+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38067 | |||||||||
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Title | Cryo-EM structure of human XPR1 in open state | |||||||||
Map data | main map | |||||||||
Sample |
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Keywords | transport open state / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information : / phosphate ion transport / intracellular phosphate ion homeostasis / inositol hexakisphosphate binding / phosphate ion transmembrane transport / cellular response to phosphate starvation / efflux transmembrane transporter activity / response to virus / trans-Golgi network / virus receptor activity ...: / phosphate ion transport / intracellular phosphate ion homeostasis / inositol hexakisphosphate binding / phosphate ion transmembrane transport / cellular response to phosphate starvation / efflux transmembrane transporter activity / response to virus / trans-Golgi network / virus receptor activity / Golgi apparatus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.61 Å | |||||||||
Authors | Jiang DH / Yan R | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Structure of transport at 3.6 Angstroms resolution. Authors: Jiang DH / Yan R | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38067.map.gz | 117.8 MB | EMDB map data format | |
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Header (meta data) | emd-38067-v30.xml emd-38067.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_38067.png | 32.8 KB | ||
Filedesc metadata | emd-38067.cif.gz | 5.3 KB | ||
Others | emd_38067_half_map_1.map.gz emd_38067_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38067 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38067 | HTTPS FTP |
-Validation report
Summary document | emd_38067_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_38067_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_38067_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | emd_38067_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38067 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38067 | HTTPS FTP |
-Related structure data
Related structure data | 8x5eMC 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_38067.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map
File | emd_38067_half_map_1.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map
File | emd_38067_half_map_2.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : transport
Entire | Name: transport |
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Components |
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-Supramolecule #1: transport
Supramolecule | Name: transport / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Solute carrier family 53 member 1
Macromolecule | Name: Solute carrier family 53 member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 54.831422 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: APAWTTFRVG LFCGIFIVLN ITLVLAAVFK LETDRSIWPL IRIYRGGFLL IEFLFLLGIN TYGWRQAGVN HVLIFELNPR SNLSHQHLF EIAGFLGILW CLSLLACFFA PISVIPTYVY PLALYGFMVF FLINPTKTFY YKSRFWLLKL LFRVFTAPFH K VGFADFWL ...String: APAWTTFRVG LFCGIFIVLN ITLVLAAVFK LETDRSIWPL IRIYRGGFLL IEFLFLLGIN TYGWRQAGVN HVLIFELNPR SNLSHQHLF EIAGFLGILW CLSLLACFFA PISVIPTYVY PLALYGFMVF FLINPTKTFY YKSRFWLLKL LFRVFTAPFH K VGFADFWL ADQLNSLSVI LMDLEYMICF YSLELKWDES KGLLPNNSEE SGICHKYTYG VRAIVQCIPA WLRFIQCLRR YR DTKRAFP HLVNAGKYST TFFMVTFAAL YSTHKERGHS DTMVFFYLWI VFYIISSCYT LIWDLKMDWG LFDKNAGENT FLR EEIVYP QKAYYYCAII EDVILRFAWT IQISITSTTL LPHSGDIIAT VFAPLEVFRR FVWNFFRLEN EHLNNCGEFR AVRD ISVAP LNADDQTLLE QMMDQDDGVR NRQKNRSWKY NQSISLRRPR LASQSKARDT KVLIEDTDDE ANT UniProtKB: Solute carrier family 53 member 1 |
-Macromolecule #2: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: PO4 |
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Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-Macromolecule #3: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...
Macromolecule | Name: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate type: ligand / ID: 3 / Number of copies: 6 / Formula: 6OU |
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Molecular weight | Theoretical: 717.996 Da |
Chemical component information | ChemComp-6OU: |
-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: OTHER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 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: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40195 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |