Coactivators through a Conserved and Modular Interface.
Authors: Parker, B.W. / Gogl, G. / Balint, M. / Hetenyi, C. / Remenyi, A. / Weiss, E.L.
History
DepositionMar 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DBF2 kinase activator protein MOB1
B: Cell cycle protein kinase DBF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3047
Polymers38,9182
Non-polymers3865
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-43 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.620, 108.620, 135.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-402-

PO4

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Components

#1: Protein DBF2 kinase activator protein MOB1 / MPS1 binder 1 / Maintenance of ploidy protein MOB1


Mass: 27584.428 Da / Num. of mol.: 1 / Fragment: UNP Residues 79-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MOB1, YIL106W / Production host: Escherichia coli (E. coli) / References: UniProt: P40484
#2: Protein Cell cycle protein kinase DBF2 / / Dumbbell forming protein 2


Mass: 11334.040 Da / Num. of mol.: 1 / Fragment: UNP Residues 85-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: DBF2, YGR092W / Production host: Escherichia coli (E. coli)
References: UniProt: P22204, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8.5
Details: 100mM Bicine/Tris, 30mM LiCl, 30mM NaCl, 30mM KCl, 30mM RbCl, 12.5% (w/v) PEG1000, 12.5% (w/v) PEG3350, 12.5% (v/v) MPD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→44.423 Å / Num. obs: 6385 / % possible obs: 99.9 % / Redundancy: 24.6 % / CC1/2: 0.99 / Rrim(I) all: 0.75 / Net I/σ(I): 9.34
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 25.8 % / Mean I/σ(I) obs: 1.49 / CC1/2: 0.791 / Rrim(I) all: 3.69 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2420: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BRK

5brk


Resolution: 3.501→44.423 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 322 5.07 %
Rwork0.2179 --
obs0.2199 6350 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.501→44.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 17 0 2041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012091
X-RAY DIFFRACTIONf_angle_d0.7562841
X-RAY DIFFRACTIONf_dihedral_angle_d13.412751
X-RAY DIFFRACTIONf_chiral_restr0.047307
X-RAY DIFFRACTIONf_plane_restr0.004366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5009-4.41010.28921630.24172915X-RAY DIFFRACTION100
4.4101-44.42640.23921590.20463113X-RAY DIFFRACTION100
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)
11.54751.4587-2.16713.6293-2.99613.52310.9246-0.2287-0.80631.22830.6248-0.41-1.07570.51070.59481.0595-0.0391-0.17320.9345-0.21870.7042-27.9219-37.9056-16.807
20.0424-0.0236-0.02090.0339-0.02230.02-0.1010.35670.2102-0.17240.4481-0.08610.16110.0574-01.4729-0.21010.24270.8537-0.00470.7818-27.6084-22.653-20.2485
30.23360.5289-0.27730.5061-0.15420.2599-0.22940.7056-0.5082-0.4440.2474-0.127-0.1544-0.575-0.01410.6712-0.1052-0.01360.2340.07950.5864-31.0405-27.2951-2.8616
40.1428-0.0872-0.04820.0513-0.01050.0486-0.6822-0.82250.5394-1.01150.11830.31830.6995-0.452500.869-0.0751-0.06230.68830.06570.7676-31.7465-37.093917.7365
50.5099-0.08-0.4652-0.02140.07310.37150.02160.3343-0.2818-0.4638-0.1569-0.1328-0.2877-0.4483-00.5162-0.00950.03980.50730.05150.6128-17.8774-29.816115.1775
60.0930.0495-0.07070.06920.12170.28430.28670.20710.3584-0.2034-0.5826-0.24020.00520.444300.5439-0.0839-0.07850.479-0.04420.5707-27.7573-22.59518.9802
70.0713-0.01820.11310.3859-0.17710.1320.09860.59760.6529-0.137-0.2292-0.91040.14240.215800.68910.06440.11380.5230.04240.6335-26.4033-12.904-6.0706
81.5793-1.0453-0.92870.3710.29520.7809-0.05380.1191-0.2841-0.6255-0.0822-0.67930.49460.0463-0.00260.4699-0.0545-0.0110.3476-0.06590.4789-24.3516-36.11430.4607
90.00410.01980.00550.01880.02240.013-0.1832-0.1146-0.9876-0.21761.01120.42920.60680.4811-01.30950.04630.21961.31550.60221.5703-17.6478-43.8984-5.3785
101.4429-0.2663-1.05431.44620.09541.0401-0.04830.1648-0.5648-0.4661-0.4899-0.0653-0.73310.5683-0.35280.6816-0.0108-0.11660.4867-0.05320.5121-39.4462-31.3636-13.0847
110.0216-0.02620.0050.00340.0017-0.00610.5553-0.55170.34960.87240.21520.50890.16010.559-01.9759-0.1747-0.02691.3377-0.21811.0527-32.6517-13.6882-42.0989
121.0063-0.2363-0.69250.2434-0.12040.61320.2209-0.38990.1067-0.52670.13010.06790.24650.65370.01331.2080.0153-0.11930.49140.08710.691-35.2253-16.21-19.713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 137 through 146 )
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 152 )
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 174 )
4X-RAY DIFFRACTION4chain 'A' and (resid 175 through 184 )
5X-RAY DIFFRACTION5chain 'A' and (resid 185 through 209 )
6X-RAY DIFFRACTION6chain 'A' and (resid 210 through 225 )
7X-RAY DIFFRACTION7chain 'A' and (resid 226 through 247 )
8X-RAY DIFFRACTION8chain 'A' and (resid 248 through 305 )
9X-RAY DIFFRACTION9chain 'A' and (resid 306 through 312 )
10X-RAY DIFFRACTION10chain 'B' and (resid 97 through 138 )
11X-RAY DIFFRACTION11chain 'B' and (resid 139 through 148 )
12X-RAY DIFFRACTION12chain 'B' and (resid 149 through 172 )

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