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- PDB-7cru: hnRNPK NLS in complex with Importin alpha 1 (KPNA2) -

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Basic information

Entry
Database: PDB / ID: 7cru
TitlehnRNPK NLS in complex with Importin alpha 1 (KPNA2)
Components
  • Heterogeneous nuclear ribonucleoprotein K
  • Importin subunit alpha-1
KeywordsTRANSPORT PROTEIN / importin alpha / hnRNPK / NLS / complex
Function / homology
Function and homology information


regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Sensing of DNA Double Strand Breaks / regulation of DNA recombination / regulation of low-density lipoprotein particle clearance / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex ...regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Sensing of DNA Double Strand Breaks / regulation of DNA recombination / regulation of low-density lipoprotein particle clearance / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / : / nuclear import signal receptor activity / podosome / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / DNA metabolic process / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of type I interferon production / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / HCMV Late Events / cell projection / mRNA splicing, via spliceosome / positive regulation of receptor-mediated endocytosis / ISG15 antiviral mechanism / histone deacetylase binding / protein import into nucleus / cytoplasmic stress granule / SARS-CoV-1 activates/modulates innate immune responses / host cell / nuclear membrane / Estrogen-dependent gene expression / cadherin binding / protein domain specific binding / ribonucleoprotein complex / Golgi membrane / focal adhesion / negative regulation of DNA-templated transcription / mRNA binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
ROK, N-terminal / ROKNT (NUC014) domain / KH domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / K Homology domain, type 1 / Importin-alpha, importin-beta-binding domain ...ROK, N-terminal / ROKNT (NUC014) domain / KH domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / K Homology domain, type 1 / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Type-1 KH domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / K Homology domain, type 1 superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / K Homology domain / K homology RNA-binding domain / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Importin subunit alpha-1 / Heterogeneous nuclear ribonucleoprotein K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYao, J. / Sun, Q.
CitationJournal: Cell.Mol.Life Sci. / Year: 2021
Title: Nuclear import receptors and hnRNPK mediates nuclear import and stress granule localization of SIRLOIN.
Authors: Yao, J. / Tu, Y. / Shen, C. / Zhou, Q. / Xiao, H. / Jia, D. / Sun, Q.
History
DepositionAug 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: 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
Revision 1.2Nov 29, 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

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Assembly

Deposited unit
B: Heterogeneous nuclear ribonucleoprotein K
A: Importin subunit alpha-1
D: Heterogeneous nuclear ribonucleoprotein K
C: Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,18210
Polymers104,7954
Non-polymers3876
Water1,74797
1
B: Heterogeneous nuclear ribonucleoprotein K
A: Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4563
Polymers52,3972
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-1 kcal/mol
Surface area18600 Å2
MethodPISA
2
D: Heterogeneous nuclear ribonucleoprotein K
C: Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7267
Polymers52,3972
Non-polymers3285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-3 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.792, 83.317, 101.372
Angle α, β, γ (deg.)90.000, 98.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Heterogeneous nuclear ribonucleoprotein K / hnRNPK NLS / hnRNP K / Transformation up-regulated nuclear protein / TUNP


Mass: 2877.194 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPK, HNRPK / Production host: Escherichia coli (E. coli) / References: UniProt: P61978
#2: Protein Importin subunit alpha-1 / Karyopherin subunit alpha-2 / RAG cohort protein 1 / SRP1-alpha


Mass: 49520.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA2, RCH1, SRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52292
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.86 Å3/Da / Density % sol: 68.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Ammonium Acetate, 0.1 M Bis-Tris pH 5.5, 17% w/v PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 36276 / % possible obs: 98.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.234 / Rpim(I) all: 0.175 / Rrim(I) all: 0.255 / Χ2: 0.927 / Net I/σ(I): 2.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.8-2.853.317550.3380.8880.79796.4
2.85-2.93.418240.2780.8180.83398.8
2.9-2.963.318130.3380.7620.83799.6
2.96-3.023.418100.4630.6650.80698.9
3.02-3.083.318270.5130.5840.81698.60.916
3.08-3.153.317660.520.5430.827970.836
3.15-3.23317240.5830.4260.90193.70.6270.762
3.23-3.323.218020.6680.4050.8998.10.6210.745
3.32-3.423.518090.7340.3520.92499.70.5640.667
3.42-3.533.518320.810.2970.89899.80.4780.564
3.53-3.653.518420.8550.2350.96199.80.3780.446
3.65-3.83.518310.90.1830.99599.70.2930.346
3.8-3.973.418540.9240.1541.04399.60.2440.29
3.97-4.183.518050.9550.1261.001990.2010.238
4.18-4.443.318320.9520.1131.06299.20.1760.21
4.44-4.793.117460.9660.0981.07294.40.1470.178
4.79-5.273.518440.9660.0990.92598.90.1580.187
5.27-6.033.518470.9690.1020.85999.20.1650.194
6.03-7.593.418600.9730.0921.02399.30.1450.172
7.59-503.218530.9730.0671.05496.70.1030.123

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WV6

4wv6


Resolution: 2.8→46.68 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.911 / SU B: 17.501 / SU ML: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.629 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 1850 5.1 %RANDOM
Rwork0.2137 ---
obs0.215 34409 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.29 Å2 / Biso mean: 51.04 Å2 / Biso min: 11.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å2-0 Å2-0.71 Å2
2---2.48 Å20 Å2
3---1.54 Å2
Refinement stepCycle: final / Resolution: 2.8→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6836 0 26 97 6959
Biso mean--61.4 33.76 -
Num. residues----893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0146977
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176522
X-RAY DIFFRACTIONr_angle_refined_deg0.9231.6479490
X-RAY DIFFRACTIONr_angle_other_deg0.7491.63415251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875887
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21724.199312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.881151194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7031528
X-RAY DIFFRACTIONr_chiral_restr0.0450.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021173
LS refinement shellResolution: 2.792→2.865 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 120 -
Rwork0.335 2387 -
all-2507 -
obs--93.72 %

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