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- PDB-4e4v: The crystal structure of the dimeric human importin alpha 1 at 2.... -

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Basic information

Entry
Database: PDB / ID: 4e4v
TitleThe crystal structure of the dimeric human importin alpha 1 at 2.5 angstrom resolution.
ComponentsImportin subunit alpha-2
KeywordsTRANSPORT PROTEIN / armadillo repeat / karyopherin / importin / nuclear import / host-virus interaction / nucleus / phosphoprotein / protein transport / transport
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / regulation of DNA recombination / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / host cell / nuclear import signal receptor activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear localization sequence binding ...Sensing of DNA Double Strand Breaks / regulation of DNA recombination / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / host cell / nuclear import signal receptor activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear localization sequence binding / DNA metabolic process / CaMK IV-mediated phosphorylation of CREB / NLS-bearing protein import into nucleus / ISG15 antiviral mechanism / protein import into nucleus / histone deacetylase binding / SARS-CoV-1 activates/modulates innate immune responses / nuclear membrane / Estrogen-dependent gene expression / Golgi membrane / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Importin subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5283 Å
AuthorsHang, P.C. / Miknis, Z.M. / Franke, W.A. / Umland, T.C. / Schultz, L.W.
CitationJournal: To be Published
Title: The crystal structure of the dimeric human importin alpha 1 at 2.5 angstrom resolution.
Authors: Hang, P.C. / Miknis, Z.J. / Franke, W.A. / Umland, T.C. / Schultz, L.W.
History
DepositionMar 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Importin subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,83717
Polymers105,3312
Non-polymers1,50615
Water2,990166
1
A: Importin subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,55710
Polymers52,6661
Non-polymers8919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Importin subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2807
Polymers52,6661
Non-polymers6156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.520, 143.520, 136.957
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Importin subunit alpha-2 / / Karyopherin subunit alpha-2 / RAG cohort protein 1 / SRP1-alpha


Mass: 52665.535 Da / Num. of mol.: 2
Fragment: Importin alpha 1 lacking IBB domain (UNP residues 70-529)
Mutation: K486R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IP0A1, KPNA2, RCH1, SRP1 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P52292
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 0.5 CITRATE PH 5.4 10 MM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9422 / Wavelength: 0.9422 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2008 / Details: VERTICAL FOCUSING MIRROR
RadiationMonochromator: SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9422 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 47596 / % possible obs: 99.7 % / Redundancy: 9.6 % / Biso Wilson estimate: 68.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 5.02 / % possible all: 97.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EJL

1ejl


Resolution: 2.5283→34.809 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 22.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 1971 4.14 %
Rwork0.1547 --
obs0.1567 47580 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.44 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5283→34.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6582 0 94 166 6842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146791
X-RAY DIFFRACTIONf_angle_d1.4999245
X-RAY DIFFRACTIONf_dihedral_angle_d15.4442474
X-RAY DIFFRACTIONf_chiral_restr0.0771122
X-RAY DIFFRACTIONf_plane_restr0.0071173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5283-2.59150.24071140.18692537X-RAY DIFFRACTION78
2.5915-2.66150.24921410.18933264X-RAY DIFFRACTION100
2.6615-2.73980.28591400.19283261X-RAY DIFFRACTION100
2.7398-2.82820.25421330.18153246X-RAY DIFFRACTION100
2.8282-2.92920.25611450.17663288X-RAY DIFFRACTION100
2.9292-3.04650.25881400.18663272X-RAY DIFFRACTION100
3.0465-3.1850.24591440.18563282X-RAY DIFFRACTION100
3.185-3.35280.2591380.19693285X-RAY DIFFRACTION100
3.3528-3.56270.26251460.18073286X-RAY DIFFRACTION100
3.5627-3.83740.19631420.15573304X-RAY DIFFRACTION100
3.8374-4.2230.17431430.13733339X-RAY DIFFRACTION100
4.223-4.83270.16031500.12253330X-RAY DIFFRACTION100
4.8327-6.08340.22211380.15633384X-RAY DIFFRACTION100
6.0834-34.8120.16391570.13843531X-RAY DIFFRACTION99
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)
11.63930.3921-0.27857.33180.54981.6736-0.2167-0.00650.1644-0.01540.23040.0506-0.0390.173-0.00460.2917-0.0117-0.1010.5424-0.07670.4003-20.9709-46.500817.1984
23.53721.2122-0.96750.87660.15720.6605-0.03470.11990.9128-0.13850.13530.3698-0.0345-0.0567-0.09490.42670.0827-0.13090.44060.05940.8695.3753-9.545319.4661
33.71270.75870.41674.5819-0.64252.6175-0.31850.460.7181-0.88980.41420.57660.0582-0.4428-0.07430.6244-0.0267-0.21490.65480.05820.573114.3335-21.95742.4861
44.26481.6373-1.77671.5352-0.75941.9840.001-0.0468-0.08220.1318-0.0889-0.04190.0759-0.16710.08250.4170.0283-0.13770.3301-0.0760.4173-4.5748-49.325233.2648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 65 through 245 )
2X-RAY DIFFRACTION2chain 'A' and (resid 246 through 497 )
3X-RAY DIFFRACTION3chain 'B' and (resid 65 through 245 )
4X-RAY DIFFRACTION4chain 'B' and (resid 246 through 497 )

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