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- EMDB-35767: Structure of the Mex67-Mtr2-3 heterodimer -

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Basic information

Entry
Database: EMDB / ID: EMD-35767
TitleStructure of the Mex67-Mtr2-3 heterodimer
Map datamap of Mex67-Mtr2-3
Sample
  • Complex: Mex67-Mtr2 heterodimer
    • Protein or peptide: Nuclear export factor
Keywordsnuclear export factor / NUCLEAR PROTEIN / RIBOSOME
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.88 Å
AuthorsLi ZQ / Chen SJ / Sui SF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionMar 30, 2023-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateJun 28, 2023-
Current statusJun 28, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35767.png

Downloads & links

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Map

FileDownload / File: emd_35767.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of Mex67-Mtr2-3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 800 pix.
= 534.4 Å		0.67 Å/pix.
x 800 pix.
= 534.4 Å		0.67 Å/pix.
x 800 pix.
= 534.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.35479867 - 1.0220047
Average (Standard dev.)-0.00008308106 (±0.007067629)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 534.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A map of Mex67-Mtr2-3

Fileemd_35767_half_map_1.map
Annotationhalf A map of Mex67-Mtr2-3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B map of Mex67-Mtr2-3

Fileemd_35767_half_map_2.map
Annotationhalf B map of Mex67-Mtr2-3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mex67-Mtr2 heterodimer

EntireName: Mex67-Mtr2 heterodimer
Components
  • Complex: Mex67-Mtr2 heterodimer
    • Protein or peptide: Nuclear export factor

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Supramolecule #1: Mex67-Mtr2 heterodimer

SupramoleculeName: Mex67-Mtr2 heterodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: Nuclear export factor

MacromoleculeName: Nuclear export factor / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MSGFHNVGNI NMMAQQQMQQ NRIKISVRNW QNATMNDLIN FISRNARVAV YDAHVEGPLV IGYVNSKAE AESLMKWNGV RFAGSNLKFE LLDNNGASAG TSDTISFLRG VLLKRYDPQT K LLNLGALH SDPELIQKGV FSSISTQSKM FPAMMKLAST EKSLIVESVN ...String:
MSGFHNVGNI NMMAQQQMQQ NRIKISVRNW QNATMNDLIN FISRNARVAV YDAHVEGPLV IGYVNSKAE AESLMKWNGV RFAGSNLKFE LLDNNGASAG TSDTISFLRG VLLKRYDPQT K LLNLGALH SDPELIQKGV FSSISTQSKM FPAMMKLAST EKSLIVESVN LADNQLKDIS AI STLAQTF PNLKNLCLAN NQIFRFRSLE VWKNKFKDLR ELLMTNNPIT TDKLYRTEML RLF PKLVVL DNVIVRDEQK LQTVYSLPMK IQQFFFENDA LGQSSTDFAT NFLNLWDNNR EQLL NLYSP QSQFSVSVDS TIPPSTVTDS DQTPAFGYYM SSSRNISKVS SEKSIQQRLS IGQES INSI FKTLPKTKHH LQEQPNEYSM ETISYPQING FVITLHGFFE ETGKPELESN KKTGKN NYQ KNRRYNHGYN STSNNKLSKK SFDRTWVIVP MNNSVIIASD LLTVRAYSTG AWKTASI AI AQPPQQQASV LPQVASMNPN ITTPPQPQPS VVPGGMSIPG APQGAMVMAP TLQLPPDV Q SRLNPVQLEL LNKLHLETKL NAEYTFMLAE QSNWNYEVAI KGFQSSMNGI PREAFVQF

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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: 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

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

0220

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86343
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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