[English] 日本語
Yorodumi
- PDB-5yf4: A kinase complex MST4-MOB4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yf4
TitleA kinase complex MST4-MOB4
Components
  • MOB-like protein phocein
  • Peptide from Serine/threonine-protein kinase 26
KeywordsPROTEIN BINDING / Kinase / Complex / Phosphorylation
Function / homology
Function and homology information


microvillus assembly / vesicle membrane / Golgi-associated vesicle / Golgi cisterna membrane / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cell periphery / kinase binding / cellular response to oxidative stress ...microvillus assembly / vesicle membrane / Golgi-associated vesicle / Golgi cisterna membrane / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cell periphery / kinase binding / cellular response to oxidative stress / regulation of apoptotic process / dendritic spine / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / apical plasma membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / protein homodimerization activity / extracellular exosome / ATP binding / membrane / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
MST4, kinase domain / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...MST4, kinase domain / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / 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
Similarity search - Domain/homology
Serine/threonine-protein kinase 26 / MOB-like protein phocein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.897 Å
AuthorsChen, M. / Zhou, Z.C.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The MST4-MOB4 complex disrupts the MST1-MOB1 complex in the Hippo-YAP pathway and plays a pro-oncogenic role in pancreatic cancer.
Authors: Chen, M. / Zhang, H. / Shi, Z. / Li, Y. / Zhang, X. / Gao, Z. / Zhou, L. / Ma, J. / Xu, Q. / Guan, J. / Cheng, Y. / Jiao, S. / Zhou, Z.C.
History
DepositionSep 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MOB-like protein phocein
B: Peptide from Serine/threonine-protein kinase 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1604
Polymers21,0292
Non-polymers1312
Water1,35175
1
A: MOB-like protein phocein
B: Peptide from Serine/threonine-protein kinase 26
hetero molecules

A: MOB-like protein phocein
B: Peptide from Serine/threonine-protein kinase 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3198
Polymers42,0584
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3420 Å2
ΔGint-34 kcal/mol
Surface area14400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.469, 33.997, 61.023
Angle α, β, γ (deg.)90.00, 122.67, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein MOB-like protein phocein / 2C4D / Class II mMOB1 / Mob1 homolog 3 / Mob3 / Mps one binder kinase activator-like 3 / ...2C4D / Class II mMOB1 / Mob1 homolog 3 / Mob3 / Mps one binder kinase activator-like 3 / Preimplantation protein 3


Mass: 18938.725 Da / Num. of mol.: 1 / Fragment: UNP residues 53-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOB4, MOB3, MOBKL3, PHOCN, PREI3, CGI-95 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus / References: UniProt: Q9Y3A3
#2: Protein/peptide Peptide from Serine/threonine-protein kinase 26 / / MST3 and SOK1-related kinase / Mammalian STE20-like protein kinase 4 / STE20-like kinase MST4 / ...MST3 and SOK1-related kinase / Mammalian STE20-like protein kinase 4 / STE20-like kinase MST4 / Serine/threonine-protein kinase MASK


Mass: 2090.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9P289, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES, pH 7.5, 30% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.897→50 Å / Num. obs: 12086 / % possible obs: 98.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.046 / Rrim(I) all: 0.119 / Net I/σ(I): 15.5
Reflection shellResolution: 1.897→1.965 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.798 / Num. unique obs: 1123 / CC1/2: 0.715 / Rpim(I) all: 0.365 / Rrim(I) all: 0.881 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.897→30.038 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.71 / Stereochemistry target values: ML
Details: The number of reflections containing anomalous reflections used in refinement is 18533. Non-anomalous reflections in data collection and refinement are 12086 and 12079 respectively.
RfactorNum. reflection% reflection
Rfree0.1977 1865 10.06 %
Rwork0.1527 --
obs0.1572 12079 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.897→30.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 2 75 1180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111168
X-RAY DIFFRACTIONf_angle_d1.2461589
X-RAY DIFFRACTIONf_dihedral_angle_d8.527912
X-RAY DIFFRACTIONf_chiral_restr0.063176
X-RAY DIFFRACTIONf_plane_restr0.007203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.897-1.94830.2598840.2432757X-RAY DIFFRACTION48
1.9483-2.00560.242900.2134823X-RAY DIFFRACTION50
2.0056-2.07030.2168950.1905847X-RAY DIFFRACTION52
2.0703-2.14430.21271030.1749912X-RAY DIFFRACTION55
2.1443-2.23010.16891150.15591020X-RAY DIFFRACTION62
2.2301-2.33160.17371380.14011252X-RAY DIFFRACTION77
2.3316-2.45450.19071650.1441428X-RAY DIFFRACTION88
2.4545-2.60820.19011850.15581607X-RAY DIFFRACTION96
2.6082-2.80940.21121760.16271548X-RAY DIFFRACTION96
2.8094-3.09190.23351790.16471631X-RAY DIFFRACTION99
3.0919-3.53870.18821740.14451617X-RAY DIFFRACTION99
3.5387-4.4560.21781770.13181607X-RAY DIFFRACTION98
4.456-30.0420.16641840.14971619X-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)
17.98430.93971.97582.12760.47484.28940.51810.803-0.9547-0.8494-0.10830.3730.98590.2336-0.35320.50240.0402-0.13670.273-0.04450.3596-0.7868.13017.9558
23.86310.88390.61265.7028-0.76233.2152-0.0047-0.17250.04890.41720.01360.2876-0.1409-0.0402-0.01250.1262-0.00150.01560.1227-0.01030.1125-0.255912.094626.7066
33.55090.0667-0.26562.9192-0.63413.03860.020.2839-0.3592-0.34020.03160.34640.3105-0.2644-0.0190.1463-0.0087-0.03070.1107-0.00990.1496-3.9039.524616.4
41.55440.35791.92372.0067-0.49628.25040.0980.61170.2402-0.54760.097-0.3207-0.21150.6246-0.30130.2695-0.05820.0650.2750.03080.17987.214220.09738.7536
57.92940.02820.95415.28560.30994.2025-0.33260.37690.2932-0.71150.1950.3544-0.2925-0.60970.16350.2856-0.0008-0.06410.23420.0340.131-6.368418.19785.0262
64.81852.26755.31487.33173.87857.2604-0.13780.22560.6801-0.0644-0.16551.1952-0.1303-1.32350.27170.24960.0181-0.05380.5330.05710.4224-11.18519.801411.9046
75.5252-2.1928-0.70973.64360.09717.17950.0431-1.32330.07321.26980.22660.4893-0.0237-0.202-0.21010.29420.01460.12870.4326-0.03780.3538-11.751711.412630.4093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 67 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 173 )
4X-RAY DIFFRACTION4chain 'A' and (resid 174 through 185 )
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 210 )
7X-RAY DIFFRACTION7chain 'B' and (resid 323 through 333 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more