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- PDB-6k06: Crystal structure of Importin-alpha and phosphomimetic GM130 -

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Basic information

Entry
Database: PDB / ID: 6k06
TitleCrystal structure of Importin-alpha and phosphomimetic GM130
Components
  • Importin subunit alpha-1
  • Peptide from Golgin subfamily A member 2
KeywordsPROTEIN BINDING / Importin alpha / GM130
Function / homology
Function and homology information


meiotic spindle assembly / Golgi cis cisterna / positive regulation of protein glycosylation / Golgi disassembly / asymmetric cell division / Golgi ribbon formation / 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 / microtubule nucleation ...meiotic spindle assembly / Golgi cis cisterna / positive regulation of protein glycosylation / Golgi disassembly / asymmetric cell division / Golgi ribbon formation / 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 / microtubule nucleation / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / cis-Golgi network / postsynapse to nucleus signaling pathway / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / COPII-mediated vesicle transport / syntaxin binding / nuclear import signal receptor activity / nuclear localization sequence binding / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Golgi cisterna membrane / NLS-bearing protein import into nucleus / COPII-coated ER to Golgi transport vesicle / Golgi organization / protein glycosylation / mitotic spindle assembly / spindle assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane / negative regulation of autophagy / negative regulation of protein binding / mitotic spindle / spindle pole / cytoplasmic stress granule / protein import into nucleus / host cell / protein transport / microtubule binding / DNA-binding transcription factor binding / protein homotetramerization / microtubule / postsynaptic density / cadherin binding / Golgi membrane / glutamatergic synapse / protein kinase binding / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Golgin subfamily A / Golgin subfamily A member 2, C-terminal binding motif / Golgin subfamily A, conserved domain / Putative golgin subfamily A member 2-like protein 5 / GM130 C-terminal binding motif / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat ...Golgin subfamily A / Golgin subfamily A member 2, C-terminal binding motif / Golgin subfamily A, conserved domain / Putative golgin subfamily A member 2-like protein 5 / GM130 C-terminal binding motif / 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 / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Golgin subfamily A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChang, C.-C. / Chen, C.-J. / Pien, Y.-C. / Tsai, S.-Y. / Hsia, K.-C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)106-2311-B-001 -038 -MY3 Taiwan
CitationJournal: Nat Commun / Year: 2019
Title: Ran pathway-independent regulation of mitotic Golgi disassembly by Importin-alpha.
Authors: Chang, C.-C. / Chen, C.-J. / Grauffel, C. / Pien, Y.-C. / Lim, C. / Tsai, S.-Y. / Hsia, K.-C.
History
DepositionMay 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: Peptide from Golgin subfamily A member 2
C: Importin subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)52,6962
Polymers52,6962
Non-polymers00
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint1 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.734, 79.001, 89.569
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Peptide from Golgin subfamily A member 2 / phosphomimetic GM130 / 130 kDa cis-Golgi matrix protein / GM130 / GM130 autoantigen / Golgin-95


Mass: 5797.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOLGA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08379
#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: 46898.656 Da / Num. of mol.: 1 / Mutation: S25D
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.2M Potassium thiocyante, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 50110 / % possible obs: 95.1 % / Redundancy: 7.3 % / CC1/2: 0.99 / Rsym value: 0.04 / Net I/σ(I): 20.7
Reflection shellResolution: 1.75→1.85 Å / Num. unique obs: 7420 / CC1/2: 0.98 / Rsym value: 0.14

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IQ1

1iq1


Resolution: 1.75→20 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.199 2000 -
Rwork0.172 --
obs-50110 95.1 %
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 0 442 3871
LS refinement shellHighest resolution: 1.75 Å
RfactorNum. reflection% reflection
Rfree0.272 --
Rwork0.244 --
obs-3305 93 %
Refinement TLS params.Method: refined / Origin x: -0.6444 Å / Origin y: -10.84 Å / Origin z: 22.5176 Å
111213212223313233
T0.2149 Å2-0.0122 Å20.0101 Å2-0.2066 Å20.0359 Å2--0.2693 Å2
L0.9073 °2-0.5568 °2-0.6202 °2-0.7907 °20.6981 °2--0.8435 °2
S-0.0216 Å °0.031 Å °0.0127 Å °0.0935 Å °-0.0028 Å °0.0173 Å °0.0545 Å °-0.0061 Å °0.023 Å °
Refinement TLS groupSelection details: all

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