[English] 日本語
Yorodumi- EMDB-28882: Cryo-EM structure of a Zinc-loaded D51A mutant of the YiiP-Fab complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28882 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of a Zinc-loaded D51A mutant of the YiiP-Fab complex | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
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) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Lopez-Redondo ML / Hussein AK / Stokes DL | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: To Be Published Title: Characterization of individual Zn2+ binding sites of YiiP Authors: Lopez-Redondo ML / Hussein AK / Stokes DL | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_28882.map.gz | 129.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-28882-v30.xml emd-28882.xml | 21.6 KB 21.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28882_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_28882.png | 43.4 KB | ||
Masks | emd_28882_msk_1.map | 137.1 MB | Mask map | |
Others | emd_28882_half_map_1.map.gz emd_28882_half_map_2.map.gz | 127.3 MB 127.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28882 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28882 | HTTPS FTP |
-Validation report
Summary document | emd_28882_validation.pdf.gz | 672.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_28882_full_validation.pdf.gz | 672.1 KB | Display | |
Data in XML | emd_28882_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | emd_28882_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28882 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28882 | HTTPS FTP |
-Related structure data
Related structure data | 8f6fMC 8f6eC 8f6hC 8f6iC 8f6jC 8f6kC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_28882.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.079 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_28882_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_28882_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_28882_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : D51A Zinc-loaded YiiP-Fab complex
Entire | Name: D51A Zinc-loaded YiiP-Fab complex |
---|---|
Components |
|
-Supramolecule #1: D51A Zinc-loaded YiiP-Fab complex
Supramolecule | Name: D51A Zinc-loaded YiiP-Fab complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 |
---|---|
Source (natural) | Organism: Shewanella oneidensis (bacteria) |
Molecular weight | Theoretical: 163.024 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: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Shewanella oneidensis (bacteria) / Strain: MR-1 |
Molecular weight | Theoretical: 32.441199 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTQTSQYDFW VKLASRASVA TALTLITIKL LAWLYSGSAS MLASLTDSFA ATLASIINFI AIRYAIVPAD HDHRYGHGKA EPLAALAQS AFIMGSAFLL LFYGGERLLN PSPVENATLG VVVSVVAIVL TLALVLLQKR ALAATNSTVV EADSLHYKSD L FLNAAVLL ...String: MTQTSQYDFW VKLASRASVA TALTLITIKL LAWLYSGSAS MLASLTDSFA ATLASIINFI AIRYAIVPAD HDHRYGHGKA EPLAALAQS AFIMGSAFLL LFYGGERLLN PSPVENATLG VVVSVVAIVL TLALVLLQKR ALAATNSTVV EADSLHYKSD L FLNAAVLL ALVLSQYGWW WADGLFAVLI ACYIGQQAFD LGYRSIQALL DRELDEDTRQ RIKLIAKEDP RVLGLHDLRT RQ AGKTVFI QFHLELDGNL SLNEAHSITD TTGLRVKAAF EDAEVIIHQD PVQVEPTTQ |
-Macromolecule #2: Fab2r light chain
Macromolecule | Name: Fab2r light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.580242 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQIWSWPLIT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQIWSWPLIT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC |
-Macromolecule #3: Fab2r heavy chain
Macromolecule | Name: Fab2r heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.406352 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EISEVQLVES GGGLVQPGGS LRLSCAASGF TIYSSSIHWV RQAPGKGLEW VASIYSSSGS TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARQSYSGLSP RRHWSYGAMD YWGQGTLVTV FNQIKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String: EISEVQLVES GGGLVQPGGS LRLSCAASGF TIYSSSIHWV RQAPGKGLEW VASIYSSSGS TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARQSYSGLSP RRHWSYGAMD YWGQGTLVTV FNQIKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKTHT |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
| |||||||||||||||
Grid | Model: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 7.0 nm / 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 |
---|---|
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: 4058 / 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: 2.75 µm / Nominal defocus min: 0.75 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 |