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- PDB-1gcj: N-TERMINAL FRAGMENT OF IMPORTIN-BETA -

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Basic information

Entry
Database: PDB / ID: 1gcj
TitleN-TERMINAL FRAGMENT OF IMPORTIN-BETA
ComponentsIMPORTIN BETA
KeywordsTRANSPORT PROTEIN / HEAT REPEAT MOTIF / NUCLEAR PORE-TARGETING COMPLEX COMPONENT / nuclear import factor
Function / homology
Function and homology information


Regulation of cholesterol biosynthesis by SREBP (SREBF) / Assembly of the ORC complex at the origin of replication / Apoptosis induced DNA fragmentation / Initiation of Nuclear Envelope (NE) Reformation / RNA import into nucleus / Interferon alpha/beta signaling / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / importin-alpha family protein binding / astral microtubule organization ...Regulation of cholesterol biosynthesis by SREBP (SREBF) / Assembly of the ORC complex at the origin of replication / Apoptosis induced DNA fragmentation / Initiation of Nuclear Envelope (NE) Reformation / RNA import into nucleus / Interferon alpha/beta signaling / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / importin-alpha family protein binding / astral microtubule organization / establishment of mitotic spindle localization / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / ribosomal protein import into nucleus / nuclear import signal receptor activity / mitotic metaphase chromosome alignment / Maturation of hRSV A proteins / mitotic spindle assembly / Neutrophil degranulation / Hsp90 protein binding / small GTPase binding / protein import into nucleus / cytoplasmic stress granule / nuclear membrane / protein domain specific binding / protein-containing complex / nucleoplasm / cytosol
Similarity search - Function
Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / Armadillo/beta-catenin-like repeats / Armadillo ...Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / 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 beta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsLee, S.J. / Imamoto, N. / Sakai, H. / Nakagawa, A. / Kose, S. / Koike, M. / Yamamoto, M. / Kumasaka, T. / Yoneda, Y. / Tsukihara, T.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The adoption of a twisted structure of importin-beta is essential for the protein-protein interaction required for nuclear transport.
Authors: Lee, S.J. / Imamoto, N. / Sakai, H. / Nakagawa, A. / Kose, S. / Koike, M. / Yamamoto, M. / Kumasaka, T. / Yoneda, Y. / Tsukihara, T.
History
DepositionJul 31, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMPORTIN BETA
B: IMPORTIN BETA


Theoretical massNumber of molelcules
Total (without water)103,7572
Polymers103,7572
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-19 kcal/mol
Surface area41640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.830, 103.780, 126.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer constructed from chain A or chain B.

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Components

#1: Protein IMPORTIN BETA


Mass: 51878.734 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN (1-449 RESIDUES)
Mutation: MET1MSE, MET146MSE,MET181MSE,MET219MSE,MET245MSE,MET252MSE,MET256MSE,MET268MSE,MET291MSE,MET353MSE,MET388MSE,MET410MSE,MET417MSE,
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL6 / Tissue: THYMUS / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P70168
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: cacodylate,PEG4000,glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
225 mMphosphate1drop
35 mM2-mercaptoethanol1drop
410 %(v/v)glycerol1drop
550 mMcacodylic acid1reservoir
615 %(w/v)PEG40001reservoir
720 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.9793
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→57.33 Å / Num. obs: 33562 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.293 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 271717
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 4.6

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→39.18 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1670 5 %RANDOM
Rwork0.215 ---
obs-33101 97.9 %-
Refinement stepCycle: LAST / Resolution: 2.6→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7178 0 0 211 7389
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.115

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