[English] 日本語
Yorodumi
- EMDB-34200: Complex Structure of Arginine Kinase McsB and McsA from Staphyloc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34200
TitleComplex Structure of Arginine Kinase McsB and McsA from Staphylococcus aureus
Map dataComplex Structure of Arginine Kinase McsB and McsA from Staphylococcus aureus
Sample
  • Complex: McsA-McsB complex
    • Protein or peptide: Protein-arginine kinase
    • Protein or peptide: Protein-arginine kinase activator protein
  • Ligand: ZINC ION
KeywordsArginine kinase / Protein quality control / Zinc finger / Enzyme activation / TRANSFERASE
Function / homology
Function and homology information


protein arginine kinase / stress response to cadmium ion / stress response to copper ion / phosphocreatine biosynthetic process / creatine kinase activity / cobalt ion binding / cadmium ion binding / kinase activity / protein kinase activity / copper ion binding ...protein arginine kinase / stress response to cadmium ion / stress response to copper ion / phosphocreatine biosynthetic process / creatine kinase activity / cobalt ion binding / cadmium ion binding / kinase activity / protein kinase activity / copper ion binding / DNA binding / extracellular space / zinc ion binding / ATP binding
Similarity search - Function
YacH protein / Protein arginine kinase / UvrB/uvrC motif / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / UVR domain ...YacH protein / Protein arginine kinase / UvrB/uvrC motif / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / UVR domain / UVR domain profile. / Zinc finger, PARP-type / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Protein-arginine kinase / Protein-arginine kinase activator protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsLu K / Luo B / Tao X / Li H / Xie Y / Zhao Z / Xia W / Su Z / Mao Z
Funding support China, 8 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077142 China
National Natural Science Foundation of China (NSFC)22022706 China
National Natural Science Foundation of China (NSFC)21837006 China
National Natural Science Foundation of China (NSFC)91953117 China
National Natural Science Foundation of China (NSFC)21877131 China
National Natural Science Foundation of China (NSFC)32070049 China
National Natural Science Foundation of China (NSFC)32222040 China
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
CitationJournal: Nat Chem Biol / Year: 2025
Title: Complex structure and activation mechanism of arginine kinase McsB by McsA.
Authors: Kai Lu / Bingnan Luo / Xuan Tao / Yongbo Luo / Mingjun Ao / Bin Zheng / Xiang Xu / Xiaoyan Ma / Jingling Niu / Huinan Li / Yanxuan Xie / Zhennan Zhao / Peng Zheng / Guanbo Wang / Song Gao / ...Authors: Kai Lu / Bingnan Luo / Xuan Tao / Yongbo Luo / Mingjun Ao / Bin Zheng / Xiang Xu / Xiaoyan Ma / Jingling Niu / Huinan Li / Yanxuan Xie / Zhennan Zhao / Peng Zheng / Guanbo Wang / Song Gao / Chao Wang / Wei Xia / Zhaoming Su / Zong-Wan Mao /
Abstract: Protein phosphorylation is a pivotal post-translational modification modulating various cellular processes. In Gram-positive bacteria, the protein arginine kinase McsB, along with its activator McsA, ...Protein phosphorylation is a pivotal post-translational modification modulating various cellular processes. In Gram-positive bacteria, the protein arginine kinase McsB, along with its activator McsA, has a key role in labeling misfolded and damaged proteins during stress. However, the activation mechanism of McsB by McsA remains elusive. Here we report the cryo-electron microscopy structure of a tetrameric McsA-McsB complex at 3.41 Å resolution. Biochemical analysis indicates that the homotetrameric assembly is essential for McsB's kinase activity. The conserved C-terminal zinc finger of McsA interacts with an extended loop in McsB, optimally orienting a critical catalytic cysteine residue. In addition, McsA binding decreases the CtsR's affinity for McsB, enhancing McsB's kinase activity and accelerating the turnover rate of CtsR phosphorylation. Furthermore, McsA binding also increases McsB's thermostability, ensuring its activity under heat stress. These findings elucidate the structural basis and activation mechanism of McsB in stress response.
History
DepositionAug 30, 2022-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_34200.png

Downloads & links

-
Map

FileDownload / File: emd_34200.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComplex Structure of Arginine Kinase McsB and McsA from Staphylococcus aureus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 208 pix.
= 228.8 Å		1.1 Å/pix.
x 208 pix.
= 228.8 Å		1.1 Å/pix.
x 208 pix.
= 228.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.2782857 - 0.4442992
Average (Standard dev.)0.00038395586 (±0.008917424)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 228.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Complex Structure of Arginine Kinase McsB and McsA...

Fileemd_34200_half_map_1.map
AnnotationComplex Structure of Arginine Kinase McsB and McsA from Staphylococcus aureus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Complex Structure of Arginine Kinase McsB and McsA...

Fileemd_34200_half_map_2.map
AnnotationComplex Structure of Arginine Kinase McsB and McsA from Staphylococcus aureus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : McsA-McsB complex

EntireName: McsA-McsB complex
Components
  • Complex: McsA-McsB complex
    • Protein or peptide: Protein-arginine kinase
    • Protein or peptide: Protein-arginine kinase activator protein
  • Ligand: ZINC ION

-
Supramolecule #1: McsA-McsB complex

SupramoleculeName: McsA-McsB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Staphylococcus aureus (bacteria)

-
Macromolecule #1: Protein-arginine kinase

MacromoleculeName: Protein-arginine kinase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: protein arginine kinase
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 38.653918 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTHNIHDNIS QWMKSNEETP IVMSSRIRLA RNLENHVHPL MYATENDGFR VINEVQDALP NFELMRLDQM DQQSKMKMVA KHLISPELI KQPAAAVLVN DDESLSVMIN EEDHIRIQAM GTDTTLQALY NQASSIDDEL DRSLDISYDE QLGYLTTCPT N IGTGMRAS ...String:
MTHNIHDNIS QWMKSNEETP IVMSSRIRLA RNLENHVHPL MYATENDGFR VINEVQDALP NFELMRLDQM DQQSKMKMVA KHLISPELI KQPAAAVLVN DDESLSVMIN EEDHIRIQAM GTDTTLQALY NQASSIDDEL DRSLDISYDE QLGYLTTCPT N IGTGMRAS VMLHLPGLSI MKRMTRIAQT INRFGYTIRG IYGEGSQVYG HTYQVSNQLT LGKSELEIIE TLTEVVNQII HE EKQIRQK LDTYNQLETQ DRVFRSLGIL QNCRMITMEE ASYRLSEVKL GIDLNYIELQ NFKFNELMVA IQSPFLLDEE DDK SVKEKR ADILREHIK

UniProtKB: Protein-arginine kinase

-
Macromolecule #2: Protein-arginine kinase activator protein

MacromoleculeName: Protein-arginine kinase activator protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 6.596689 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
KRCPSCHMTL KDIAHVGKFG CANCYATFKD DIIDIVRRVQ GGQFEHVGKT PHSSHKKIA

UniProtKB: Protein-arginine kinase activator protein

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78.2 K
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4563787
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 268536
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8gqd:
Complex Structure of Arginine Kinase McsB and McsA from Staphylococcus aureus

+
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