[English] 日本語
Yorodumi
- PDB-4lqp: Crystal structure of the Cbk1(T743E)-Mob2 kinase-coactivator comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lqp
TitleCrystal structure of the Cbk1(T743E)-Mob2 kinase-coactivator complex, in crystal form A
Components
  • CBK1 kinase activator protein MOB2
  • Serine/threonine-protein kinase CBK1
KeywordsTRANSFERASE/TRANSFERASE activator / Kinase / TRANSFERASE-TRANSFERASE activator complex
Function / homology
Function and homology information


budding cell apical bud growth / regulation of fungal-type cell wall organization / cellular bud / establishment or maintenance of actin cytoskeleton polarity / prospore membrane / incipient cellular bud site / cellular bud tip / septum digestion after cytokinesis / cellular bud neck / serine/threonine protein kinase complex ...budding cell apical bud growth / regulation of fungal-type cell wall organization / cellular bud / establishment or maintenance of actin cytoskeleton polarity / prospore membrane / incipient cellular bud site / cellular bud tip / septum digestion after cytokinesis / cellular bud neck / serine/threonine protein kinase complex / mating projection tip / regulation of protein secretion / establishment or maintenance of cell polarity / protein kinase activator activity / cytoplasmic stress granule / cell cortex / non-specific serine/threonine protein kinase / intracellular signal transduction / cell division / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / : / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / : / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / CBK1 kinase activator protein MOB2 / Serine/threonine-protein kinase CBK1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsGogl, G. / Remenyi, A.
CitationJournal: Plos Biol. / Year: 2015
Title: The Structure of an NDR/LATS Kinase-Mob Complex Reveals a Novel Kinase-Coactivator System and Substrate Docking Mechanism.
Authors: Gogl, G. / Schneider, K.D. / Yeh, B.J. / Alam, N. / Nguyen Ba, A.N. / Moses, A.M. / Hetenyi, C. / Remenyi, A. / Weiss, E.L.
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase CBK1
B: CBK1 kinase activator protein MOB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7063
Polymers87,2002
Non-polymers5061
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-9 kcal/mol
Surface area31850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.380, 129.380, 231.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Serine/threonine-protein kinase CBK1 / Cell wall biosynthesis kinase


Mass: 58784.582 Da / Num. of mol.: 1 / Fragment: UNP residues 251-756 / Mutation: D475A, T743E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CBK1, N1727, YNL161W / Production host: Escherichia coli (E. coli)
References: UniProt: P53894, non-specific serine/threonine protein kinase
#2: Protein CBK1 kinase activator protein MOB2 / MPS1 binder 2 / Maintenance of ploidy protein MOB2


Mass: 28415.197 Da / Num. of mol.: 1 / Fragment: UNP residues 46-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MOB2, YFL034C-B, YFL035C, YFL035C-A / Production host: Escherichia coli (E. coli) / References: UniProt: P43563
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.56 Å3/Da / Density % sol: 77.88 %
Crystal growTemperature: 296 K / Method: microbatch under oil / pH: 5.5
Details: 25% PEG 20,000 buffered with 0.1M Na-citrate, pH 5.5, Microbatch under oil, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 28, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.5→49.591 Å / Num. all: 12243 / Num. obs: 12238 / % possible obs: 98.9 % / Observed criterion σ(F): 2.83 / Observed criterion σ(I): 2.83
Reflection shellResolution: 4.5→4.66 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.5→49.59 Å / SU ML: 0.6 / σ(F): 1.35 / Phase error: 39.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3104 587 4.8 %RANDOM
Rwork0.2876 ---
obs0.2887 12110 99.79 %-
all-12243 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.5→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 31 0 4131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064237
X-RAY DIFFRACTIONf_angle_d1.6655781
X-RAY DIFFRACTIONf_dihedral_angle_d22.2011455
X-RAY DIFFRACTIONf_chiral_restr0.127643
X-RAY DIFFRACTIONf_plane_restr0.006743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5-4.95260.3461470.27912825X-RAY DIFFRACTION100
4.9526-5.66840.31771450.26942864X-RAY DIFFRACTION100
5.6684-7.13820.39351580.36652881X-RAY DIFFRACTION100
7.1382-49.59430.27691370.27093081X-RAY DIFFRACTION100

+
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