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- PDB-4b8j: rImp_alpha1a -

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Basic information

Entry
Database: PDB / ID: 4b8j
TitlerImp_alpha1a
ComponentsIMPORTIN SUBUNIT ALPHA-1A
KeywordsTRANSPORT PROTEIN / NUCLEAR LOCALIZATION SIGNAL
Function / homology
Function and homology information


NLS-bearing protein import into nucleus / nuclear localization sequence binding / nuclear import signal receptor activity / perinuclear region of cytoplasm / nucleus
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
Importin subunit alpha-1a
Similarity search - Component
Biological speciesORYZA SATIVA JAPONICA GROUP (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsChang, C.-W. / Counago, R.L.M. / Williams, S.J. / Boden, M. / Kobe, B.
CitationJournal: Plant Cell / Year: 2012
Title: Crystal Structure of Rice Importin-Alpha and Structural Basis of its Interaction with Plant-Specific Nuclear Localization Signals.
Authors: Chang, C.-W. / Counago, R.L.M. / Williams, S.J. / Boden, M. / Kobe, B.
History
DepositionAug 28, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMPORTIN SUBUNIT ALPHA-1A


Theoretical massNumber of molelcules
Total (without water)57,7761
Polymers57,7761
Non-polymers00
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.252, 72.736, 62.425
Angle α, β, γ (deg.)90.00, 91.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein IMPORTIN SUBUNIT ALPHA-1A / RICE IMPORTIN ALPHA1A


Mass: 57776.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYZA SATIVA JAPONICA GROUP (Japanese rice)
Plasmid: PGEX2T_RIMPALPHA1A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q71VM4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 3.03 Å3/Da / Density % sol: 59.03 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M BIS-TRIS PROPANE PH 7.0, 15-17% PEG 3350, 0.2 M NAF, 0.2 M NDSB-221.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→19.84 Å / Num. obs: 40273 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.4 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EE4

1ee4


Resolution: 2.001→19.841 Å / SU ML: 0.16 / σ(F): 1.33 / Phase error: 16.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1778 2015 5 %
Rwork0.1481 --
obs0.1496 40259 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Refinement stepCycle: LAST / Resolution: 2.001→19.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 0 278 3597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013372
X-RAY DIFFRACTIONf_angle_d1.184580
X-RAY DIFFRACTIONf_dihedral_angle_d14.2031254
X-RAY DIFFRACTIONf_chiral_restr0.076544
X-RAY DIFFRACTIONf_plane_restr0.007592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0009-2.05090.24321220.18662471X-RAY DIFFRACTION91
2.0509-2.10630.18111260.15492757X-RAY DIFFRACTION100
2.1063-2.16820.18331490.13572771X-RAY DIFFRACTION100
2.1682-2.23810.16211250.12912754X-RAY DIFFRACTION100
2.2381-2.3180.14331460.132722X-RAY DIFFRACTION100
2.318-2.41060.18071410.13272752X-RAY DIFFRACTION100
2.4106-2.52010.17431370.1362754X-RAY DIFFRACTION100
2.5201-2.65270.1611460.13822735X-RAY DIFFRACTION100
2.6527-2.81850.17771540.14682749X-RAY DIFFRACTION100
2.8185-3.03540.17151520.15122737X-RAY DIFFRACTION100
3.0354-3.33950.16431440.15912763X-RAY DIFFRACTION100
3.3395-3.81980.19231460.14842774X-RAY DIFFRACTION100
3.8198-4.80120.17381720.13272755X-RAY DIFFRACTION100
4.8012-19.84170.19271550.17722750X-RAY DIFFRACTION98
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)
10.0003-0.0099-0.0090.15180.15670.16260.31720.14830.0311-0.0494-0.14040.2111-0.0168-0.095700.37830.06980.04160.5382-0.03340.615813.95466.077237.5745
21.0482-0.115-0.74411.65320.52930.9632-0.09810.0116-0.14220.0432-0.09380.26990.1274-0.1875-0.03230.1699-0.02570.00720.1888-0.01680.220815.84215.740943.9524
30.4712-0.1267-0.36620.37790.11851.10510.04120.04130.04380.0148-0.0150.0439-0.0390.0880.00010.1499-0.0053-0.01380.1329-0.00220.161341.2882-4.921618.8481
40.2909-0.27450.47210.9163-0.16670.8821-0.06870.23060.174-0.0122-0.0279-0.0011-0.35710.3347-0.09810.2448-0.0274-0.0170.27390.04260.176950.43643.3958-7.1858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 25 THROUGH 85)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 86 THROUGH 236)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 237 THROUGH 425)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 426 THROUGH 494)

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