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- EMDB-29936: CRYO-EM STRUCTURE OF IMPORTIN ALPHA1/BETA HETERODIMER -

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Basic information

Entry
Database: EMDB / ID: EMD-29936
TitleCRYO-EM STRUCTURE OF IMPORTIN ALPHA1/BETA HETERODIMER
Map data
Sample
  • Complex: Importin Alpha1/Beta Heterodimer
    • Protein or peptide: Importin subunit beta-1
    • Protein or peptide: Importin subunit alpha-1
KeywordsImportins / TRANSPORT PROTEIN
Function / homology
Function and homology information


RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / Sensing of DNA Double Strand Breaks / regulation of DNA recombination / astral microtubule organization / establishment of mitotic spindle localization / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / Sensing of DNA Double Strand Breaks / regulation of DNA recombination / astral microtubule organization / establishment of mitotic spindle localization / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / ribosomal protein import into nucleus / NS1 Mediated Effects on Host Pathways / Initiation of Nuclear Envelope (NE) Reformation / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear import signal receptor activity / DNA metabolic process / CaMK IV-mediated phosphorylation of CREB / mitotic metaphase chromosome alignment / nuclear localization sequence binding / NLS-bearing protein import into nucleus / positive regulation of type I interferon production / mitotic spindle assembly / nuclear pore / Assembly of the ORC complex at the origin of replication / Hsp90 protein binding / small GTPase binding / ISG15 antiviral mechanism / histone deacetylase binding / cytoplasmic stress granule / specific granule lumen / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / host cell / Interferon alpha/beta signaling / nuclear envelope / nuclear membrane / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / protein domain specific binding / Golgi membrane / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / enzyme binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain ...Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / HEAT repeat profile. / IBB domain profile. / HEAT, type 2 / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Importin subunit alpha-1 / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsKo Y / Cingolani G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Sci Adv / Year: 2024
Title: Structural basis for nuclear import of hepatitis B virus (HBV) nucleocapsid core.
Authors: Ruoyu Yang / Ying-Hui Ko / Fenglin Li / Ravi K Lokareddy / Chun-Feng David Hou / Christine Kim / Shelby Klein / Santiago Antolínez / Juan F Marín / Carolina Pérez-Segura / Martin F ...Authors: Ruoyu Yang / Ying-Hui Ko / Fenglin Li / Ravi K Lokareddy / Chun-Feng David Hou / Christine Kim / Shelby Klein / Santiago Antolínez / Juan F Marín / Carolina Pérez-Segura / Martin F Jarrold / Adam Zlotnick / Jodi A Hadden-Perilla / Gino Cingolani /
Abstract: Nuclear import of the hepatitis B virus (HBV) nucleocapsid is essential for replication that occurs in the nucleus. The ~360-angstrom HBV capsid translocates to the nuclear pore complex (NPC) as an ...Nuclear import of the hepatitis B virus (HBV) nucleocapsid is essential for replication that occurs in the nucleus. The ~360-angstrom HBV capsid translocates to the nuclear pore complex (NPC) as an intact particle, hijacking human importins in a reaction stimulated by host kinases. This paper describes the mechanisms of HBV capsid recognition by importins. We found that importin α1 binds a nuclear localization signal (NLS) at the far end of the HBV coat protein Cp183 carboxyl-terminal domain (CTD). This NLS is exposed to the capsid surface through a pore at the icosahedral quasi-sixfold vertex. Phosphorylation at serine-155, serine-162, and serine-170 promotes CTD compaction but does not affect the affinity for importin α1. The binding of 30 importin α1/β1 augments HBV capsid diameter to ~620 angstroms, close to the maximum size trafficable through the NPC. We propose that phosphorylation favors CTD externalization and prompts its compaction at the capsid surface, exposing the NLS to importins.
History
DepositionMar 2, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29936.png

Downloads & links

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Map

FileDownload / File: emd_29936.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 208 pix.
= 181.376 Å		0.87 Å/pix.
x 208 pix.
= 181.376 Å		0.87 Å/pix.
x 208 pix.
= 181.376 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.872 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.1564849 - 0.29756916
Average (Standard dev.)0.0021789935 (±0.014354405)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 181.37599 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29936_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29936_half_map_2.map
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Sample components

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Entire : Importin Alpha1/Beta Heterodimer

EntireName: Importin Alpha1/Beta Heterodimer
Components
  • Complex: Importin Alpha1/Beta Heterodimer
    • Protein or peptide: Importin subunit beta-1
    • Protein or peptide: Importin subunit alpha-1

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Supramolecule #1: Importin Alpha1/Beta Heterodimer

SupramoleculeName: Importin Alpha1/Beta Heterodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Importin subunit beta-1

MacromoleculeName: Importin subunit beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.257812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MELITILEKT VSPDRLELEA AQKFLERAAV ENLPTFLVEL SRVLANPGNS QVARVAAGLQ IKNSLTSKDP DIKAQYQQRW LAIDANARR EVKNYVLQTL GTETYRPSSA SQCVAGIACA EIPVNQWPEL IPQLVANVTN PNSTEHMKES TLEAIGYICQ D IDPEQLQD ...String:
MELITILEKT VSPDRLELEA AQKFLERAAV ENLPTFLVEL SRVLANPGNS QVARVAAGLQ IKNSLTSKDP DIKAQYQQRW LAIDANARR EVKNYVLQTL GTETYRPSSA SQCVAGIACA EIPVNQWPEL IPQLVANVTN PNSTEHMKES TLEAIGYICQ D IDPEQLQD KSNEILTAII QGMRKEEPSN NVKLAATNAL LNSLEFTKAN FDKESERHFI MQVVCEATQC PDTRVRVAAL QN LVKIMSL YYQYMETYMG PALFAITIEA MKSDIDEVAL QGIEFWSNVC DEEMDLAIEA SEAAEQGRPP EHTSKFYAKG ALQ YLVPIL TQTLTKQDEN DDDDDWNPCK AAGVCLMLLA TCCEDDIVPH VLPFIKEHIK NPDWRYRDAA VMAFGCILEG PEPS QLKPL VIQAMPTLIE LMKDPSVVVR DTAAWTVGRI CELLPEAAIN DVYLAPLLQC LIEGLSAEPR VASNVCWAFS SLAEA AYEA ADVADDQEEP ATYCLSSSFE LIVQKLLETT DRPDGHQNNL RSSAYESLME IVKNSAKDCY PAVQKTTLVI MERLQQ VLQ MESHIQSTSD RIQFNDLQSL LCATLQNVLR KVQHQDALQI SDVVMASLLR MFQSTAGSGG VQEDALMAVS TLVEVLG GE FLKYMEAFKP FLGIGLKNYA EYQVCLAAVG LVGDLCRALQ SNIIPFCDEV MQLLLENLGN ENVHRSVKPQ ILSVFGDI A LAIGGEFKKY LEVVLNTLQQ ASQAQVDKSD YDMVDYLNEL RESCLEAYTG IVQGLKGDQE NVHPDVMLVQ PRVEFILSF IDHIAGDEDH TDGVVACAAG LIGDLCTAFG KDVLKLVEAR PMIHELLTEG RRSKTNKAKT LATWATKELR KLKNQA

UniProtKB: Importin subunit beta-1

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Macromolecule #2: Importin subunit alpha-1

MacromoleculeName: Importin subunit alpha-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.296262 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AARLHRFKNK GKDSTEMRRR RIEVNVELRK AKKDDQMLKR RNV

UniProtKB: Importin subunit alpha-1

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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: 8
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1qgk

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1009142
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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