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- PDB-7jvo: Importin alpha bound to the C-terminus of ACE2 -

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Basic information

Entry
Database: PDB / ID: 7jvo
TitleImportin alpha bound to the C-terminus of ACE2
Components
  • ARG-LYS-LYS-LYS-ASN-LYS-ALA
  • Importin subunit alpha-1
KeywordsTRANSPORT PROTEIN / Importin / karyopherin / ACE2
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 / nuclear localization sequence binding / NLS-bearing protein import into nucleus / positive regulation of amino acid transport / angiotensin-converting enzyme 2 ...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 / nuclear localization sequence binding / NLS-bearing protein import into nucleus / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / host cell / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / angiotensin maturation / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / Attachment and Entry / carboxypeptidase activity / negative regulation of signaling receptor activity / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / cilium / negative regulation of ERK1 and ERK2 cascade / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / endocytic vesicle membrane / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / nuclear membrane / DNA-binding transcription factor binding / endopeptidase activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / postsynaptic density / Attachment and Entry / membrane fusion / receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / glutamatergic synapse / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / 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 / Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Importin subunit alpha-1 / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsForwood, J.K. / Cross, E.M. / Tsimbalyuk, S.
CitationJournal: Cell Discov / Year: 2021
Title: Targeting novel LSD1-dependent ACE2 demethylation domains inhibits SARS-CoV-2 replication.
Authors: Tu, W.J. / McCuaig, R.D. / Melino, M. / Rawle, D.J. / Le, T.T. / Yan, K. / Suhrbier, A. / Johnston, R.L. / Koufariotis, L.T. / Waddell, N. / Cross, E.M. / Tsimbalyuk, S. / Bain, A. / Ahern, ...Authors: Tu, W.J. / McCuaig, R.D. / Melino, M. / Rawle, D.J. / Le, T.T. / Yan, K. / Suhrbier, A. / Johnston, R.L. / Koufariotis, L.T. / Waddell, N. / Cross, E.M. / Tsimbalyuk, S. / Bain, A. / Ahern, E. / Collinson, N. / Phipps, S. / Forwood, J.K. / Seddiki, N. / Rao, S.
History
DepositionAug 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha-1
B: ARG-LYS-LYS-LYS-ASN-LYS-ALA


Theoretical massNumber of molelcules
Total (without water)56,9622
Polymers56,9622
Non-polymers00
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.938, 89.948, 100.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: 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: 55268.473 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 (E. coli) / References: UniProt: P52293
#2: Protein/peptide ARG-LYS-LYS-LYS-ASN-LYS-ALA


Mass: 1693.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BYF1*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 600 mM citrate, pH 7.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→29.98 Å / Num. obs: 36873 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 37.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.9
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 3125 / CC1/2: 0.807

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BVT

6bvt


Resolution: 2.2→29.67 Å / SU ML: 0.2253 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9425 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2099 1803 4.9 %
Rwork0.1863 35003 -
obs0.1874 36806 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 0 210 3434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373286
X-RAY DIFFRACTIONf_angle_d0.66534483
X-RAY DIFFRACTIONf_chiral_restr0.041549
X-RAY DIFFRACTIONf_plane_restr0.0043573
X-RAY DIFFRACTIONf_dihedral_angle_d2.1772705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.27831320.24942645X-RAY DIFFRACTION99.75
2.26-2.330.29541320.24152644X-RAY DIFFRACTION100
2.33-2.40.27321290.23292676X-RAY DIFFRACTION100
2.4-2.490.24771290.21472666X-RAY DIFFRACTION100
2.49-2.590.2921520.21472635X-RAY DIFFRACTION99.96
2.59-2.70.29091590.21712656X-RAY DIFFRACTION99.93
2.7-2.850.23291500.20672660X-RAY DIFFRACTION100
2.85-3.020.27931250.21192691X-RAY DIFFRACTION100
3.02-3.260.22011440.20412674X-RAY DIFFRACTION100
3.26-3.590.23141360.1912705X-RAY DIFFRACTION100
3.59-4.10.17211240.1612744X-RAY DIFFRACTION99.93
4.1-5.160.16331360.14962741X-RAY DIFFRACTION100
5.16-29.670.15591550.16782866X-RAY DIFFRACTION99.83

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