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Yorodumi- EMDB-28886: Cryo-EM structure of a Zinc-loaded H263A/D287A mutant of the YiiP... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28886 | |||||||||
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Title | Cryo-EM structure of a Zinc-loaded H263A/D287A mutant of the YiiP-Fab complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Zinc transporter / cation diffusion facilitator / membrane protein / transport protein | |||||||||
Function / homology | Function and homology information zinc efflux active transmembrane transporter activity / cadmium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / intracellular zinc ion homeostasis / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Shewanella oneidensis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||
Authors | Lopez-Redondo ML / Hussein AK / Stokes DL | |||||||||
Funding support | United States, 2 items
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Citation | Journal: To Be Published Title: Characterization of individual Zn2+ binding sites of YiiP Authors: Lopez-Redondo ML / Hussein AK / Stokes DL | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28886.map.gz | 168.1 MB | EMDB map data format | |
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Header (meta data) | emd-28886-v30.xml emd-28886.xml | 19.4 KB 19.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28886_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_28886.png | 37.1 KB | ||
Masks | emd_28886_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-28886.cif.gz | 6.6 KB | ||
Others | emd_28886_half_map_1.map.gz emd_28886_half_map_2.map.gz | 165.3 MB 165.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28886 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28886 | HTTPS FTP |
-Validation report
Summary document | emd_28886_validation.pdf.gz | 836.7 KB | Display | EMDB validaton report |
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Full document | emd_28886_full_validation.pdf.gz | 836.2 KB | Display | |
Data in XML | emd_28886_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | emd_28886_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28886 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28886 | HTTPS FTP |
-Related structure data
Related structure data | 8f6kMC 8f6eC 8f6fC 8f6hC 8f6iC 8f6jC 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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-Map
File | Download / File: emd_28886.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.079 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28886_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28886_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28886_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : D287A_H263A Zinc-loaded YiiP-Fab complex
Entire | Name: D287A_H263A Zinc-loaded YiiP-Fab complex |
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Components |
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-Supramolecule #1: D287A_H263A Zinc-loaded YiiP-Fab complex
Supramolecule | Name: D287A_H263A Zinc-loaded YiiP-Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Shewanella oneidensis (bacteria) |
Molecular weight | Theoretical: 325.261 KDa |
-Macromolecule #1: Cadmium and zinc efflux pump FieF
Macromolecule | Name: Cadmium and zinc efflux pump FieF / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Shewanella oneidensis (bacteria) |
Molecular weight | Theoretical: 32.374137 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTQTSQYDFW VKLASRASVA TALTLITIKL LAWLYSGSAS MLASLTDSFA DTLASIINFI AIRYAIVPAD HDHRYGHGKA EPLAALAQS AFIMGSAFLL LFYGGERLLN PSPVENATLG VVVSVVAIVL TLALVLLQKR ALAATNSTVV EADSLHYKSD L FLNAAVLL ...String: MTQTSQYDFW VKLASRASVA TALTLITIKL LAWLYSGSAS MLASLTDSFA DTLASIINFI AIRYAIVPAD HDHRYGHGKA EPLAALAQS AFIMGSAFLL LFYGGERLLN PSPVENATLG VVVSVVAIVL TLALVLLQKR ALAATNSTVV EADSLHYKSD L FLNAAVLL ALVLSQYGWW WADGLFAVLI ACYIGQQAFD LGYRSIQALL DRELDEDTRQ RIKLIAKEDP RVLGLHDLRT RQ AGKTVFI QFHLELDGNL SLNEAASITD TTGLRVKAAF EDAEVIIHQA PVQVEPTTQ UniProtKB: Cation-efflux pump FieF |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / 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
Concentration | 4 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 7 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa / Details: PELCO easiGlow | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 4113 / Average exposure time: 2.5 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
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
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: BACKBONE TRACE / Overall B value: 135.2 / Target criteria: cross-correlation |
Output model | PDB-8f6k: |