[English] 日本語
Yorodumi
- EMDB-30407: The LAT2-4F2hc complex in complex with leucine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30407
TitleThe LAT2-4F2hc complex in complex with leucine
Map datacryo EM map of the LAT2-4F2hc complex in complex with Leucine
Sample
  • Complex: The LAT2-4F2hc complex in complex with leucine
    • Protein or peptide: 4F2 cell-surface antigen heavy chain
    • Protein or peptide: Large neutral amino acids transporter small subunit 2
  • Ligand: LEUCINE
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: water
Keywordsamino acid transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


proline transmembrane transport / glycine transmembrane transporter activity / : / glycine transport / apical pole of neuron / tyrosine transport / L-histidine transport / amino acid transport complex / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity ...proline transmembrane transport / glycine transmembrane transporter activity / : / glycine transport / apical pole of neuron / tyrosine transport / L-histidine transport / amino acid transport complex / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / aromatic amino acid transmembrane transporter activity / phenylalanine transport / methionine transport / L-leucine transmembrane transporter activity / amino acid transmembrane transport / thyroid hormone transmembrane transporter activity / isoleucine transport / valine transport / toxin transmembrane transporter activity / proline transport / L-amino acid transmembrane transporter activity / L-leucine transport / thyroid hormone transport / neutral amino acid transport / amino acid import across plasma membrane / neutral L-amino acid transmembrane transporter activity / Tryptophan catabolism / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / exogenous protein binding / anchoring junction / antiporter activity / Basigin interactions / microvillus membrane / response to exogenous dsRNA / amino acid transport / tryptophan transport / transport across blood-brain barrier / basal plasma membrane / peptide antigen binding / calcium ion transport / melanosome / double-stranded RNA binding / virus receptor activity / basolateral plasma membrane / carbohydrate metabolic process / apical plasma membrane / cadherin binding / protein heterodimerization activity / lysosomal membrane / synapse / symbiont entry into host cell / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / nucleoplasm / membrane / plasma membrane
Similarity search - Function
L-type amino acid transporter / Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / : / Amino acid/polyamine transporter I / Amino acid permease / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain ...L-type amino acid transporter / Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / : / Amino acid/polyamine transporter I / Amino acid permease / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Amino acid transporter heavy chain SLC3A2 / Large neutral amino acids transporter small subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYan RH / Zhou JY
Funding support China, 4 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31971123 China
National Science Foundation (NSF, China)81920108015 China
National Science Foundation (NSF, China)31930059 China
National Science Foundation (NSF, China)31800139 China
CitationJournal: 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
DepositionJul 27, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7cmi
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30407.png

Downloads & links

-
Map

FileDownload / File: emd_30407.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo EM map of the LAT2-4F2hc complex in complex with Leucine
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.0545551 - 0.11389984
Average (Standard dev.)-0.00014709633 (±0.002803402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 278.272 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z278.272278.272278.272
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0550.114-0.000

-
Supplemental data

-
Sample components

-
Entire : The LAT2-4F2hc complex in complex with leucine

EntireName: The LAT2-4F2hc complex in complex with leucine
Components
  • Complex: The LAT2-4F2hc complex in complex with leucine
    • Protein or peptide: 4F2 cell-surface antigen heavy chain
    • Protein or peptide: Large neutral amino acids transporter small subunit 2
  • Ligand: LEUCINE
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: water

-
Supramolecule #1: The LAT2-4F2hc complex in complex with leucine

SupramoleculeName: The LAT2-4F2hc complex in complex with leucine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

-
Macromolecule #1: 4F2 cell-surface antigen heavy chain

MacromoleculeName: 4F2 cell-surface antigen heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.160828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

UniProtKB: Amino acid transporter heavy chain SLC3A2

-
Macromolecule #2: Large neutral amino acids transporter small subunit 2

MacromoleculeName: Large neutral amino acids transporter small subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.560273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

UniProtKB: Large neutral amino acids transporter small subunit 2

-
Macromolecule #4: LEUCINE

MacromoleculeName: LEUCINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: LEU
Molecular weightTheoretical: 131.173 Da
Chemical component information

ChemComp-LEU:
LEUCINE

-
Macromolecule #5: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: OTHER / Spherical aberration corrector: 2.7
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 751924
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more