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- EMDB-27780: Cryo-EM structure of Importin-4 bound to RanGTP -

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Basic information

Entry
Database: EMDB / ID: EMD-27780
TitleCryo-EM structure of Importin-4 bound to RanGTP
Map data
Sample
  • Complex: Complex of Importin-4 bound to RanGTP
    • Protein or peptide: Importin-4
    • Protein or peptide: GTP-binding nuclear protein GSP1/CNR1
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
KeywordsImportin / Karyopherin / GTPase / nuclear import / PROTEIN TRANSPORT
Function / homology
Function and homology information


regulation of cell cycle phase transition / Postmitotic nuclear pore complex (NPC) reformation / regulation of nucleocytoplasmic transport / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / nucleus organization / protein localization to nucleus / ribosomal subunit export from nucleus ...regulation of cell cycle phase transition / Postmitotic nuclear pore complex (NPC) reformation / regulation of nucleocytoplasmic transport / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / nucleus organization / protein localization to nucleus / ribosomal subunit export from nucleus / small GTPase binding / protein import into nucleus / GTPase activity / chromatin / GTP binding / protein-containing complex / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Importin beta family / TOG domain / TOG / HEAT-like repeat / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain ...Importin beta family / TOG domain / TOG / HEAT-like repeat / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GTP-binding nuclear protein GSP1/CNR1 / Importin-4
Similarity search - Component
Biological speciesHomo sapiens (human) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsBernardes NE / Fung HYJ / Li Y / Chen Z / Chook YM
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141461 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069909 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP170644 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structure of IMPORTIN-4 bound to the H3-H4-ASF1 histone-histone chaperone complex.
Authors: Natália Elisa Bernardes / Ho Yee Joyce Fung / Yang Li / Zhe Chen / Yuh Min Chook /
Abstract: IMPORTIN-4, the primary nuclear import receptor of core histones H3 and H4, binds the H3-H4 dimer and histone chaperone ASF1 prior to nuclear import. However, how H3-H3-ASF1 is recognized for ...IMPORTIN-4, the primary nuclear import receptor of core histones H3 and H4, binds the H3-H4 dimer and histone chaperone ASF1 prior to nuclear import. However, how H3-H3-ASF1 is recognized for transport cannot be explained by available crystal structures of IMPORTIN-4-histone tail peptide complexes. Our 3.5-Å IMPORTIN-4-H3-H4-ASF1 cryoelectron microscopy structure reveals the full nuclear import complex and shows a binding mode different from suggested by previous structures. The N-terminal half of IMPORTIN-4 clamps the globular H3-H4 domain and H3 αN helix, while its C-terminal half binds the H3 N-terminal tail weakly; tail contribution to binding energy is negligible. ASF1 binds H3-H4 without contacting IMPORTIN-4. Together, ASF1 and IMPORTIN-4 shield nucleosomal H3-H4 surfaces to chaperone and import it into the nucleus where RanGTP binds IMPORTIN-4, causing large conformational changes to release H3-H4-ASF1. This work explains how full-length H3-H4 binds IMPORTIN-4 in the cytoplasm and how it is released in the nucleus.
History
DepositionAug 4, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27780.png

Downloads & links

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Map

FileDownload / File: emd_27780.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.094 Å
Density
Contour LevelBy AUTHOR: 0.49
Minimum - Maximum-1.3807737 - 1.6915183
Average (Standard dev.)0.002120981 (±0.074448854)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 273.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27780_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27780_half_map_2.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 : Complex of Importin-4 bound to RanGTP

EntireName: Complex of Importin-4 bound to RanGTP
Components
  • Complex: Complex of Importin-4 bound to RanGTP
    • Protein or peptide: Importin-4
    • Protein or peptide: GTP-binding nuclear protein GSP1/CNR1
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Complex of Importin-4 bound to RanGTP

SupramoleculeName: Complex of Importin-4 bound to RanGTP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Importin-4

