+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31251 | ||||||||||||
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Title | Overall structure of Erastin-bound xCT-4F2hc complex | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information cystine:glutamate antiporter activity / regulation of neutrophil apoptotic process / L-kynurenine transmembrane transport / L-kynurenine transmembrane transporter activity / regulation of cysteine metabolic process / regulation of glutathione biosynthetic process / regulation of glutamate metabolic process / regulation of melanin biosynthetic process / regulation of AMPA glutamate receptor clustering / L-cystine transport ...cystine:glutamate antiporter activity / regulation of neutrophil apoptotic process / L-kynurenine transmembrane transport / L-kynurenine transmembrane transporter activity / regulation of cysteine metabolic process / regulation of glutathione biosynthetic process / regulation of glutamate metabolic process / regulation of melanin biosynthetic process / regulation of AMPA glutamate receptor clustering / L-cystine transport / neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / methionine transport / tyrosine transport / L-histidine transport / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / L-amino acid transmembrane transporter activity / dipeptide import across plasma membrane / : / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / isoleucine transport / L-alanine import across plasma membrane / regulation of protein transport / phenylalanine transport / valine transport / L-leucine transmembrane transporter activity / amino acid transmembrane transport / calcium:sodium antiporter activity / L-leucine transport / thyroid hormone transport / proline transport / L-glutamate transmembrane transport / glutathione transmembrane transport / regulation of cellular response to oxidative stress / negative regulation of ferroptosis / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / ventricular system development / intracellular glutamate homeostasis / lens fiber cell differentiation / L-glutamate import across plasma membrane / Tryptophan catabolism / striatum development / astrocyte projection / exogenous protein binding / anchoring junction / limb development / Basigin interactions / response to redox state / NFE2L2 regulating anti-oxidant/detoxification enzymes / microvillus membrane / adult behavior / amino acid transport / regulation of synapse organization / lung alveolus development / response to exogenous dsRNA / tryptophan transport / glutathione metabolic process / basal plasma membrane / brush border membrane / response to nicotine / visual learning / modulation of chemical synaptic transmission / response to organic cyclic compound / response to toxic substance / platelet aggregation / calcium ion transport / double-stranded RNA binding / melanosome / apical part of cell / virus receptor activity / regulation of cell population proliferation / cellular response to oxidative stress / basolateral plasma membrane / carbohydrate metabolic process / cadherin binding / symbiont entry into host cell / apical plasma membrane / protein heterodimerization activity / lysosomal membrane / synapse / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / nucleoplasm / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Yan RH / Li YN / Zhang YY / Chi XM / Zhou Q | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Cell Res / Year: 2022 Title: The structure of erastin-bound xCT-4F2hc complex reveals molecular mechanisms underlying erastin-induced ferroptosis. Authors: Renhong Yan / Enjun Xie / Yaning Li / Jin Li / Yuanyuan Zhang / Ximin Chi / Xueping Hu / Lei Xu / Tingjun Hou / Brent R Stockwell / Junxia Min / Qiang Zhou / Fudi Wang / | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31251.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-31251-v30.xml emd-31251.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_31251.png | 40.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31251 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31251 | HTTPS FTP |
-Validation report
Summary document | emd_31251_validation.pdf.gz | 487.4 KB | Display | EMDB validaton report |
