+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34638 | |||||||||
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Title | Structure of the Mex67-Mtr2-1 heterodimer | |||||||||
Map data | Mex67-Mtr2-1 heterodimer | |||||||||
Sample |
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Keywords | nuclear export factor / NUCLEAR PROTEIN | |||||||||
Function / homology | Function and homology information nuclear RNA export factor complex / nuclear pore central transport channel / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA export from nucleus / U4 snRNA binding / tRNA processing / poly(A)+ mRNA export from nucleus / porin activity / ribosomal large subunit export from nucleus ...nuclear RNA export factor complex / nuclear pore central transport channel / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA export from nucleus / U4 snRNA binding / tRNA processing / poly(A)+ mRNA export from nucleus / porin activity / ribosomal large subunit export from nucleus / U5 snRNA binding / U2 snRNA binding / mRNA export from nucleus / U6 snRNA binding / nuclear pore / ribosomal small subunit export from nucleus / U1 snRNA binding / tRNA binding / mRNA binding / RNA binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.81 Å | |||||||||
Authors | Li ZQ / Chen SJ / Sui SF | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nature / Year: 2023 Title: Nuclear export of pre-60S particles through the nuclear pore complex. Authors: Zongqiang Li / Shuaijiabin Chen / Liang Zhao / Guoqiang Huang / Huiqin Xu / Xiaoyun Yang / Peiyi Wang / Ning Gao / Sen-Fang Sui / Abstract: The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm. The assembly intermediates of the ribosomal ...The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm. The assembly intermediates of the ribosomal subunits, pre-60S and pre-40S particles, are among the largest cargoes of the NPC and the export of these gigantic ribonucleoproteins requires numerous export factors. Here we report the cryo-electron microscopy structure of native pre-60S particles trapped in the channel of yeast NPCs. In addition to known assembly factors, multiple factors with export functions are also included in the structure. These factors in general bind to either the flexible regions or subunit interface of the pre-60S particle, and virtually form many anchor sites for NPC binding. Through interactions with phenylalanine-glycine (FG) repeats from various nucleoporins of NPC, these factors collectively facilitate the passage of the pre-60S particle through the central FG repeat network of the NPC. Moreover, in silico analysis of the axial and radial distribution of pre-60S particles within the NPC shows that a single NPC can take up to four pre-60S particles simultaneously, and pre-60S particles are enriched in the inner ring regions close to the wall of the NPC with the solvent-exposed surface facing the centre of the nuclear pore. Our data suggest a translocation model for the export of pre-60S particles through the NPC. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34638.map.gz | 122.5 MB | EMDB map data format | |
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Header (meta data) | emd-34638-v30.xml emd-34638.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34638_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_34638.png | 63.1 KB | ||
Filedesc metadata | emd-34638.cif.gz | 5.5 KB | ||
Others | emd_34638_half_map_1.map.gz emd_34638_half_map_2.map.gz | 226.6 MB 226.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34638 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34638 | HTTPS FTP |
-Related structure data
Related structure data | 8hbnMC 8hfrC 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_34638.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Mex67-Mtr2-1 heterodimer | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.336 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Mex67-Mtr2-1 heterodimer half B map
File | emd_34638_half_map_1.map | ||||||||||||
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Annotation | Mex67-Mtr2-1 heterodimer half B map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Mex67-Mtr2-1 heterodimer half B map
File | emd_34638_half_map_2.map | ||||||||||||
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Annotation | Mex67-Mtr2-1 heterodimer half B map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mex67-Mtr2-1
Entire | Name: Mex67-Mtr2-1 |
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Components |
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-Supramolecule #1: Mex67-Mtr2-1
Supramolecule | Name: Mex67-Mtr2-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
-Macromolecule #1: mRNA export factor MEX67
Macromolecule | Name: mRNA export factor MEX67 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Molecular weight | Theoretical: 67.417477 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae S288C (yeast) |
Sequence | String: MSGFHNVGNI NMMAQQQMQQ NRIKISVRNW QNATMNDLIN FISRNARVAV YDAHVEGPLV IGYVNSKAEA ESLMKWNGVR FAGSNLKFE LLDNNGASAG TSDTISFLRG VLLKRYDPQT KLLNLGALHS DPELIQKGVF SSISTQSKMF PAMMKLASTE K SLIVESVN ...String: MSGFHNVGNI NMMAQQQMQQ NRIKISVRNW QNATMNDLIN FISRNARVAV YDAHVEGPLV IGYVNSKAEA ESLMKWNGVR FAGSNLKFE LLDNNGASAG TSDTISFLRG VLLKRYDPQT KLLNLGALHS DPELIQKGVF SSISTQSKMF PAMMKLASTE K SLIVESVN LADNQLKDIS AISTLAQTFP NLKNLCLANN QIFRFRSLEV WKNKFKDLRE LLMTNNPITT DKLYRTEMLR LF PKLVVLD NVIVRDEQKL QTVYSLPMKI QQFFFENDAL GQSSTDFATN FLNLWDNNRE QLLNLYSPQS QFSVSVDSTI PPS TVTDSD QTPAFGYYMS SSRNISKVSS EKSIQQRLSI GQESINSIFK TLPKTKHHLQ EQPNEYSMET ISYPQINGFV ITLH GFFEE TGKPELESNK KTGKNNYQKN RRYNHGYNST SNNKLSKKSF DRTWVIVPMN NSVIIASDLL TVRAYSTGAW KTASI AIAQ PPQQQASVLP QVASMNPNIT TPPQPQPSVV PGGMSIPGAP QGAMVMAPTL QLPPDVQSRL NPVQLELLNK LHLETK LNA EYTFMLAEQS NWNYEVAIKG FQSSMNGIPR EAFVQF UniProtKB: mRNA export factor MEX67 |
-Macromolecule #2: mRNA transport regulator MTR2
Macromolecule | Name: mRNA transport regulator MTR2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Molecular weight | Theoretical: 20.802506 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae S288C (yeast) |
Sequence | String: MNTNSNTMVM NDANQAQITA TFTKKILAHL DDPDSNKLAQ FVQLFNPNNC RIIFNATPFA QATVFLQMWQ NQVVQTQHAL TGVDYHAIP GSGTLICNVN CKVRFDESGR DKMGQDATVP IQPNNTGNRN RPNDMNKPRP LWGPYFGISL QLIIDDRIFR N DFNGVISG FNYNMVYKPE DSLLKI UniProtKB: mRNA transport regulator MTR2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |