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- PDB-5h43: Structural and mechanistical studies of the nuclear import by Imp... -

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Basic information

Entry
Database: PDB / ID: 5h43
TitleStructural and mechanistical studies of the nuclear import by Importin-alpha
Components
  • (Histone acetyltransferase KAT8) x 2
  • Importin subunit alpha-1
KeywordsPROTEIN TRANSPORT/TRANSFERASE / importin alpha / nuclear import / PROTEIN TRANSPORT-TRANSFERASE complex
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / MSL complex / regulation of DNA recombination / histone H4K16 acetyltransferase activity / entry of viral genome into host nucleus through nuclear pore complex via importin / regulation of mRNA processing / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / myeloid cell differentiation / NLS-dependent protein nuclear import complex ...Sensing of DNA Double Strand Breaks / MSL complex / regulation of DNA recombination / histone H4K16 acetyltransferase activity / entry of viral genome into host nucleus through nuclear pore complex via importin / regulation of mRNA processing / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / myeloid cell differentiation / NLS-dependent protein nuclear import complex / host cell / NSL complex / : / nuclear import signal receptor activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear localization sequence binding / DNA metabolic process / peptide-lysine-N-acetyltransferase activity / CaMK IV-mediated phosphorylation of CREB / NLS-bearing protein import into nucleus / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / neurogenesis / regulation of autophagy / transcription coregulator activity / ISG15 antiviral mechanism / kinetochore / nuclear matrix / protein import into nucleus / histone deacetylase binding / SARS-CoV-1 activates/modulates innate immune responses / HATs acetylate histones / nuclear membrane / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / Golgi membrane / negative regulation of DNA-templated transcription / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily ...MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / 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. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Chromo-like domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Acyl-CoA N-acyltransferase / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Winged helix-like DNA-binding domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, R. / Li, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Natural Science Foundation of China31470726 China
CitationJournal: Traffic / Year: 2018
Title: Structural insights into the nuclear import of the histone acetyltransferase males-absent-on-the-first by importin alpha 1
Authors: Zheng, W. / Wang, R. / Liu, X. / Tian, S. / Yao, B. / Chen, A. / Jin, S. / Li, Y.
History
DepositionOct 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Histone acetyltransferase KAT8
C: Histone acetyltransferase KAT8


Theoretical massNumber of molelcules
Total (without water)49,4903
Polymers49,4903
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint3 kcal/mol
Surface area19180 Å2
Unit cell
Length a, b, c (Å)82.222, 82.222, 169.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Importin subunit alpha-1 / / Karyopherin subunit alpha-2 / RAG cohort protein 1 / SRP1-alpha


Mass: 46359.945 Da / Num. of mol.: 1 / Fragment: UNP residues 70-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA2, RCH1, SRP1 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P52292
#2: Protein/peptide Histone acetyltransferase KAT8 / Lysine acetyltransferase 8 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / hMOF


Mass: 1328.500 Da / Num. of mol.: 1 / Fragment: UNP residues 140-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT8, MOF, MYST1 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H7Z6, histone acetyltransferase
#3: Protein/peptide Histone acetyltransferase KAT8 / Lysine acetyltransferase 8 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / hMOF


Mass: 1801.974 Da / Num. of mol.: 1 / Fragment: UNP residues 128-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT8, MOF, MYST1 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H7Z6, histone acetyltransferase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.89 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 3%(v/v) Tacsimate pH5.0, 0.1M Sodium citrate tribasic dehydrate pH5.6, 16%(w/v) PEG 3350
PH range: 5.0-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.005 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 34657 / % possible obs: 99.9 % / Redundancy: 18.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 34
Reflection shellResolution: 2.31→2.37 Å / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KND

3knd


Resolution: 2.3→47.9 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.164 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24253 1301 4.9 %RANDOM
Rwork0.21144 ---
obs0.21298 25226 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.447 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.3→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 0 146 3614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193526
X-RAY DIFFRACTIONr_bond_other_d0.0060.023477
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9654800
X-RAY DIFFRACTIONr_angle_other_deg1.03838000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.49725.724145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07915612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9411515
X-RAY DIFFRACTIONr_chiral_restr0.1070.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213977
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02738
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.6676.5851809
X-RAY DIFFRACTIONr_mcbond_other6.6646.5841808
X-RAY DIFFRACTIONr_mcangle_it9.0499.8422256
X-RAY DIFFRACTIONr_mcangle_other9.0499.8442257
X-RAY DIFFRACTIONr_scbond_it7.2747.1161717
X-RAY DIFFRACTIONr_scbond_other7.2727.1181718
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.12510.4182545
X-RAY DIFFRACTIONr_long_range_B_refined13.18252.9594215
X-RAY DIFFRACTIONr_long_range_B_other13.19752.8684190
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 90 -
Rwork0.356 1831 -
obs--100 %

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