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- PDB-4b8p: rImp_alpha_A89NLS -

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Basic information

Entry
Database: PDB / ID: 4b8p
TitlerImp_alpha_A89NLS
Components
  • A89NLS
  • IMPORTIN SUBUNIT ALPHA-1A
KeywordsPROTEIN TRANSPORT / 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)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 29, 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
B: IMPORTIN SUBUNIT ALPHA-1A
C: A89NLS
D: A89NLS


Theoretical massNumber of molelcules
Total (without water)109,0934
Polymers109,0934
Non-polymers00
Water3,963220
1
A: IMPORTIN SUBUNIT ALPHA-1A
C: A89NLS


Theoretical massNumber of molelcules
Total (without water)54,5472
Polymers54,5472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-0.2 kcal/mol
Surface area18440 Å2
MethodPISA
2
B: IMPORTIN SUBUNIT ALPHA-1A
D: A89NLS


Theoretical massNumber of molelcules
Total (without water)54,5472
Polymers54,5472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-0.5 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.425, 140.967, 73.167
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein IMPORTIN SUBUNIT ALPHA-1A


Mass: 53026.848 Da / Num. of mol.: 2 / Fragment: NLS BINDING DOMAIN, RESIDUES 73-526
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYZA SATIVA JAPONICA GROUP (Japanese rice)
Plasmid: PET30A_RIMPALPHA1A_DIBB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q71VM4
#2: Protein/peptide A89NLS


Mass: 1519.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PGEX2T-A89NLS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.95 Å3/Da / Density % sol: 58.29 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M BIS-TRIS PROPANE PH 7.0, 15% PEG 3350, 0.2 M NDSB-221 AND 0.2 M NAF

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.3→19.82 Å / Num. obs: 55804 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.5
Reflection shellResolution: 2.3→19.82 Å / Redundancy: 3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EE4

1ee4


Resolution: 2.3→19.818 Å / σ(F): 1.38 / Phase error: 20.6 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2038 2848 5.1 %
Rwork0.1888 --
obs0.1896 55640 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 0 220 6780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096668
X-RAY DIFFRACTIONf_angle_d1.1459072
X-RAY DIFFRACTIONf_dihedral_angle_d14.0092460
X-RAY DIFFRACTIONf_chiral_restr0.0661088
X-RAY DIFFRACTIONf_plane_restr0.0061170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33960.26981440.27332588X-RAY DIFFRACTION93
2.3396-2.38210.23881190.26382589X-RAY DIFFRACTION94
2.3821-2.42780.31541350.25272572X-RAY DIFFRACTION93
2.4278-2.47730.26911360.25372645X-RAY DIFFRACTION94
2.4773-2.5310.2881330.24992659X-RAY DIFFRACTION94
2.531-2.58980.28761390.24212603X-RAY DIFFRACTION94
2.5898-2.65440.25571460.23682613X-RAY DIFFRACTION94
2.6544-2.72590.21221470.22342644X-RAY DIFFRACTION94
2.7259-2.80590.2281530.22042614X-RAY DIFFRACTION94
2.8059-2.89620.22941220.21772668X-RAY DIFFRACTION95
2.8962-2.99930.23631450.22022671X-RAY DIFFRACTION95
2.9993-3.1190.21121330.2142647X-RAY DIFFRACTION95
3.119-3.26020.23851570.21042609X-RAY DIFFRACTION94
3.2602-3.43120.23571380.20422664X-RAY DIFFRACTION95
3.4312-3.64480.1771660.18542637X-RAY DIFFRACTION94
3.6448-3.92410.17911360.16192660X-RAY DIFFRACTION95
3.9241-4.31490.15891470.14042670X-RAY DIFFRACTION95
4.3149-4.93010.18341380.13372662X-RAY DIFFRACTION95
4.9301-6.17690.17051600.16282663X-RAY DIFFRACTION94
6.1769-19.22160.14981370.13932721X-RAY DIFFRACTION95

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