MacromoleculeName: Importin-4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.83207 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MESAGLEQLL RELLLPDTER IRRATEQLQI VLRAPAALPA LCDLLASAAD PQIRQFAAVL TRRRLNTRWR RLAAEQRESL KSLILTALQ RETEHCVSLS LAQLSATIFR KEGLEAWPQL LQLLQHSTHS PHSPEREMGL LLLSVVVTSR PEAFQPHHRE L LRLLNETL ...String:
MESAGLEQLL RELLLPDTER IRRATEQLQI VLRAPAALPA LCDLLASAAD PQIRQFAAVL TRRRLNTRWR RLAAEQRESL KSLILTALQ RETEHCVSLS LAQLSATIFR KEGLEAWPQL LQLLQHSTHS PHSPEREMGL LLLSVVVTSR PEAFQPHHRE L LRLLNETL GEVGSPGLLF YSLRTLTTMA PYLSTEDVPL ARMLVPKLIM AMQTLIPIDE AKACEALEAL DELLESEVPV IT PYLSEVL TFCLEVARNV ALGNAIRIRI LCCLTFLVKV KSKALLKNRL LPPLLHTLFP IVAAEPPPGQ LDPEDQDSEE EEL EIELMG ETPKHFAVQV VDMLALHLPP EKLCPQLMPM LEEALRSESP YQRKAGLLVL AVLSDGAGDH IRQRLLPPLL QIVC KGLED PSQVVRNAAL FALGQFSENL QPHISSYSRE VMPLLLAYLK SVPLGHTHHL AKACYALENF VENLGPKVQP YLPEL MECM LQLLRNPSSP RAKELAVSAL GAIATAAQAS LLPYFPAIME HLREFLLTGR EDLQPVQIQS LETLGVLARA VGEPMR PLA EECCQLGLGL CDQVDDPDLR RCTYSLFAAL SGLMGEGLAP HLEQITTLML LSLRSTEGIV PQYDGSSSFL LFDDESD GE EEEELMDEDV EEEDDSEISG YSVENAFFDE KEDTCAAVGE ISVNTSVAFL PYMESVFEEV FKLLECPHLN VRKAAHEA L GQFCCALHKA CQSCPSEPNT AALQAALARV VPSYMQAVNR ERERQVVMAV LEALTGVLRS CGTLTLKPPG RLAELCGVL KAVLQRKTAC QDTDEEEEEE DDDQAEYDAM LLEHAGEAIP ALAAAAGGDS FAPFFAGFLP LLVCKTKQGC TVAEKSFAVG TLAETIQGL GAASAQFVSR LLPVLLSTAQ EADPEVRSNA IFGMGVLAEH GGHPAQEHFP KLLGLLFPLL ARERHDRVRD N ICGALARL LMASPTRKPE PQVLAALLHA LPLKEDLEEW VTIGRLFSFL YQSSPDQVID VAPELLRICS LILADNKIPP DT KAALLLL LTFLAKQHTD SFQAALGSLP VDKAQELQAV LGLS

UniProtKB: Importin-4

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Macromolecule #2: GTP-binding nuclear protein GSP1/CNR1

MacromoleculeName: GTP-binding nuclear protein GSP1/CNR1 / type: protein_or_peptide / ID: 2
Details: Truncated yeast Ran (residues 1-179) with the Q71L mutation
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.825357 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSAPAANGEV PTFKLVLVGD GGTGKTTFVK RHLTGEFEKK YIATIGVEVH PLSFYTNFGE IKFDVWDTAG LEKFGGLRDG YYINAQCAI IMFDVTSRIT YKNVPNWHRD LVRVCENIPI VLCGNKVDVK ERKVKAKTIT FHRKKNLQYY DISAKSNYNF E KPFLWLAR ...String:
MSAPAANGEV PTFKLVLVGD GGTGKTTFVK RHLTGEFEKK YIATIGVEVH PLSFYTNFGE IKFDVWDTAG LEKFGGLRDG YYINAQCAI IMFDVTSRIT YKNVPNWHRD LVRVCENIPI VLCGNKVDVK ERKVKAKTIT FHRKKNLQYY DISAKSNYNF E KPFLWLAR KLAGNPQLEF VASPALAPPE VQVDEQLMQQ YQQEMEQATA LPLPDEDDAD L

UniProtKB: GTP-binding nuclear protein GSP1/CNR1

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16089
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3.1)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8dyo:
Cryo-EM structure of Importin-4 bound to RanGTP

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