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- PDB-4jiz: Human Mob1-phosphopeptide complex -

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Basic information

Entry
Database: PDB / ID: 4jiz
TitleHuman Mob1-phosphopeptide complex
Components
  • MOB kinase activator 1A
  • phosphopeptide
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


hippo signaling / Signaling by Hippo / protein kinase activator activity / positive regulation of protein phosphorylation / extracellular exosome / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
MOB kinase activator 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStach, L. / Ogrodowicz, R.W. / Rock, J.M. / Lim, D. / Yaffe, M.B. / Amon, A. / Smerdon, S.J.
CitationJournal: Science / Year: 2013
Title: Activation of the yeast Hippo pathway by phosphorylation-dependent assembly of signaling complexes.
Authors: Rock, J.M. / Lim, D. / Stach, L. / Ogrodowicz, R.W. / Keck, J.M. / Jones, M.H. / Wong, C.C. / Yates, J.R. / Winey, M. / Smerdon, S.J. / Yaffe, M.B. / Amon, A.
History
DepositionMar 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Nov 27, 2013Group: Structure summary
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_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
B: phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3783
Polymers21,3122
Non-polymers651
Water88349
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-6 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.490, 59.600, 53.420
Angle α, β, γ (deg.)90.00, 104.65, 90.00
Int Tables number4
Space group name H-MP1211

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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: 20236.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C2orf6, MOB1, MOB1A, MOB4B, MOBK1B, MOBKL1B / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H8S9
#2: Protein/peptide phosphopeptide


Mass: 1076.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.: 49 / 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: 2.49 Å3/Da / Density % sol: 50.65 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→60 Å / Num. all: 12390 / Num. obs: 10903 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39.047 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.38 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 505 4.79 %random
Rwork0.178 ---
all0.231 10562 --
obs0.1803 10057 87.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 1 49 1549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031541
X-RAY DIFFRACTIONf_angle_d0.7352090
X-RAY DIFFRACTIONf_dihedral_angle_d16.887564
X-RAY DIFFRACTIONf_chiral_restr0.043224
X-RAY DIFFRACTIONf_plane_restr0.003265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.21070.3046790.23991711X-RAY DIFFRACTION52
2.2107-2.34920.30641130.21992410X-RAY DIFFRACTION74
2.3492-2.53060.24891700.20183040X-RAY DIFFRACTION93
2.5306-2.78520.23081510.19643231X-RAY DIFFRACTION100
2.7852-3.1880.25431740.19523260X-RAY DIFFRACTION100
3.188-4.01590.21331700.16193251X-RAY DIFFRACTION100
4.0159-39.05350.19981540.15913210X-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)
12.3878-0.2531-1.23840.813-0.11197.2984-0.2937-0.1972-0.54570.36350.2077-0.25651.18150.7101-1.55051.05270.0835-0.120.4684-0.3157-0.0633-1.0335-6.9941-24.3958
20.2519-0.37660.07340.4775-0.14460.0316-0.03980.0843-0.5997-0.84540.02810.93410.0165-0.2854-0.03190.4178-0.0734-0.08280.3581-0.03360.3752-11.6559-0.5936-14.1605
30.2142-0.1040.19590.2726-0.19630.1918-0.14780.0339-0.29170.42260.2010.0448-0.0358-0.07670.00060.26120.01640.03820.2270.02070.2766-9.14958.90344.6559
40.1102-0.27680.03720.6038-0.14440.23430.0419-0.0933-0.0772-0.24590.14210.626-0.2146-0.28360.00660.18840.0357-0.03130.29070.04560.3779-14.778314.7965-7.4947
50.14340.0486-0.016-0.0001-0.01040.0069-0.02290.0883-0.0079-0.23250.04170.0912-0.017-0.87610.01021.0087-0.0705-0.37040.7109-0.01660.5631-18.80186.9256-26.3994
60.15260.0254-0.03730.40660.30710.24680.26230.0356-0.1095-0.31750.12090.4749-0.2181-0.18540.03930.25240.0269-0.06470.17750.02370.2051-7.51657.5671-13.8089
70.08350.11340.13740.1620.18750.2585-0.0304-0.21050.0770.4345-0.12480.24980.1087-0.3504-0.01730.33160.0101-0.00360.27420.10660.345-9.5065-6.42435.3172
80.5614-0.19730.27950.1458-0.1730.19770.29570.0232-0.498-0.7579-0.080.31440.24010.12850.01050.3364-0.0015-0.00830.2147-0.05310.2212-2.3953-4.0319-11.0541
90.10910.11590.09350.16130.0490.21720.1396-0.3238-0.1586-0.33240.0724-0.41430.00290.124-0.00030.20610.0270.01550.20640.00860.2634.49614.3166-7.7935
100.07610.0766-0.00560.0758-0.04590.0340.03610.21740.5033-0.103-0.1702-0.2008-0.18620.05860.00090.27010.0297-0.00690.23030.06780.2774-1.573619.3451-2.5518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 54 )
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 74 )
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 105 )
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 115 )
6X-RAY DIFFRACTION6chain 'A' and (resid 116 through 144 )
7X-RAY DIFFRACTION7chain 'A' and (resid 145 through 154 )
8X-RAY DIFFRACTION8chain 'A' and (resid 155 through 172 )
9X-RAY DIFFRACTION9chain 'A' and (resid 173 through 190 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 8 )

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