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Yorodumi- EMDB-39232: Cryo EM structure of human phosphate channel XPR1 at inward-facin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39232 | |||||||||||||||
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Title | Cryo EM structure of human phosphate channel XPR1 at inward-facing state | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | phosphate channel / membrane protein / phosphate homeostasis / TRANSPORT PROTEIN | |||||||||||||||
Function / homology | Function and homology information phosphate transmembrane transporter 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 / virus receptor activity / Golgi apparatus ...phosphate transmembrane transporter 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 / virus receptor activity / Golgi apparatus / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.56 Å | |||||||||||||||
Authors | Lu Y / Yue C / Zhang L / Yao D / Yu Y / Cao Y | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: Science / Year: 2024 Title: Structural basis for inositol pyrophosphate gating of the phosphate channel XPR1. Authors: Yi Lu / Chen-Xi Yue / Li Zhang / Deqiang Yao / Ying Xia / Qing Zhang / Xinchen Zhang / Shaobai Li / Yafeng Shen / Mi Cao / Chang-Run Guo / An Qin / Jie Zhao / Lu Zhou / Ye Yu / Yu Cao / Abstract: Precise regulation of intracellular phosphate (Pi) is critical for cellular function, with XPR1 serving as the sole Pi exporter in humans. The mechanism of Pi efflux, activated by inositol ...Precise regulation of intracellular phosphate (Pi) is critical for cellular function, with XPR1 serving as the sole Pi exporter in humans. The mechanism of Pi efflux, activated by inositol pyrophosphates (PP-IPs), has remained unclear. This study presents cryo-electron microscopy structures of XPR1 in multiple conformations, revealing a transmembrane pathway for Pi export and a dual-binding activation pattern by PP-IPs. A canonical binding site is located at the dimeric interface of SPX domains, and a second site, biased toward PP-IPs, is found between the transmembrane and SPX domains. By integrating structural studies with electrophysiological analyses, we characterize XPR1 as an IPs/PP-IPs-activated phosphate channel. The interplay among its TMDs, SPX domains, and IPs/PP-IPs orchestrates the conformational transition between its closed and open states. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39232.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-39232-v30.xml emd-39232.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_39232_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_39232.png | 102.3 KB | ||
Filedesc metadata | emd-39232.cif.gz | 5.5 KB | ||
Others | emd_39232_half_map_1.map.gz emd_39232_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39232 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39232 | HTTPS FTP |
-Validation report
Summary document | emd_39232_validation.pdf.gz | 763.3 KB | Display | EMDB validaton report |
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Full document | emd_39232_full_validation.pdf.gz | 762.9 KB | Display | |
Data in XML | emd_39232_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_39232_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39232 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39232 | HTTPS FTP |
-Related structure data
Related structure data | 8yfxMC 8yetC 8yexC 8yf4C 8yfdC 8yfuC 8yfwC 9iwsC 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_39232.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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: #1
File | emd_39232_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_39232_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo EM structure of human phosphate channel XPR1 at inward-facin...
Entire | Name: Cryo EM structure of human phosphate channel XPR1 at inward-facing state |
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Components |
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-Supramolecule #1: Cryo EM structure of human phosphate channel XPR1 at inward-facin...
Supramolecule | Name: Cryo EM structure of human phosphate channel XPR1 at inward-facing state type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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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: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 46.469188 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QPAPAWTTFR VGLFCGIFIV LNITLVLAAV FKLETDRSIW PLIRIYRGGF LLIEFLFLLG INTYGWRQAG VNHVLIFELN PRSNLSHQH LFEIAGFLGI LWCLSLLACF FAPISVIPTY VYPLALYGFM VFFLINPTKT FYYKSRFWLL KLLFRVFTAP F HKVGFADF ...String: QPAPAWTTFR VGLFCGIFIV LNITLVLAAV FKLETDRSIW PLIRIYRGGF LLIEFLFLLG INTYGWRQAG VNHVLIFELN PRSNLSHQH LFEIAGFLGI LWCLSLLACF FAPISVIPTY VYPLALYGFM VFFLINPTKT FYYKSRFWLL KLLFRVFTAP F HKVGFADF WLADQLNSLS VILMDLEYMI CFYSLELKWD ESKGLLPNNS EESGICHKYT YGVRAIVQCI PAWLRFIQCL RR YRDTKRA FPHLVNAGKY STTFFMVTFA ALYSTHKERG HSDTMVFFYL WIVFYIISSC YTLIWDLKMD WGLFDKNAGE NTF LREEIV YPQKAYYYCA IIEDVILRFA WTIQISITST TLLPHSGDII ATVFAPLEVF RRFVWNFFRL ENEHLNNCGE UniProtKB: Solute carrier family 53 member 1 |
-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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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |