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- PDB-5k9s: Importin-alpha in complex with HNF1-beta peptide -

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Basic information

Entry
Database: PDB / ID: 5k9s
TitleImportin-alpha in complex with HNF1-beta peptide
Components
  • HNF1 beta A splice variant 2
  • Importin subunit alpha-1
KeywordsTRANSPORT PROTEIN / Nuclear transport
Function / homology
Function and homology information


regulation of pronephros size / pronephric nephron tubule development / pronephros development / Regulation of gene expression in early pancreatic precursor cells / Nephron development / endocrine pancreas development / Developmental Lineage of Pancreatic Acinar Cells / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / Sensing of DNA Double Strand Breaks / genitalia development ...regulation of pronephros size / pronephric nephron tubule development / pronephros development / Regulation of gene expression in early pancreatic precursor cells / Nephron development / endocrine pancreas development / Developmental Lineage of Pancreatic Acinar Cells / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / Sensing of DNA Double Strand Breaks / genitalia development / regulation of transcription by glucose / entry of viral genome into host nucleus through nuclear pore complex via importin / pancreas development / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / insulin secretion / NLS-bearing protein import into nucleus / nuclear import signal receptor activity / nuclear localization sequence binding / non-canonical NF-kappaB signal transduction / positive regulation of transcription initiation by RNA polymerase II / kidney development / positive regulation of type I interferon production / liver development / transcription coregulator binding / Developmental Lineage of Pancreatic Ductal Cells / promoter-specific chromatin binding / protein import into nucleus / histone deacetylase binding / cytoplasmic stress granule / host cell / nuclear membrane / transcription regulator complex / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / postsynaptic density / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / glutamatergic synapse / protein homodimerization activity / DNA-templated transcription / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Hepatocyte nuclear factor 1, beta isoform, C-terminal / Hepatocyte nuclear factor 1, N-terminal domain superfamily / Hepatocyte nuclear factor 1 / Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus / Hepatocyte nuclear factor 1, N-terminal / HNF-1, dimerization domain / HNF-1, POU-specific (POUs) atypical domain / Hepatocyte nuclear factor 1 (HNF-1), N terminus / POU-specific (POUs) atypical domain profile. / HNF-1 dimerization (HNF-p1) domain profile. ...Hepatocyte nuclear factor 1, beta isoform, C-terminal / Hepatocyte nuclear factor 1, N-terminal domain superfamily / Hepatocyte nuclear factor 1 / Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus / Hepatocyte nuclear factor 1, N-terminal / HNF-1, dimerization domain / HNF-1, POU-specific (POUs) atypical domain / Hepatocyte nuclear factor 1 (HNF-1), N terminus / POU-specific (POUs) atypical domain profile. / HNF-1 dimerization (HNF-p1) domain profile. / 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. / 'Homeobox' domain signature. / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily / Alpha Horseshoe / Armadillo-like helical / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Hepatocyte nuclear factor 1-beta / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWiedmann, M.M. / Aibara, S. / Spring, D.R. / Stewart, M. / Brenton, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105178939 United Kingdom
CitationJournal: To Be Published
Title: Importin-alpha in complex with HNF1-beta peptide
Authors: Wiedmann, M.M. / Aibara, S. / Spring, D.R. / Stewart, M. / Brenton, J.
History
DepositionJun 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: 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: HNF1 beta A splice variant 2
C: HNF1 beta A splice variant 2


Theoretical massNumber of molelcules
Total (without water)52,6143
Polymers52,6143
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint3 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.380, 111.394, 129.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 49644.406 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
#2: Protein/peptide HNF1 beta A splice variant 2


Mass: 1484.815 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNF1B / Production host: synthetic construct (others) / References: UniProt: P35680*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 8K, 0.09 M NPS, 20% ethylene glycol, 0.1 M Buffer 1 (Morpheus I)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.4→129.4 Å / Num. obs: 23388 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.997 / Net I/σ(I): 10.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
Aimless0.5.16data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U54

4u54


Resolution: 2.4→65.712 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 1204 5.15 %Random
Rwork0.1852 ---
obs0.1872 23358 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→65.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 0 53 3500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083505
X-RAY DIFFRACTIONf_angle_d0.7974761
X-RAY DIFFRACTIONf_dihedral_angle_d16.651302
X-RAY DIFFRACTIONf_chiral_restr0.043568
X-RAY DIFFRACTIONf_plane_restr0.005610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.49610.35481170.26192426X-RAY DIFFRACTION100
2.4961-2.60970.2841410.23772419X-RAY DIFFRACTION100
2.6097-2.74730.24091110.22112454X-RAY DIFFRACTION100
2.7473-2.91940.26971310.22032442X-RAY DIFFRACTION100
2.9194-3.14480.26391310.21762460X-RAY DIFFRACTION100
3.1448-3.46130.24391340.22092434X-RAY DIFFRACTION100
3.4613-3.96210.21291540.18692444X-RAY DIFFRACTION100
3.9621-4.99160.19161460.14812482X-RAY DIFFRACTION100
4.9916-65.73680.19471390.16212593X-RAY DIFFRACTION100

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