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Full document | emd_31251_full_validation.pdf.gz | 487 KB | Display | |
Data in XML | emd_31251_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_31251_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31251 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31251 | HTTPS FTP |
-Related structure data
Related structure data | 7epzMC 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_31251.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Overall structure of Erastin-bound xCT-4F2hc complex
Entire | Name: Overall structure of Erastin-bound xCT-4F2hc complex |
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Components |
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-Supramolecule #1: Overall structure of Erastin-bound xCT-4F2hc complex
Supramolecule | Name: Overall structure of Erastin-bound xCT-4F2hc complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: 4F2 cell-surface antigen heavy chain
Macromolecule | Name: 4F2 cell-surface antigen heavy chain / 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: 70.160828 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAHHHHHHHH HHSGRELQPP EASIAVVSIP RQLPGSHSEA GVQGLSAGDD SETGSDCVTQ AGLQLLASSD PPALASKNAE VTVETGFHH VSQADIEFLT SIDPTASASG SAGITGTMSQ DTEVDMKEVE LNELEPEKQP MNAASGAAMS LAGAEKNGLV K IKVAEDEA ...String: MAHHHHHHHH HHSGRELQPP EASIAVVSIP RQLPGSHSEA GVQGLSAGDD SETGSDCVTQ AGLQLLASSD PPALASKNAE VTVETGFHH VSQADIEFLT SIDPTASASG SAGITGTMSQ DTEVDMKEVE LNELEPEKQP MNAASGAAMS LAGAEKNGLV K IKVAEDEA EAAAAAKFTG LSKEELLKVA GSPGWVRTRW ALLLLFWLGW LGMLAGAVVI IVRAPRCREL PAQKWWHTGA LY RIGDLQA FQGHGAGNLA GLKGRLDYLS SLKVKGLVLG PIHKNQKDDV AQTDLLQIDP NFGSKEDFDS LLQSAKKKSI RVI LDLTPN YRGENSWFST QVDTVATKVK DALEFWLQAG VDGFQVRDIE NLKDASSFLA EWQNITKGFS EDRLLIAGTN SSDL QQILS LLESNKDLLL TSSYLSDSGS TGEHTKSLVT QYLNATGNRW CSWSLSQARL LTSFLPAQLL RLYQLMLFTL PGTPV FSYG DEIGLDAAAL PGQPMEAPVM LWDESSFPDI PGAVSANMTV KGQSEDPGSL LSLFRRLSDQ RSKERSLLHG DFHAFS AGP GLFSYIRHWD QNERFLVVLN FGDVGLSAGL QASDLPASAS LPAKADLLLS TQPGREEGSP LELERLKLEP HEGLLLR FP YAALE |
-Macromolecule #2: Cystine/glutamate transporter
Macromolecule | Name: Cystine/glutamate transporter / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 57.609777 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MADYKDDDDK SGPDEVDASG RVRKPVVSTI SKGGYLQGNV NGRLPSLGNK EPPGQEKVQL KRKVTLLRGV SIIIGTIIGA GIFISPKGV LQNTGSVGMS LTIWTVCGVL SLFGALSYAE LGTTIKKSGG HYTYILEVFG PLPAFVRVWV ELLIIRPAAT A VISLAFGR ...String: MADYKDDDDK SGPDEVDASG RVRKPVVSTI SKGGYLQGNV NGRLPSLGNK EPPGQEKVQL KRKVTLLRGV SIIIGTIIGA GIFISPKGV LQNTGSVGMS LTIWTVCGVL SLFGALSYAE LGTTIKKSGG HYTYILEVFG PLPAFVRVWV ELLIIRPAAT A VISLAFGR YILEPFFIQC EIPELAIKLI TAVGITVVMV LNSMSVSWSA RIQIFLTFCK LTAILIIIVP GVMQLIKGQT QN FKDAFSG RDSSITRLPL AFYYGMYAYA GWFYLNFVTE EVENPEKTIP LAICISMAIV TIGYVLTNVA YFTTINAEEL LLS NAVAVT FSERLLGNFS LAVPIFVALS CFGSMNGGVF AVSRLFYVAS REGHLPEILS MIHVRKHTPL PAVIVLHPLT MIML FSGDL DSLLNFLSFA RWLFIGLAVA GLIYLRYKCP DMHRPFKVPL FIPALFSFTC LFMVALSLYS DPFSTGIGFV ITLTG VPAY YLFIIWDKKP RWFRIMSEKI TRTLQIILEV VPEEDKL |
-Macromolecule #4: 2-[(1S)-1-[4-[2-(4-chloranylphenoxy)ethanoyl]piperazin-1-yl]ethyl...
Macromolecule | Name: 2-[(1S)-1-[4-[2-(4-chloranylphenoxy)ethanoyl]piperazin-1-yl]ethyl]-3-(2-ethoxyphenyl)quinazolin-4-one type: ligand / ID: 4 / Number of copies: 1 / Formula: J9O |
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Molecular weight | Theoretical: 547.045 Da |
Chemical component information | ChemComp-J9O: |
-Macromolecule #5: 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE
Macromolecule | Name: 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: PX8 |
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Molecular weight | Theoretical: 703.99 Da |
Chemical component information | ChemComp-PX8: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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 BIOQUANTUM (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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
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
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 114524 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |