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- PDB-3zin: Gu_alpha_helicase -

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Basic information

Entry
Database: PDB / ID: 3zin
TitleGu_alpha_helicase
Components
  • IMPORTIN SUBUNIT ALPHA-2
  • NUCLEOLAR RNA HELICASE 2
KeywordsTRANSPORT PROTEIN/HYDROLASE / TRANSPORT PROTEIN-HYDROLASE COMPLEX
Function / homology
Function and homology information


B-WICH complex positively regulates rRNA expression / Major pathway of rRNA processing in the nucleolus and cytosol / R-loop processing / 7SK snRNA binding / positive regulation of myeloid dendritic cell cytokine production / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway ...B-WICH complex positively regulates rRNA expression / Major pathway of rRNA processing in the nucleolus and cytosol / R-loop processing / 7SK snRNA binding / positive regulation of myeloid dendritic cell cytokine production / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / host cell / miRNA binding / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / snoRNA binding / response to exogenous dsRNA / response to virus / rRNA processing / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / double-stranded RNA binding / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / nuclear membrane / DNA-binding transcription factor binding / RNA helicase activity / postsynaptic density / transcription by RNA polymerase II / rRNA binding / RNA helicase / innate immune response / glutamatergic synapse / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
GUCT / GUCT (NUC152) domain / 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. ...GUCT / GUCT (NUC152) domain / 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 / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / RNA-binding domain superfamily / Armadillo-like helical / Alpha Horseshoe / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Nucleolar RNA helicase 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChang, C.-W. / Counago, R.M. / Williams, S.J. / Kobe, B.
CitationJournal: Traffic / Year: 2013
Title: Distinctive Conformation of Minor Site-Specific Nuclear Localization Signals Bound to Importin-Alpha
Authors: Chang, C.-W. / Counago, R.M. / Williams, S.J. / Boden, M. / Kobe, B.
History
DepositionJan 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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-2
B: NUCLEOLAR RNA HELICASE 2
C: NUCLEOLAR RNA HELICASE 2


Theoretical massNumber of molelcules
Total (without water)53,0483
Polymers53,0483
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-0.3 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.094, 90.262, 100.704
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 SUBUNIT ALPHA-2 / / IMPORTIN ALPHA P1 / KARYOPHERIN SUBUNIT ALPHA-2 / PENDULIN / PORE TARGETING COMPLEX 58 KDA SUBUNIT ...IMPORTIN ALPHA P1 / KARYOPHERIN SUBUNIT ALPHA-2 / PENDULIN / PORE TARGETING COMPLEX 58 KDA SUBUNIT / PTAC58 / RAG COHORT PROTEIN 1 / SRP1-ALPHA / IMPORTIN ALPHA_IBB


Mass: 49872.836 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET30A_MIMPALPHA_DIBB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52293
#2: Protein/peptide NUCLEOLAR RNA HELICASE 2 / DEAD BOX PROTEIN 21 / GU-ALPHA / NUCLEOLAR RNA HELICASE GU / NUCLEOLAR RNA HELICASE II / RH II/GU


Mass: 1587.782 Da / Num. of mol.: 2 / Fragment: RESIDUES 839-851
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET30A_MIMPALPHA_DIBB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JIK5, RNA helicase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 3.27 Å3/Da / Density % sol: 62.38 % / Description: NONE
Crystal growpH: 6.5
Details: 0.8 M SODIUM CITRATE, 0.1 M HEPES BUFFER (PH 6.5) AND 10 MM DTT

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536
DetectorDate: Jul 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2→19.83 Å / Num. obs: 49123 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 33.84 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 14.55 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 6.5 / % possible all: 99.3

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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 1IAL

1ial


Resolution: 2→19.83 Å / Cor.coef. Fo:Fc: 0.9521 / Cor.coef. Fo:Fc free: 0.9417 / SU R Cruickshank DPI: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.116 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 2488 5.07 %RANDOM
Rwork0.1788 ---
obs0.1799 49062 99.46 %-
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.3573 Å20 Å20 Å2
2--4.0398 Å20 Å2
3----4.3971 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3398 0 0 188 3586
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013457HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.944698HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1614SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes490HARMONIC5
X-RAY DIFFRACTIONt_it3457HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion2.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion478SEMIHARMONIC5
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_contact4282SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2392 171 5.12 %
Rwork0.1834 3168 -
all0.1862 3339 -
obs--99.46 %
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)
10.9127-0.19720.63225.9587-1.93413.63410.160.0473-0.1458-0.4605-0.0493-0.17590.17490.2758-0.1107-0.02750.0254-0.0523-0.0903-0.0082-0.103-5.4991-8.246315.5457
21.40970.28490.33891.8487-0.53560.6470.0968-0.03960.05560.1659-0.0295-0.01220.02290.0225-0.0673-0.0074-0.0133-0.0066-0.0368-0.0098-0.0506-4.737814.843616.6464
31.11820.5823-0.69012.7324-1.47382.45630.16560.05930.19650.1272-0.0690.0954-0.11670.0667-0.0966-0.0766-0.01110.0505-0.08210.0158-0.01413.615128.83976.1203
41.78950.4137-0.95382.3963-0.731.97220.0310.61770.252-0.42910.17750.3727-0.0082-0.4488-0.2085-0.13780.0052-0.0370.00420.1336-0.11298.681637.5397-19.0085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|72 - 156}
2X-RAY DIFFRACTION2{A|157 - 262}
3X-RAY DIFFRACTION3{A|263 - 329}
4X-RAY DIFFRACTION4{A|330 - 497}

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