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- PDB-6iwa: Crystal structure of Importin-alpha and phosphoserine GM130 -

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Basic information

Entry
Database: PDB / ID: 6iwa
TitleCrystal structure of Importin-alpha and phosphoserine GM130
Components
  • Importin subunit alpha-1
  • PHOSPHOSERINE GM130
KeywordsPROTEIN BINDING / Importin alpha / GM130
Function / homology
Function and homology information


Golgi cis cisterna / meiotic spindle assembly / 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 ...Golgi cis cisterna / meiotic spindle assembly / 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 / cis-Golgi network / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / COPII-coated ER to Golgi transport vesicle / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / syntaxin binding / centrosome cycle / nuclear import signal receptor activity / Golgi cisterna membrane / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / : / Golgi organization / mitotic spindle assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / negative regulation of protein binding / spindle assembly / endoplasmic reticulum-Golgi intermediate compartment membrane / negative regulation of autophagy / protein import into nucleus / cytoplasmic stress granule / spindle pole / mitotic spindle / protein transport / host cell / protein homotetramerization / microtubule binding / DNA-binding transcription factor binding / microtubule / postsynaptic density / cadherin binding / Golgi membrane / protein kinase binding / glutamatergic synapse / Golgi apparatus / nucleoplasm / identical protein binding / 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 / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / 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: 2.4 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
DepositionDec 5, 2018Deposition 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOSERINE GM130
C: Importin subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)50,2152
Polymers50,2152
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint3 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.657, 89.797, 99.422
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 PHOSPHOSERINE GM130 / 130 kDa cis-Golgi matrix protein / GM130 / GM130 autoantigen / Golgin-95


Mass: 3315.868 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
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.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.5 Å3/Da / Density % sol: 64.82 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.1M Sodium citrate tribasic dihydrate, 16% w/v Polyethylene glycol 8000 (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 28211 / % possible obs: 99.9 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rsym value: 0.042 / Net I/σ(I): 21.5
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 2744 / CC1/2: 0.983 / Rsym value: 0.142

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Processing

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

1iq1


Resolution: 2.4→20 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.216 1996 -
Rwork0.171 --
obs-28196 99.9 %
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3483 0 0 152 3635
LS refinement shellHighest resolution: 2.4 Å
RfactorNum. reflection% reflection
Rfree0.239 --
Rwork0.203 --
obs-1744 95 %
Refinement TLS params.Method: refined / Origin x: -1.3191 Å / Origin y: 23.8423 Å / Origin z: 0.5434 Å
111213212223313233
T0.2725 Å20.0298 Å20.0427 Å2-0.2805 Å2-0.017 Å2--0.3205 Å2
L1.2803 °21.015 °20.6998 °2-1.7046 °20.8906 °2--0.8861 °2
S0.0038 Å °0.2368 Å °-0.2375 Å °-0.1278 Å °0.1525 Å °-0.1336 Å °-0.0437 Å °0.129 Å °-0.1646 Å °
Refinement TLS groupSelection details: ALL

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