+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30406 | |||||||||||||||
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Title | The LAT2-4F2hc complex in complex with tryptophan | |||||||||||||||
Map data | cryo EM map of the LAT2-4F2hc complex in complex Tryptophan | |||||||||||||||
Sample |
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Function / homology | Function and homology information proline transmembrane transport / glycine transmembrane transporter activity / thyroid hormone transmembrane transporter activity / L-amino acid transmembrane transporter activity / amino acid import across plasma membrane / amino acid transmembrane transport / organic cation transmembrane transporter activity / glycine transport / neutral L-amino acid secondary active transmembrane transporter activity / tyrosine transport ...proline transmembrane transport / glycine transmembrane transporter activity / thyroid hormone transmembrane transporter activity / L-amino acid transmembrane transporter activity / amino acid import across plasma membrane / amino acid transmembrane transport / organic cation transmembrane transporter activity / glycine transport / neutral L-amino acid secondary active transmembrane transporter activity / tyrosine transport / L-histidine transport / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / aromatic amino acid transmembrane transporter activity / methionine transport / apical pole of neuron / amino acid transport complex / L-leucine import across plasma membrane / isoleucine transport / L-alanine transmembrane transporter activity / L-leucine transmembrane transporter activity / L-alanine import across plasma membrane / phenylalanine transport / valine transport / L-leucine transport / calcium:sodium antiporter activity / thyroid hormone transport / proline transport / neutral amino acid transport / toxin transmembrane transporter activity / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / Tryptophan catabolism / exogenous protein binding / antiporter activity / anchoring junction / Basigin interactions / microvillus membrane / amino acid transport / response to exogenous dsRNA / transport across blood-brain barrier / tryptophan transport / basal plasma membrane / peptide antigen binding / calcium ion transport / double-stranded RNA binding / melanosome / virus receptor activity / 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 / Zhou JY / Li YN / Lei JL / Zhou Q | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: Cell Discov / Year: 2020 Title: Structural insight into the substrate recognition and transport mechanism of the human LAT2-4F2hc complex. Authors: Renhong Yan / Jiayao Zhou / Yaning Li / Jianlin Lei / Qiang Zhou / | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30406.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-30406-v30.xml emd-30406.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
Images | emd_30406.png | 39.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30406 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30406 | HTTPS FTP |
-Validation report
Summary document | emd_30406_validation.pdf.gz | 461.1 KB | Display | EMDB validaton report |
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Full document | emd_30406_full_validation.pdf.gz | 460.6 KB | Display | |
Data in XML | emd_30406_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_30406_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30406 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30406 | HTTPS FTP |
-Related structure data
Related structure data | 7cmhMC 7cmiC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30406.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryo EM map of the LAT2-4F2hc complex in complex Tryptophan | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : The LAT2-4F2hc complex in complex with leucine
Entire | Name: The LAT2-4F2hc complex in complex with leucine |
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Components |
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-Supramolecule #1: The LAT2-4F2hc complex in complex with leucine
Supramolecule | Name: The LAT2-4F2hc complex in complex with leucine / 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) |
Molecular weight | Experimental: 100 KDa |
-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: Large neutral amino acids transporter small subunit 2
Macromolecule | Name: Large neutral amino acids transporter small subunit 2 / 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: 60.560273 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MADYKDDDDK SGPDEVDASG REEGARHRNN TEKKHPGGGE SDASPEAGSG GGGVALKKEI GLVSACGIIV GNIIGSGIFV SPKGVLENA GSVGLALIVW IVTGFITVVG ALCYAELGVT IPKSGGDYSY VKDIFGGLAG FLRLWIAVLV IYPTNQAVIA L TFSNYVLQ ...String: MADYKDDDDK SGPDEVDASG REEGARHRNN TEKKHPGGGE SDASPEAGSG GGGVALKKEI GLVSACGIIV GNIIGSGIFV SPKGVLENA GSVGLALIVW IVTGFITVVG ALCYAELGVT IPKSGGDYSY VKDIFGGLAG FLRLWIAVLV IYPTNQAVIA L TFSNYVLQ PLFPTCFPPE SGLRLLAAIC LLLLTWVNCS SVRWATRVQD IFTAGKLLAL ALIIIMGIVQ ICKGEYFWLE PK NAFENFQ EPDIGLVALA FLQGSFAYGG WNFLNYVTEE LVDPYKNLPR AIFISIPLVT FVYVFANVAY VTAMSPQELL ASN AVAVTF GEKLLGVMAW IMPISVALST FGGVNGSLFT SSRLFFAGAR EGHLPSVLAM IHVKRCTPIP ALLFTCISTL LMLV TSDMY TLINYVGFIN YLFYGVTVAG QIVLRWKKPD IPRPIKINLL FPIIYLLFWA FLLVFSLWSE PVVCGIGLAI MLTGV PVYF LGVYWQHKPK CFSDFIELLT LVSQKMCVVV YPEVERGSGT EEANEDMEEQ QQPMYQPTPT KDKDVAGQPQ P |
-Macromolecule #4: TRYPTOPHAN
Macromolecule | Name: TRYPTOPHAN / type: ligand / ID: 4 / Number of copies: 1 / Formula: TRP |
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Molecular weight | Theoretical: 204.225 Da |
Chemical component information | ChemComp-TRP: |
-Macromolecule #5: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
Macromolecule | Name: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: 3PH |
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Molecular weight | Theoretical: 704.998 Da |
Chemical component information | ChemComp-3PH: |
-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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Specialist optics | Phase plate: OTHER / Spherical aberration corrector: 2.7 |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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 |
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 / Number images used: 713248 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |