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- PDB-3lww: Structure of an open and closed conformation of Human Importin Be... -

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Basic information

Entry
Database: PDB / ID: 3lww
TitleStructure of an open and closed conformation of Human Importin Beta bound to the Snurportin1 IBB-domain trapped in the same crystallographic asymmetric unit
Components
  • Importin subunit beta-1
  • Snurportin-1
KeywordsPROTEIN TRANSPORT / HEAT repeat / IBB-domain / Importin beta / Karyopherin / Snurportin
Function / homology
Function and homology information


RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / establishment of mitotic spindle localization / astral microtubule organization / RNA cap binding / snRNA import into nucleus / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / establishment of mitotic spindle localization / astral microtubule organization / RNA cap binding / snRNA import into nucleus / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / ribosomal protein import into nucleus / Initiation of Nuclear Envelope (NE) Reformation / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / mitotic spindle assembly / nuclear pore / Assembly of the ORC complex at the origin of replication / Hsp90 protein binding / ISG15 antiviral mechanism / small GTPase binding / cytoplasmic stress granule / specific granule lumen / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / nuclear envelope / snRNP Assembly / nuclear membrane / ficolin-1-rich granule lumen / protein domain specific binding / Neutrophil degranulation / enzyme binding / RNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain ...Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Importin-alpha, importin-beta-binding domain / IBB domain profile. / HEAT repeat profile. / HEAT, type 2 / 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
Snurportin-1 / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsBhardwaj, A. / Cingolani, G.
CitationJournal: Biochemistry / Year: 2010
Title: Conformational selection in the recognition of the snurportin importin beta binding domain by importin beta.
Authors: Bhardwaj, A. / Cingolani, G.
History
DepositionFeb 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit beta-1
B: Snurportin-1
C: Importin subunit beta-1
D: Snurportin-1


Theoretical massNumber of molelcules
Total (without water)204,5714
Polymers204,5714
Non-polymers00
Water00
1
A: Importin subunit beta-1
B: Snurportin-1


Theoretical massNumber of molelcules
Total (without water)102,2862
Polymers102,2862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-10 kcal/mol
Surface area41460 Å2
MethodPISA
2
C: Importin subunit beta-1
D: Snurportin-1


Theoretical massNumber of molelcules
Total (without water)102,2862
Polymers102,2862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-4 kcal/mol
Surface area39480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.650, 101.735, 101.963
Angle α, β, γ (deg.)90.00, 110.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Importin subunit beta-1 / Karyopherin subunit beta-1 / Nuclear factor p97 / Pore targeting complex 97 kDa subunit / PTAC97 / Importin-90


Mass: 97257.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNB1, NTF97 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14974
#2: Protein/peptide Snurportin-1 / RNA U transporter 1


Mass: 5027.755 Da / Num. of mol.: 2 / Fragment: Snurportin1 N-terminal domain (25-64) / Source method: obtained synthetically / References: UniProt: O95149

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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: 2.41 Å3/Da / Density % sol: 48.92 % / Description: Structure factors file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 8000, 50 mM sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.918
SYNCHROTRONNSLS X6A20.918
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDNov 28, 2008
ADSC QUANTUM 42CCDMay 15, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Horizontal focusing 5.05 asymmetric cut Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111) channel cut monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.15→15 Å / Num. all: 63234 / Num. obs: 32721 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 73.9 Å2 / Rsym value: 0.123 / Net I/σ(I): 16.3
Reflection shellHighest resolution: 3.15 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 2P8Q

2p8q


Resolution: 3.15→14.957 Å / SU ML: 0.49 / σ(F): 0.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3129 3334 5.59 %Random
Rwork0.2635 ---
obs0.2663 32721 91.24 %-
all-63234 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.2 Å2 / ksol: 0.236 e/Å3
Refinement stepCycle: LAST / Resolution: 3.15→14.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14127 0 0 0 14127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314352
X-RAY DIFFRACTIONf_angle_d0.71619464
X-RAY DIFFRACTIONf_dihedral_angle_d17.1875353
X-RAY DIFFRACTIONf_chiral_restr0.0462265
X-RAY DIFFRACTIONf_plane_restr0.0042540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.19460.3821080.33931808X-RAY DIFFRACTION69
3.1946-3.24180.38241180.33521886X-RAY DIFFRACTION76
3.2418-3.29190.34871300.30722152X-RAY DIFFRACTION82
3.2919-3.34530.32861240.30732221X-RAY DIFFRACTION86
3.3453-3.40230.33931430.32272291X-RAY DIFFRACTION89
3.4023-3.46340.34411300.31562249X-RAY DIFFRACTION90
3.4634-3.52920.38091310.28842340X-RAY DIFFRACTION91
3.5292-3.60030.33751360.28122365X-RAY DIFFRACTION90
3.6003-3.67740.30151350.27082314X-RAY DIFFRACTION92
3.6774-3.76160.32251350.27862392X-RAY DIFFRACTION92
3.7616-3.85410.30121520.25472428X-RAY DIFFRACTION94
3.8541-3.95650.24441380.25132377X-RAY DIFFRACTION94
3.9565-4.07060.30351440.2482456X-RAY DIFFRACTION94
4.0706-4.19920.29361340.24772371X-RAY DIFFRACTION94
4.1992-4.34570.30611470.24482464X-RAY DIFFRACTION95
4.3457-4.51510.33941400.25482464X-RAY DIFFRACTION96
4.5151-4.71450.25521430.24092449X-RAY DIFFRACTION96
4.7145-4.95450.28391550.23992518X-RAY DIFFRACTION96
4.9545-5.25220.35951380.27312463X-RAY DIFFRACTION97
5.2522-5.63750.32321520.28012513X-RAY DIFFRACTION97
5.6375-6.16840.41891530.29222497X-RAY DIFFRACTION97
6.1684-6.98040.29411510.28252470X-RAY DIFFRACTION97
6.9804-8.51550.31891520.22652500X-RAY DIFFRACTION96
8.5155-14.95730.19561450.17782350X-RAY DIFFRACTION92

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