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- EMDB-34200: Complex Structure of Arginine Kinase McsB and McsA from Staphyloc... -

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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 / phosphocreatine biosynthetic process / stress response to copper ion / 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 / phosphocreatine biosynthetic process / stress response to copper ion / creatine kinase activity / cobalt ion binding / cadmium ion binding / kinase activity / protein kinase activity / copper ion binding / phosphorylation / DNA binding / 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: To Be Published
Title: Complex Structure and Activation Mechanism of Arginine Kinase McsB by McsA
Authors: Lu K / Luo B / Tao X / Li H / Xie Y / Zhao Z / Xia W / Su Z / Mao Z
History
DepositionAug 30, 2022-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34200.png

Downloads & links

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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
Voxel sizeX=Y=Z: 1.1 Å
Density
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 °

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Supplemental data

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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)

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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)

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Sample components

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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

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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)

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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

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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

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Macromolecule #3: ZINC ION

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4563787
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
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

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

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

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