[English] 日本語
Yorodumi
- PDB-5b5v: Structure of full-length MOB1b -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b5v
TitleStructure of full-length MOB1b
ComponentsMOB kinase activator 1B
KeywordsMETAL BINDING PROTEIN / MOB1 Hippo pathway
Function / homology
Function and homology information


regulation of protein autophosphorylation / Signaling by Hippo / hippo signaling / kinase activator activity / protein kinase activator activity / kinase binding / positive regulation of protein phosphorylation / nucleus / metal ion binding / cytoplasm
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 1B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.193 Å
AuthorsKIM, S.-Y. / Tachioka, Y. / Mori, T. / Hakoshima, T.
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for autoinhibition and its relief of MOB1 in the Hippo pathway
Authors: Kim, S.Y. / Tachioka, Y. / Mori, T. / Hakoshima, T.
History
DepositionMay 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MOB kinase activator 1B
B: MOB kinase activator 1B
C: MOB kinase activator 1B
D: MOB kinase activator 1B
E: MOB kinase activator 1B
F: MOB kinase activator 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,99412
Polymers151,6626
Non-polymers3336
Water2,684149
1
A: MOB kinase activator 1B
C: MOB kinase activator 1B
E: MOB kinase activator 1B
F: MOB kinase activator 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3108
Polymers101,1084
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-18 kcal/mol
Surface area18440 Å2
MethodPISA
2
B: MOB kinase activator 1B
D: MOB kinase activator 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6854
Polymers50,5542
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-15 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.355, 127.686, 59.294
Angle α, β, γ (deg.)90.00, 91.03, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 25276.984 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mob1b, Mobkl1a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BPB0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 1.48 Å3/Da / Density % sol: 16.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ammonium fluoride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.19→30 Å / Num. obs: 44345 / % possible obs: 99.3 % / Redundancy: 3.6 % / Net I/σ(I): 37.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.193→29.673 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.63 / Stereochemistry target values: ML
Details: AUTHORS STATE THAT THE LINKERS BETWEEN THE CAHIN E/F AND CHAIN A/C WERE POORLY DEFINED ON THE CURRENT MAP.
RfactorNum. reflection% reflection
Rfree0.2463 2209 5.03 %
Rwork0.2333 --
obs0.234 43936 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.193→29.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6170 0 6 149 6325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146360
X-RAY DIFFRACTIONf_angle_d1.3918596
X-RAY DIFFRACTIONf_dihedral_angle_d20.2792300
X-RAY DIFFRACTIONf_chiral_restr0.061920
X-RAY DIFFRACTIONf_plane_restr0.0061102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1928-2.24050.3789890.34081826X-RAY DIFFRACTION69
2.2405-2.29260.31861410.29812677X-RAY DIFFRACTION100
2.2926-2.34990.31871510.29152671X-RAY DIFFRACTION100
2.3499-2.41340.31991320.28852648X-RAY DIFFRACTION100
2.4134-2.48440.30971320.2742719X-RAY DIFFRACTION100
2.4844-2.56450.33981500.28732674X-RAY DIFFRACTION100
2.5645-2.65610.35381400.28092631X-RAY DIFFRACTION100
2.6561-2.76240.2781500.27092674X-RAY DIFFRACTION100
2.7624-2.8880.30521350.27262655X-RAY DIFFRACTION100
2.888-3.04010.33961620.27662663X-RAY DIFFRACTION100
3.0401-3.23040.28251290.26762691X-RAY DIFFRACTION100
3.2304-3.47950.25741470.2342703X-RAY DIFFRACTION100
3.4795-3.82890.21081460.22512636X-RAY DIFFRACTION100
3.8289-4.38150.18191290.19182703X-RAY DIFFRACTION99
4.3815-5.51440.19971450.19262654X-RAY DIFFRACTION99
5.5144-29.67540.21461310.21712502X-RAY DIFFRACTION91

+
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://pdbjlvh1.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