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- PDB-8gqd: Complex Structure of Arginine Kinase McsB and McsA from Staphyloc... -

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Basic information

Entry
Database: PDB / ID: 8gqd
TitleComplex Structure of Arginine Kinase McsB and McsA from Staphylococcus aureus
Components
  • Protein-arginine kinase
  • Protein-arginine kinase activator protein
KeywordsTRANSFERASE / Arginine kinase / Protein quality control / Zinc finger / Enzyme activation
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)
MethodELECTRON MICROSCOPY / single 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, 8items
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, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Protein-arginine kinase
A: Protein-arginine kinase
B: Protein-arginine kinase
C: Protein-arginine kinase
E: Protein-arginine kinase activator protein
F: Protein-arginine kinase activator protein
G: Protein-arginine kinase activator protein
H: Protein-arginine kinase activator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,26412
Polymers181,0028
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Protein-arginine kinase


Mass: 38653.918 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mcsB / Plasmid: pET47b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G0P6, protein arginine kinase
#2: Protein
Protein-arginine kinase activator protein


Mass: 6596.689 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mcsA / Plasmid: pET47b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G0P7
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: McsA-McsB complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET47b
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 78.2 K
Image recordingElectron dose: 53 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
1EMAN23.12particle selection
2EPU2.8image acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.15model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13Coot0.9model refinement
14PHENIX1.15model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4563787
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 268536 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00625439
ELECTRON MICROSCOPYf_angle_d1.4245983
ELECTRON MICROSCOPYf_dihedral_angle_d10.19610211
ELECTRON MICROSCOPYf_chiral_restr0.0611960
ELECTRON MICROSCOPYf_plane_restr0.0043780

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