[English] 日本語
Yorodumi
- PDB-5ncl: Crystal structure of the Cbk1-Mob2 kinase-coactivator complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ncl
TitleCrystal structure of the Cbk1-Mob2 kinase-coactivator complex with an SSD1 peptide
Components
  • CBK1 kinase activator protein MOB2
  • Protein SSD1
  • Serine/threonine-protein kinase CBK1
KeywordsSIGNALING PROTEIN / kinase
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 / septum digestion after cytokinesis / cellular bud tip / intracellular mRNA localization / cellular bud neck ...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 / septum digestion after cytokinesis / cellular bud tip / intracellular mRNA localization / cellular bud neck / serine/threonine protein kinase complex / mating projection tip / regulation of G1 to G0 transition / regulation of protein secretion / establishment or maintenance of cell polarity / mRNA catabolic process / protein kinase activator activity / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / P-body / mRNA 5'-UTR binding / cytoplasmic stress granule / cell cortex / 3'-5'-RNA exonuclease activity / non-specific serine/threonine protein kinase / negative regulation of translation / intracellular signal transduction / cell division / protein serine kinase activity / protein serine/threonine kinase activity / mRNA binding / signal transduction / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
DIS3-like exonuclease 2, C-terminal / DIS3-like exonuclease 2 C terminal / MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site ...DIS3-like exonuclease 2, C-terminal / DIS3-like exonuclease 2 C terminal / MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / : / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Nucleic acid-binding, OB-fold / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Protein SSD1 / 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: 3.15 Å
AuthorsGogl, G. / Remenyi, A. / Parker, B. / Weiss, E.
CitationJournal: Biochemistry / Year: 2020
Title: Ndr/Lats Kinases Bind Specific Mob-Family Coactivators through a Conserved and Modular Interface.
Authors: Parker, B.W. / Gogl, G. / Balint, M. / Hetenyi, C. / Remenyi, A. / Weiss, E.L.
History
DepositionMar 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase CBK1
B: CBK1 kinase activator protein MOB2
D: Protein SSD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8784
Polymers88,3723
Non-polymers5061
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-25 kcal/mol
Surface area30820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.430, 79.990, 117.590
Angle α, β, γ (deg.)90.00, 117.60, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 58756.566 Da / Num. of mol.: 1 / Fragment: UNP Residues 251-756
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CBK1, YNL161W, N1727 / 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)
Gene: MOB2, YFL034C-B, YFL035C, YFL035C-A / Production host: Escherichia coli (E. coli) / References: UniProt: P43563
#3: Protein/peptide Protein SSD1 / Protein SRK1


Mass: 1200.273 Da / Num. of mol.: 1 / Fragment: UNP Residues 205-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SSD1, CLA1, RLD1, SRK1, YDR293C, D9819.4 / Production host: Escherichia coli (E. coli) / References: UniProt: P24276
#4: 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: 4.06 Å3/Da / Density % sol: 69.7 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 5.5 / Details: 25% PEG 20,000 BUFFERED WITH 0.1M NA-CITRATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→44.595 Å / Num. obs: 19888 / % possible obs: 99.7 % / Redundancy: 7.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.168 / Net I/σ(I): 9.37
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1455 / CC1/2: 0.804 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(dev_2420: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BRK

5brk


Resolution: 3.15→44.595 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.74
RfactorNum. reflection% reflection
Rfree0.2982 1000 5.03 %
Rwork0.2333 --
obs0.2367 19880 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.15→44.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4715 0 31 0 4746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014871
X-RAY DIFFRACTIONf_angle_d1.2926629
X-RAY DIFFRACTIONf_dihedral_angle_d18.2232851
X-RAY DIFFRACTIONf_chiral_restr0.061728
X-RAY DIFFRACTIONf_plane_restr0.008848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1502-3.31620.42561350.33262707X-RAY DIFFRACTION100
3.3162-3.52390.32231500.27382643X-RAY DIFFRACTION100
3.5239-3.79590.35621330.25532699X-RAY DIFFRACTION100
3.7959-4.17760.29511310.23272694X-RAY DIFFRACTION100
4.1776-4.78150.33461350.21182687X-RAY DIFFRACTION100
4.7815-6.02190.27581600.23932698X-RAY DIFFRACTION100
6.0219-44.59960.24711560.20262752X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.7981 Å / Origin y: -13.6636 Å / Origin z: 19.783 Å
111213212223313233
T0.5771 Å20.0641 Å2-0.0951 Å2-0.4364 Å2-0.0049 Å2--0.6904 Å2
L3.0984 °21.2111 °20.084 °2-1.364 °2-0.0843 °2--1.7696 °2
S0.0937 Å °-0.9606 Å °0.278 Å °0.3043 Å °-0.2705 Å °-0.1846 Å °-0.0896 Å °0.3524 Å °0.0467 Å °
Refinement TLS groupSelection details: all

+
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