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- PDB-6d7m: Crystal structure of the W184R/W231R Importin alpha mutant -

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Basic information

Entry
Database: PDB / ID: 6d7m
TitleCrystal structure of the W184R/W231R Importin alpha mutant
ComponentsPeroxidase,Importin subunit alpha-1
KeywordsTRANSPORT PROTEIN / IMPORTIN / NLS / BIPARTITE / PROTEIN BINDING
Function / homology
Function and homology information


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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / host cell / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule ...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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / host cell / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / nuclear membrane / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / nucleus / cytosol
Similarity search - Function
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 ...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
SUCCINIC ACID / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.187 Å
AuthorsPedersen, L.C. / London, R.E. / Gabel, S.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES050111 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIA ES102645 United States
CitationJournal: Traffic / Year: 2018
Title: Variations in nuclear localization strategies among pol X family enzymes.
Authors: Kirby, T.W. / Pedersen, L.C. / Gabel, S.A. / Gassman, N.R. / London, R.E.
History
DepositionApr 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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

Downloads & links

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Assembly

Deposited unit
B: Peroxidase,Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6126
Polymers55,2731
Non-polymers3405
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.813, 90.162, 98.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peroxidase,Importin subunit alpha-1 / Importin alpha P1


Mass: 55272.535 Da / Num. of mol.: 1 / Mutation: W184R, W231R
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, peroxidase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Bis-Tris-Propane, 1.0M Sodium Succinate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 7, 2018 / Details: VariMaxHF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.187→50 Å / Num. obs: 35979 / % possible obs: 99.1 % / Redundancy: 6.3 % / Rpim(I) all: 0.043 / Rsym value: 0.101 / Net I/σ(I): 9.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1705 / CC1/2: 0.814 / Rpim(I) all: 0.336 / Rrim(I) all: 0.843 / Rsym value: 0.772 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E6Q

5e6q


Resolution: 2.187→38.907 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 23.92
RfactorNum. reflection% reflection
Rfree0.2222 1803 5.02 %
Rwork0.1914 --
obs0.193 35928 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.187→38.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 19 162 3281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063201
X-RAY DIFFRACTIONf_angle_d0.8084376
X-RAY DIFFRACTIONf_dihedral_angle_d10.4251932
X-RAY DIFFRACTIONf_chiral_restr0.044539
X-RAY DIFFRACTIONf_plane_restr0.005568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1874-2.24660.29691300.2492355X-RAY DIFFRACTION90
2.2466-2.31270.27011320.24012543X-RAY DIFFRACTION98
2.3127-2.38730.28081330.23242597X-RAY DIFFRACTION98
2.3873-2.47260.25031440.23642577X-RAY DIFFRACTION99
2.4726-2.57160.26491330.23952617X-RAY DIFFRACTION99
2.5716-2.68860.30291400.24812619X-RAY DIFFRACTION100
2.6886-2.83030.27311370.22162639X-RAY DIFFRACTION100
2.8303-3.00760.25931420.22882656X-RAY DIFFRACTION100
3.0076-3.23970.26481400.20642661X-RAY DIFFRACTION100
3.2397-3.56550.22681380.18572651X-RAY DIFFRACTION100
3.5655-4.0810.20131440.16292697X-RAY DIFFRACTION100
4.081-5.13970.15821420.15542701X-RAY DIFFRACTION100
5.1397-38.91260.19831480.17312812X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.12680.1509-0.95153.00091.07235.51850.3333-0.01830.10250.3937-0.0906-0.1077-0.32090.1527-0.12890.4273-0.06510.09150.37660.00270.4237-6.395416.3684-18.7581
21.5103-0.2803-0.03063.5969-0.59140.2710.0937-0.01430.070.0542-0.0575-0.059-0.12130.0989-0.04630.3733-0.00280.02760.36270.02740.2609-7.0989-1.445-15.9382
33.1076-0.3319-0.40042.1547-0.25922.59660.0146-0.0217-0.2741-0.1609-0.0249-0.09510.0442-0.0940.01710.34730.0082-0.01090.2939-0.00430.3548-2.4413-19.4814-15.5618
42.3067-0.50870.41142.5857-0.4482.4280.2246-0.0583-0.2823-0.0033-0.08640.06550.01720.0443-0.11760.33260.0202-0.03430.34350.00080.41551.4114-25.0465-10.1673
53.5250.63080.71693.9520.30822.67670.15190.13140.1613-0.1806-0.14030.06180.10280.23920.02230.37180.0238-0.02920.36120.04940.41367.1667-28.2145-6.879
61.3081-0.45251.03260.5408-0.75231.37790.114-0.1868-0.2912-0.09250.07890.33370.1694-0.1925-0.1450.3779-0.0204-0.04580.40770.07370.51328.0429-36.33424.3419
73.0220.00830.7522.9286-0.5152.4931-0.1098-0.6108-0.20070.15260.31080.3115-0.002-0.4705-0.16890.39260.04810.02840.57230.10310.44027.7618-36.819216.0084
83.2517-0.1079-0.19381.17980.4451.69160.2799-0.9328-0.02830.48410.02960.3757-0.3817-0.679-0.25960.59830.05170.12980.78440.15470.52518.0089-38.253323.4047
93.3006-1.32340.85591.6063-1.04761.09-0.4329-1.6488-0.30211.38750.66410.49650.0172-0.3248-0.1310.9354-0.03330.1151.26390.14820.59416.4887-40.842531.9632
100.1099-0.2857-0.55390.71551.40512.82860.6982-0.4410.68230.53620.14460.1508-0.2059-0.6718-0.54220.9153-0.11960.26511.42130.17640.75241.8939-43.753634.3403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain B and resid 73:93)
2X-RAY DIFFRACTION2(chain B and resid 94:213)
3X-RAY DIFFRACTION3(chain B and resid 214:256)
4X-RAY DIFFRACTION4(chain B and resid 257:287)
5X-RAY DIFFRACTION5(chain B and resid 288:315)
6X-RAY DIFFRACTION6(chain B and resid 316:384)
7X-RAY DIFFRACTION7(chain B and resid 385:414)
8X-RAY DIFFRACTION8(chain B and resid 415:450)
9X-RAY DIFFRACTION9(chain B and resid 451:486)
10X-RAY DIFFRACTION10(chain B and resid 487:496)

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