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- PDB-7umi: Importin a1 bound to Cp183-CTD -

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Basic information

Entry
Database: PDB / ID: 7umi
TitleImportin a1 bound to Cp183-CTD
Components
  • HBV-NLS
  • Importin subunit alpha-1
KeywordsPROTEIN TRANSPORT / nuclear import / viral replication / peptide binding / nuclear localization signal binding / NUCLEAR PROTEIN
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding ...Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / cytosol
Similarity search - Function
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 / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats ...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 / IBB domain profile. / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
Hepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsYang, R. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM122844-04 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
DepositionApr 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HBV-NLS
E: Importin subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)52,1082
Polymers52,1082
Non-polymers00
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.436, 90.688, 97.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide HBV-NLS


Mass: 1261.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hepatitis B virus
#2: Protein Importin subunit alpha-1 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 50846.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52293
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.6 M sodium citrate, 0.1 M HEPES pH 7.2, 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 47594 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.2 Å2 / CC1/2: 0.736 / Rpim(I) all: 0.033 / Rsym value: 0.052 / Net I/av σ(I): 22.5 / Net I/σ(I): 11.5
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 47594 / Rpim(I) all: 0.605 / Rsym value: 0.739 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LEU

7leu


Resolution: 1.99→41.09 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 2019 4.25 %
Rwork0.1837 --
obs0.185 47537 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→41.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 0 274 3579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083371
X-RAY DIFFRACTIONf_angle_d0.9454592
X-RAY DIFFRACTIONf_dihedral_angle_d4.754455
X-RAY DIFFRACTIONf_chiral_restr0.052553
X-RAY DIFFRACTIONf_plane_restr0.008591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.29291440.2733034X-RAY DIFFRACTION93
2.04-2.090.29341420.26413215X-RAY DIFFRACTION99
2.09-2.160.28081450.2423263X-RAY DIFFRACTION100
2.16-2.220.24821380.21553242X-RAY DIFFRACTION100
2.22-2.30.24331510.1943264X-RAY DIFFRACTION99
2.3-2.40.21281390.1883227X-RAY DIFFRACTION99
2.4-2.510.22141390.1893229X-RAY DIFFRACTION98
2.51-2.640.2231410.19343235X-RAY DIFFRACTION99
2.64-2.80.26711510.1933290X-RAY DIFFRACTION100
2.8-3.020.24731410.19083295X-RAY DIFFRACTION99
3.02-3.320.20411480.19623279X-RAY DIFFRACTION99
3.32-3.80.19441430.18013198X-RAY DIFFRACTION96
3.8-4.790.18451500.15143359X-RAY DIFFRACTION100
4.79-41.090.19421470.16453388X-RAY DIFFRACTION96

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