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- PDB-4bpl: rice importin_alpha in complex with nucleoplasmin NLS -

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Basic information

Entry
Database: PDB / ID: 4bpl
Titlerice importin_alpha in complex with nucleoplasmin NLS
Components
  • IMPORTIN SUBUNIT ALPHA-1A
  • NUCLEOPLASMIN NLS
KeywordsTRANSPORT PROTEIN / NUCLEAR IMPORT / NUCLEAR LOCALIZATION SIGNAL
Function / homology
Function and homology information


sperm DNA decondensation / histone chaperone activity / importin-alpha family protein binding / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / nucleosome binding / positive regulation of DNA replication / histone binding / chromatin remodeling ...sperm DNA decondensation / histone chaperone activity / importin-alpha family protein binding / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / nucleosome binding / positive regulation of DNA replication / histone binding / chromatin remodeling / nucleolus / perinuclear region of cytoplasm / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / 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 ...Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / 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
Nucleoplasmin / Importin subunit alpha-1a
Similarity search - Component
Biological speciesORYZA SATIVA (Asian cultivated rice)
XENOPUS (frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChang, C.-W. / Counago, R.M. / Williams, S.J. / Kobe, B.
CitationJournal: Mol.Plant / Year: 2014
Title: Structural Basis of Interaction of Bipartite Nuclear Localization Signal from Agrobacterium Vird2 with Rice Importin-Alpha
Authors: Chang, C.-W. / Williams, S.J. / Counago, R.M. / Kobe, B.
History
DepositionMay 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: 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

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Assembly

Deposited unit
A: IMPORTIN SUBUNIT ALPHA-1A
B: NUCLEOPLASMIN NLS


Theoretical massNumber of molelcules
Total (without water)51,4742
Polymers51,4742
Non-polymers00
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-2.1 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.221, 74.093, 138.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein IMPORTIN SUBUNIT ALPHA-1A


Mass: 49240.801 Da / Num. of mol.: 1 / Fragment: RESIDUES 73-526
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYZA SATIVA (Asian cultivated rice) / Plasmid: PET30A_RIMPALPHA1A_DIBB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q71VM4
#2: Protein/peptide NUCLEOPLASMIN NLS


Mass: 2232.710 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS (frog) / Plasmid: PGEX2T-NUCLEOPLASMINNLS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05221*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 3.09 Å3/Da / Density % sol: 60.2 % / Description: NONE
Crystal growpH: 6.2 / Details: 0.1 M MES PH 6.2 AND 1.35 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.3→19.89 Å / Num. obs: 29058 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 14.5 % / Biso Wilson estimate: 44.22 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B8O

4b8o


Resolution: 2.3→19.89 Å / Cor.coef. Fo:Fc: 0.9365 / Cor.coef. Fo:Fc free: 0.9193 / SU R Cruickshank DPI: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.183
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 1478 5.09 %RANDOM
Rwork0.2002 ---
obs0.2014 29016 99.99 %-
Displacement parametersBiso mean: 48.97 Å2
Baniso -1Baniso -2Baniso -3
1-4.0014 Å20 Å20 Å2
2--4.8802 Å20 Å2
3----8.8816 Å2
Refine analyzeLuzzati coordinate error obs: 0.321 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 0 289 3675
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013441HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084677HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1625SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes484HARMONIC5
X-RAY DIFFRACTIONt_it3441HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion3.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion475SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4319SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2672 153 5.47 %
Rwork0.2186 2642 -
all0.2212 2795 -
obs--99.99 %
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)
10.06170.20770.53691.28641.44141.8833-0.00270.00870.05180.1606-0.00120.005-0.13330.02730.0040.11360.01640.257-0.2085-0.1938-0.1903-17.914310.510266.1359
20.39621.0008-0.61372.4813-1.42781.88220.08770.0130.24570.4479-0.07480.312-0.3064-0.0932-0.0129-0.1913-0.03060.1022-0.2212-0.0662-0.16-12.92429.275847.9572
31.61710.2657-0.81750.5687-0.18020.7750.06650.1354-0.12220.0213-0.1118-0.03020.04680.00680.0453-0.22130.0072-0.0175-0.20310.0101-0.086610.091721.063626.8132
41.1881-0.86240.05931.67330.07010.0080.09540.1068-0.08130.0055-0.0787-0.03180.01080.038-0.0166-0.33050.08990.0518-0.10610.11710.002536.66617.075318.2789
50-0.1522-0.11650.2003-0.44250.0679-0.0010.0634-0.0613-0.0119-0.00790.02340.01510.01290.0089-0.1270.1755-0.1557-0.0820.01650.024939.25395.441518.1021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 73:104)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 105:237)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 238:404)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 405:476)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 477:494)

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