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- EMDB-34641: Structure of Crm1-RanGTP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-34641
TitleStructure of Crm1-RanGTP complex
Map dataCrm1-RanGTP complex half A map
Sample
  • Complex: Crm1-RanGTP complex
    • Protein or peptide: Nuclear export factor
KeywordsNuclear export factor / NUCLEAR PROTEIN
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.61 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
DepositionOct 29, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateJun 28, 2023-
Current statusJun 28, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34641.png

Downloads & links

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Map

FileDownload / File: emd_34641.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCrm1-RanGTP complex half A map
Voxel sizeX=Y=Z: 0.668 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.8762228 - 2.2869954
Average (Standard dev.)0.014123883 (±0.07200416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 213.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Crm1-RanGTP complex

Fileemd_34641_half_map_1.map
AnnotationCrm1-RanGTP complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Crm1-RanGTP complex half B map

Fileemd_34641_half_map_2.map
AnnotationCrm1-RanGTP complex half B map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Crm1-RanGTP complex

EntireName: Crm1-RanGTP complex
Components
  • Complex: Crm1-RanGTP complex
    • Protein or peptide: Nuclear export factor

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Supramolecule #1: Crm1-RanGTP complex

SupramoleculeName: Crm1-RanGTP complex / 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
Details: Author stated this map is a local refinement map from the peripheric region of the larger pre-60S particle (EMD-34725) with a high resolution. It is likely that the unmasked-calculated curve ...Details: Author stated this map is a local refinement map from the peripheric region of the larger pre-60S particle (EMD-34725) with a high resolution. It is likely that the unmasked-calculated curve has a higher resolution due to the influence of pre-60S particle.
Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MEGILDFSND LDIALLDQVV STFYQGSGVQ QKQAQEILTK FQDNPDAWQK ADQILQFSTN PQSKFIALS ILDKLITRKW KLLPNDHRIG IRNFVVGMII SMCQDDEVFK TQKNLINKSD L TLVQILKQ EWPQNWPEFI PELIGSSSSS VNVCENNMIV LKLLSEEVFD ...String:
MEGILDFSND LDIALLDQVV STFYQGSGVQ QKQAQEILTK FQDNPDAWQK ADQILQFSTN PQSKFIALS ILDKLITRKW KLLPNDHRIG IRNFVVGMII SMCQDDEVFK TQKNLINKSD L TLVQILKQ EWPQNWPEFI PELIGSSSSS VNVCENNMIV LKLLSEEVFD FSAEQMTQAK AL HLKNSMS KEFEQIFKLC FQVLEQGSSS SLIVATLESL LRYLHWIPYR YIYETNILEL LST KFMTSP DTRAITLKCL TEVSNLKIPQ DNDLIKRQTV LFFQNTLQQI ATSVMPVTAD LKAT YANAN GNDQSFLQDL AMFLTTYLAR NRALLESDES LRELLLNAHQ YLIQLSKIEE RELFK TTLD YWHNLVADLF YEVQRLPATE MSPLIQLSVG SQAISTGSGA LNPEYMKRFP LKKHIY EEI CSQLRLVIIE NMVRPEEVLV VENDEGEIVR EFVKESDTIQ LYKSEREVLV YLTHLNV ID TEEIMISKLA RQIDGSEWSW HNINTLSWAI GSISGTMSED TEKRFVVTVI KDLLDLTV K KRGKDNKAVV ASDIMYVVGQ YPRFLKAHWN FLRTVILKLF EFMHETHEGV QDMACDTFI KIVQKCKYHF VIQQPRESEP FIQTIIRDIQ KTTADLQPQQ VHTFYKACGI IISEERSVAE RNRLLSDLM QLPNMAWDTI VEQSTANPTL LLDSETVKII ANIIKTNVAV CTSMGADFYP Q LGHIYYNM LQLYRAVSSM ISAQVAAEGL IATKTPKVRG LRTIKKEILK LVETYISKAR NL DDVVKVL VEPLLNAVLE DYMNNVPDAR DAEVLNCMTT VVEKVGHMIP QGVILILQSV FEC TLDMIN KDFTEYPEHR VEFYKLLKVI NEKSFAAFLE LPPAAFKLFV DAICWAFKHN NRDV EVNGL QIALDLVKNI ERMGNVPFAN EFHKNYFFIF VSETFFVLTD SDHKSGFSKQ ALLLM KLIS LVYDNKISVP LYQEAEVPQG TSNQVYLSQY LANMLSNAFP HLTSEQIASF LSALTK QYK DLVVFKGTLR DFLVQIKEVG GDPTDYLFAE DKENALMEQN RLEREKAAKI GGLLKPS EL DD

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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: 9.61 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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