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- PDB-5gxw: Importin and NuMA complex -

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Basic information

Entry
Database: PDB / ID: 5gxw
TitleImportin and NuMA complex
Components
  • Importin subunit alpha-1
  • Peptide from Nuclear mitotic apparatus protein 1
KeywordsPROTEIN BINDING / Importin NuMA complex
Function / homology
Function and homology information


anastral spindle assembly / positive regulation of protein localization to spindle pole body / positive regulation of mitotic spindle elongation / cytoplasmic microtubule bundle / positive regulation of chromosome separation / Mitotic Prophase / positive regulation of chromosome segregation / microtubule minus-end / cortical microtubule / microtubule bundle ...anastral spindle assembly / positive regulation of protein localization to spindle pole body / positive regulation of mitotic spindle elongation / cytoplasmic microtubule bundle / positive regulation of chromosome separation / Mitotic Prophase / positive regulation of chromosome segregation / microtubule minus-end / cortical microtubule / microtubule bundle / lateral cell cortex / cell cortex region / mitotic spindle astral microtubule / positive regulation of intracellular transport / regulation of metaphase plate congression / mitotic spindle midzone / positive regulation of hair follicle development / astral microtubule organization / positive regulation of spindle assembly / microtubule minus-end binding / Sensing of DNA Double Strand Breaks / microtubule plus-end / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / positive regulation of BMP signaling pathway / positive regulation of keratinocyte differentiation / spindle pole centrosome / microtubule bundle formation / microtubule plus-end binding / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / dynein complex binding / nucleus organization / mitotic spindle pole / establishment of mitotic spindle orientation / lateral plasma membrane / positive regulation of protein localization to cell cortex / regulation of mitotic spindle organization / positive regulation of microtubule polymerization / Recruitment of NuMA to mitotic centrosomes / tubulin binding / phosphatidylinositol binding / meiotic cell cycle / spindle microtubule / mitotic spindle / nuclear matrix / spindle pole / cytoplasmic stress granule / spindle / protein import into nucleus / host cell / disordered domain specific binding / chromosome / cell cortex / microtubule binding / DNA-binding transcription factor binding / postsynaptic density / protein domain specific binding / cell division / centrosome / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex binding / structural molecule activity / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
: / : / NuMA N-terminal hook domain / 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. ...: / : / NuMA N-terminal hook domain / 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 / Nuclear mitotic apparatus protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.394 Å
AuthorsChang, C.-C. / Huang, T.-L. / Hsia, K.-C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
MOST Taiwan
CitationJournal: J. Cell Biol. / Year: 2017
Title: Regulation of mitotic spindle assembly factor NuMA by Importin-beta
Authors: Chang, C.-C. / Huang, T.-L. / Shimamoto, Y. / Tsai, S.-Y. / Hsia, K.-C.
History
DepositionSep 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Peptide from Nuclear mitotic apparatus protein 1


Theoretical massNumber of molelcules
Total (without water)49,4472
Polymers49,4472
Non-polymers00
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint2 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.065, 89.658, 101.187
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 46386.055 Da / Num. of mol.: 1 / Fragment: UNP residues 70-497
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
#2: Protein/peptide Peptide from Nuclear mitotic apparatus protein 1 / Nuclear matrix protein-22 / NMP-22 / Nuclear mitotic apparatus protein / NuMA protein / SP-H antigen


Mass: 3060.468 Da / Num. of mol.: 1 / Fragment: UNP residues 1984-2010
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUMA1, NMP22, NUMA / Production host: Escherichia coli (E. coli) / References: UniProt: Q14980
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 3.58 Å3/Da / Density % sol: 65.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1M KCl, 0.8M ammonium sulfate, 100mM Hepes, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 28006 / % possible obs: 98.3 % / Redundancy: 5.8 % / Rsym value: 0.079 / Net I/σ(I): 29.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 4.3 / Num. unique obs: 2392 / CC1/2: 0.833 / Rsym value: 0.476 / Χ2: 1.7 / % possible all: 85.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.394→19.822 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 1999 7.14 %
Rwork0.1834 25979 -
obs0.1859 27978 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.97 Å2 / Biso mean: 43.2619 Å2 / Biso min: 15.69 Å2
Refinement stepCycle: final / Resolution: 2.394→19.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3476 0 0 246 3722
Biso mean---42.46 -
Num. residues----455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093538
X-RAY DIFFRACTIONf_angle_d0.9894816
X-RAY DIFFRACTIONf_chiral_restr0.053575
X-RAY DIFFRACTIONf_plane_restr0.006621
X-RAY DIFFRACTIONf_dihedral_angle_d14.8652157
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3938-2.45360.31121140.24041478159279
2.4536-2.51980.2731340.21761756189094
2.5198-2.59380.24411430.210718551998100
2.5938-2.67730.22821430.198518572000100
2.6773-2.77280.24881430.190318572000100
2.7728-2.88350.23351450.199818892034100
2.8835-3.01430.24981440.210618742018100
3.0143-3.17260.22281440.212118672011100
3.1726-3.37050.25361460.207119022048100
3.3705-3.62920.23061450.193818742019100
3.6292-3.99180.22811460.18171896204299
3.9918-4.56330.171470.154419102057100
4.5633-5.72610.21211490.167819402089100
5.7261-19.82240.16621560.147320242180100

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