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- PDB-1ukl: Crystal structure of Importin-beta and SREBP-2 complex -

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Basic information

Entry
Database: PDB / ID: 1ukl
TitleCrystal structure of Importin-beta and SREBP-2 complex
Components
  • Importin beta-1 subunit
  • Sterol regulatory element binding protein-2
KeywordsPROTEIN TRANSPORT/DNA BINDING PROTEIN / Transcription factor / Nuclear transport factor / HEAT repeat / Helix-Loop-Helix Leucine zipper / PROTEIN TRANSPORT-DNA BINDING PROTEIN COMPLEX
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 / SREBP-SCAP-Insig complex / positive regulation of cholesterol storage / Interferon alpha/beta signaling / RNA import into nucleus / mitotic chromosome movement towards spindle pole / negative regulation of cholesterol efflux ...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 / SREBP-SCAP-Insig complex / positive regulation of cholesterol storage / Interferon alpha/beta signaling / RNA import into nucleus / mitotic chromosome movement towards spindle pole / negative regulation of cholesterol efflux / endoplasmic reticulum tubular network / SREBP signaling pathway / negative regulation of amyloid-beta clearance / astral microtubule organization / regulation of Notch signaling pathway / regulation of mitophagy / establishment of mitotic spindle localization / cellular response to laminar fluid shear stress / Cholesterol biosynthesis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / 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 / E-box binding / Maturation of hRSV A proteins / cellular response to low-density lipoprotein particle stimulus / mitotic spindle assembly / cholesterol metabolic process / Neutrophil degranulation / Activation of gene expression by SREBF (SREBP) / cholesterol homeostasis / cellular response to starvation / ER to Golgi transport vesicle membrane / Hsp90 protein binding / PPARA activates gene expression / positive regulation of cholesterol biosynthetic process / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / small GTPase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / lipid metabolic process / protein import into nucleus / cytoplasmic stress granule / sequence-specific double-stranded DNA binding / nuclear membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / chromatin / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / 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 / Helix-loop-helix DNA-binding domain / HEAT repeat profile. ...Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / 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 / Helix-loop-helix DNA-binding domain / HEAT repeat profile. / HEAT, type 2 / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Few Secondary Structures / Irregular / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit beta-1 / Sterol regulatory element-binding protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsLee, S.J. / Sekimoto, T. / Yamashita, E. / Nagoshi, E. / Nakagawa, A. / Imamoto, N. / Yoshimura, M. / Sakai, H. / Tsukihara, T. / Yoneda, Y.
CitationJournal: Science / Year: 2003
Title: The Structure of Importin-beta Bound to SREBP-2: Nuclear Import of a Transcription Factor
Authors: Lee, S.J. / Sekimoto, T. / Yamashita, E. / Nagoshi, E. / Nakagawa, A. / Imamoto, N. / Yoshimura, M. / Sakai, H. / Chong, K.T. / Tsukihara, T. / Yoneda, Y.
History
DepositionAug 26, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 23, 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-1 subunit
B: Importin beta-1 subunit
C: Sterol regulatory element binding protein-2
D: Sterol regulatory element binding protein-2
E: Sterol regulatory element binding protein-2
F: Sterol regulatory element binding protein-2


Theoretical massNumber of molelcules
Total (without water)223,6526
Polymers223,6526
Non-polymers00
Water00
1
A: Importin beta-1 subunit
C: Sterol regulatory element binding protein-2
D: Sterol regulatory element binding protein-2


Theoretical massNumber of molelcules
Total (without water)111,8263
Polymers111,8263
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Importin beta-1 subunit
E: Sterol regulatory element binding protein-2
F: Sterol regulatory element binding protein-2


Theoretical massNumber of molelcules
Total (without water)111,8263
Polymers111,8263
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.092, 113.285, 240.044
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 Importin beta-1 subunit / Importin-beta


Mass: 97271.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P70168
#2: Protein
Sterol regulatory element binding protein-2 / SREBP-2


Mass: 7277.164 Da / Num. of mol.: 4 / Fragment: residues 343-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q12772
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PEG 8000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMMES1reservoirpH6.6
25-6 %PEG80001reservoir
330 mM1reservoirSrCl2
420 %glycerol1reservoir
550 mMMES1droppH6.6
65-6 %PEG80001drop
730 mM1dropSrCl2
810 %glycerol1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9794
SYNCHROTRONSPring-8 BL44XU20.9796
Detector
TypeIDDetectorDate
Bruker DIP-60401CCDNov 24, 2002
Bruker DIP-60402CCDDec 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 3→80 Å / Num. obs: 105485 / % possible obs: 99.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 93.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 27.7
Reflection shellResolution: 3→3.1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3 / % possible all: 97.5
Reflection
*PLUS
Lowest resolution: 80 Å / Num. obs: 55607
Reflection shell
*PLUS
% possible obs: 97.5 % / Num. unique obs: 5720 / Rmerge(I) obs: 0.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 1QGK, 1AM9

1qgk

1am9


Resolution: 3→19.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2985930.88 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.297 5259 5 %RANDOM
Rwork0.239 ---
obs-105485 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.0847 Å2 / ksol: 0.258279 e/Å3
Displacement parametersBiso mean: 105.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å20 Å2
2--5.22 Å20 Å2
3----7.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15606 0 0 0 15606
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d1.07
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 875 5.1 %
Rwork0.34 16333 -
obs--97.2 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.427
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.07
LS refinement shell
*PLUS
Rfactor Rfree: 0.389 / Rfactor Rwork: 0.352

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