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- PDB-5twh: human MOB1A bound to MST1 phosphorylated T367 peptide -

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Basic information

Entry
Database: PDB / ID: 5twh
Titlehuman MOB1A bound to MST1 phosphorylated T367 peptide
Components
  • MOB kinase activator 1A
  • T367 peptide
KeywordsSIGNALING PROTEIN / complex
Function / homology
Function and homology information


positive regulation of hepatocyte apoptotic process / cell differentiation involved in embryonic placenta development / regulation of 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 substrate-dependent cell migration, cell attachment to substrate / endocardium development / negative regulation of organ growth / hippo signaling ...positive regulation of hepatocyte apoptotic process / cell differentiation involved in embryonic placenta development / regulation of 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 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 / hepatocyte apoptotic process / protein kinase activator activity / 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 protein binding / positive regulation of peptidyl-serine phosphorylation / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / protein autophosphorylation / nuclear body / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / 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 / cytoplasm / cytosol
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. / Butyryl-CoA Dehydrogenase, subunit A; domain 3 ...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: 2.5 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: T367 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0763
Polymers27,0112
Non-polymers651
Water39622
1
A: MOB kinase activator 1A
E: T367 peptide
hetero molecules

A: MOB kinase activator 1A
E: T367 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1526
Polymers54,0214
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4500 Å2
ΔGint-33 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.986, 60.986, 138.486
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-402-

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 T367 peptide


Mass: 1898.934 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.: 22 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
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: 16434 / % possible obs: 98.2 % / Redundancy: 2.8 % / Net I/σ(I): 30

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.5→26.997 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 455 4.81 %
Rwork0.2283 --
obs0.2298 9451 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→26.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 1 22 1579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051597
X-RAY DIFFRACTIONf_angle_d0.7952177
X-RAY DIFFRACTIONf_dihedral_angle_d15.672930
X-RAY DIFFRACTIONf_chiral_restr0.053243
X-RAY DIFFRACTIONf_plane_restr0.005279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.86160.33571530.27242828X-RAY DIFFRACTION95
2.8616-3.60390.27561460.26562997X-RAY DIFFRACTION99
3.6039-26.99890.23361560.20273171X-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)
12.0005-0.324-1.44938.1686-2.33956.10820.0681-0.23230.09060.8211-0.2883-0.1649-0.38620.1410.27650.3991-0.1197-0.08070.3739-0.03740.336423.542840.471442.9249
23.08231.07920.37923.8077-0.37814.9059-0.45680.08240.32670.1905-0.19390.48260.0506-0.20880.18730.3225-0.0250.06790.32150.02730.392612.793236.175739.4364
30.19190.5463-0.88452.2719-3.60875.7477-0.18540.3867-0.2104-0.33170.21780.71450.7092-0.9433-0.05920.6694-0.3973-0.0141.1035-0.12590.69230.012424.552224.889
41.88211.6973-0.32594.6208-0.10763.16770.11760.3641-0.6144-0.020.1250.76711.1769-0.86540.02670.807-0.27820.01310.6494-0.10010.67341.922916.916536.6466
50.9866-1.29531.16775.5141.60434.0158-0.55650.218-0.60710.52250.15410.79540.2152-1.0457-0.03240.7748-0.35750.17521.1653-0.12150.9777-7.243826.77142.5778
66.52672.2314-1.23591.0769-0.44690.6791-0.26530.11790.3933-0.0997-0.11931.04490.1452-1.0268-0.26950.4658-0.10750.10840.7174-0.01840.7136-0.181233.684438.7557
70.0332-0.5083-0.34288.93065.65573.65910.0177-0.36350.13650.58920.13420.6671-0.5039-0.41710.25040.68330.02110.190.541-0.07710.62416.561146.405649.4914
83.12850.6502-0.27414.27870.15654.85-0.10670.1967-0.35490.4006-0.04070.27420.9115-0.45610.20750.3902-0.10650.11620.3064-0.02350.435112.391727.545739.8153
90.13350.10220.40550.08450.31851.2271-0.143-0.2616-0.4781.4403-0.11280.3771.0845-0.28550.00231.0634-0.00470.3989-0.2735-0.16720.734216.594916.828238.5247
102.7726-3.86583.43955.3908-4.79754.2695-0.373-1.5935-0.12941.845-0.7641-0.8845-1.0151.12621.0541.0688-0.2752-0.21071.59060.11750.98390.116813.992542.0997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 86 )
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 95 )
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 110 )
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 126 )
7X-RAY DIFFRACTION7chain 'A' and (resid 127 through 136 )
8X-RAY DIFFRACTION8chain 'A' and (resid 137 through 201 )
9X-RAY DIFFRACTION9chain 'A' and (resid 202 through 211 )
10X-RAY DIFFRACTION10chain 'E' and (resid 6 through 9 )

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