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- PDB-5twg: human MOB1A bound to human MST1 phosphorylated T353 peptide -

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Basic information

Entry
Database: PDB / ID: 5twg
Titlehuman MOB1A bound to human MST1 phosphorylated T353 peptide
Components
  • MOB kinase activator 1A
  • T353 peptide
KeywordsSIGNALING PROTEIN / complex
Function / homology
Function and homology information


positive regulation of hepatocyte apoptotic process / regulation of cell differentiation involved in embryonic placenta development / cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of hippo signaling / positive regulation of substrate-dependent cell migration, cell attachment to substrate / endocardium development / negative regulation of organ growth ...positive regulation of hepatocyte apoptotic process / regulation of cell differentiation involved in embryonic placenta development / cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of hippo signaling / positive regulation of substrate-dependent cell migration, cell attachment to substrate / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / organ growth / branching involved in blood vessel morphogenesis / protein kinase activator activity / hepatocyte apoptotic process / regulation of MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of fat cell differentiation / canonical Wnt signaling pathway / keratinocyte differentiation / protein serine/threonine kinase activator activity / epithelial cell proliferation / central nervous system development / protein tetramerization / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / protein import into nucleus / negative regulation of epithelial cell proliferation / positive regulation of peptidyl-serine phosphorylation / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / protein autophosphorylation / nuclear body / non-specific serine/threonine protein kinase / protein stabilization / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / magnesium ion binding / signal transduction / protein homodimerization activity / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
MOB kinase activator / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / SARAH domain / SARAH domain profile. / : ...MOB kinase activator / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / SARAH domain / SARAH domain profile. / : / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / p53-like tetramerisation domain superfamily / 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
Serine/threonine-protein kinase 4 / MOB kinase activator 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsXiong, S. / Sicheri, F.
CitationJournal: Mol. Cell Proteomics / Year: 2017
Title: MOB1 Mediated Phospho-recognition in the Core Mammalian Hippo Pathway.
Authors: Couzens, A.L. / Xiong, S. / Knight, J.D.R. / Mao, D.Y. / Guettler, S. / Picaud, S. / Kurinov, I. / Filippakopoulos, P. / Sicheri, F. / Gingras, A.C.
History
DepositionNov 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MOB kinase activator 1A
E: T353 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7953
Polymers26,7292
Non-polymers651
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-8 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.660, 60.660, 138.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-418-

HOH

31A-423-

HOH

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Components

#1: Protein MOB kinase activator 1A / Mob1 alpha / Mob1A / Mob1 homolog 1B / Mps one binder kinase activator-like 1B


Mass: 25111.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOB1A, C2orf6, MOB4B, MOBK1B, MOBKL1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8S9
#2: Protein/peptide T353 peptide


Mass: 1617.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13043*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.1 M MES pH 6.0, 0.2 M LiCl and 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→56 Å / Num. obs: 11982 / % possible obs: 96.5 % / Redundancy: 2.8 % / Net I/σ(I): 30

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.3→45.602 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 578 4.82 %
Rwork0.2153 --
obs0.2172 11981 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→45.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 1 23 1596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131613
X-RAY DIFFRACTIONf_angle_d1.2992197
X-RAY DIFFRACTIONf_dihedral_angle_d18.434946
X-RAY DIFFRACTIONf_chiral_restr0.064242
X-RAY DIFFRACTIONf_plane_restr0.008282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.53140.35081490.28512794X-RAY DIFFRACTION100
2.5314-2.89770.31871340.25692787X-RAY DIFFRACTION98
2.8977-3.65060.2771360.24072843X-RAY DIFFRACTION99
3.6506-45.61140.21721590.18552979X-RAY DIFFRACTION98
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)
16.4484-1.42970.15158.06893.6419.422-0.1963-0.61150.64490.33380.2046-0.0988-0.30940.73250.20840.48420.0668-0.01440.53460.00340.409244.1378-21.9755.0905
24.06920.7032-0.05274.0147-2.05427.454-0.0363-0.2491-0.0971-0.0713-0.20860.0565-0.0175-0.17450.19180.39990.08250.05190.4745-0.06560.514535.1644-17.37097.3648
33.63781.11182.00361.9414-0.6822.4314-0.0004-0.37120.8103-0.2289-0.13960.0937-1.2452-0.52910.18791.05870.4618-0.14530.9069-0.11230.902523.02812.73010.5278
48.2905-1.96843.33993.2679-1.69296.9648-0.02750.22241.39340.1794-0.73610.0195-1.45030.01680.58210.81550.1366-0.12130.5229-0.11540.729133.48160.2964.0906
51.679-0.78041.51920.6951-0.73924.0320.60690.2126-0.01820.4009-0.0969-0.6973-0.41771.1787-0.50720.52780.0556-0.07240.9704-0.20150.8746.0629-6.460514.8301
64.7554-0.7488-0.87882.49590.63275.2428-0.2911-0.73150.8584-0.0415-0.17790.2201-1.0791-1.01160.65290.48050.1366-0.01530.5214-0.15960.694129.8939-8.06069.5768
74.9958-0.0898-3.05494.4672-0.04647.22570.37030.27660.0082-0.557-0.07030.43720.4307-1.2880.02010.45630.0697-0.06740.575-0.17250.602626.2967-16.6254-1.563
85.1739-0.67-2.06012.2626-2.03163.2474-0.151-0.5043-0.49120.3075-0.05651.418-0.186-1.24880.49950.44550.1008-0.04321.0293-0.2550.841918.7543-14.01868.9119
97.109-1.3375.39022.8604-0.15874.373-0.39132.4005-0.17580.16740.41330.98541.22590.74890.27281.09990.407-0.13021.3466-0.07910.90213.2684-0.23647.2218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 110 )
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 126 )
5X-RAY DIFFRACTION5chain 'A' and (resid 127 through 136 )
6X-RAY DIFFRACTION6chain 'A' and (resid 137 through 165 )
7X-RAY DIFFRACTION7chain 'A' and (resid 166 through 193 )
8X-RAY DIFFRACTION8chain 'A' and (resid 194 through 211 )
9X-RAY DIFFRACTION9chain 'E' and (resid 6 through 9 )

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