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Yorodumi- EMDB-34200: Complex Structure of Arginine Kinase McsB and McsA from Staphyloc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34200 | |||||||||||||||||||||||||||
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Title | Complex Structure of Arginine Kinase McsB and McsA from Staphylococcus aureus | |||||||||||||||||||||||||||
Map data | Complex Structure of Arginine Kinase McsB and McsA from Staphylococcus aureus | |||||||||||||||||||||||||||
Sample |
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Keywords | Arginine 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 | |||||||||||||||||||||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.41 Å | |||||||||||||||||||||||||||
Authors | Lu K / Luo B / Tao X / Li H / Xie Y / Zhao Z / Xia W / Su Z / Mao Z | |||||||||||||||||||||||||||
Funding support | China, 8 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34200.map.gz | 22.3 MB | EMDB map data format | |
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Header (meta data) | emd-34200-v30.xml emd-34200.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
Images | emd_34200.png | 160.2 KB | ||
Filedesc metadata | emd-34200.cif.gz | 5.6 KB | ||
Others | emd_34200_half_map_1.map.gz emd_34200_half_map_2.map.gz | 25.5 MB 25.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34200 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34200 | HTTPS FTP |
-Validation report
Summary document | emd_34200_validation.pdf.gz | 717.5 KB | Display | EMDB validaton report |
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Full document | emd_34200_full_validation.pdf.gz | 717.1 KB | Display | |
Data in XML | emd_34200_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_34200_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34200 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34200 | HTTPS FTP |
-Related structure data
Related structure data | 8gqdMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34200.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Complex Structure of Arginine Kinase McsB and McsA from Staphylococcus aureus | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Complex Structure of Arginine Kinase McsB and McsA...
File | emd_34200_half_map_1.map | ||||||||||||
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Annotation | Complex Structure of Arginine Kinase McsB and McsA from Staphylococcus aureus | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Complex Structure of Arginine Kinase McsB and McsA...
File | emd_34200_half_map_2.map | ||||||||||||
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Annotation | Complex Structure of Arginine Kinase McsB and McsA from Staphylococcus aureus | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : McsA-McsB complex
Entire | Name: McsA-McsB complex |
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Components |
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-Supramolecule #1: McsA-McsB complex
Supramolecule | Name: McsA-McsB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
-Macromolecule #1: Protein-arginine kinase
Macromolecule | Name: Protein-arginine kinase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: protein arginine kinase |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Molecular weight | Theoretical: 38.653918 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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
Macromolecule | Name: Protein-arginine kinase activator protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Molecular weight | Theoretical: 6.596689 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: KRCPSCHMTL KDIAHVGKFG CANCYATFKD DIIDIVRRVQ GGQFEHVGKT PHSSHKKIA UniProtKB: Protein-arginine kinase activator protein |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 78.2 K |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-8gqd: |