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- PDB-8g4j: Crystal structure of Cavia porcellus (guinea pig) importin-alpha ... -

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Basic information

Entry
Database: PDB / ID: 8g4j
TitleCrystal structure of Cavia porcellus (guinea pig) importin-alpha 1 in cargo-free state
ComponentsImportin subunit alpha
KeywordsTRANSPORT PROTEIN / importin-alpha1 / cargo-free / nuclear transport
Function / homology
Function and homology information


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 / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / positive regulation of type I interferon production / histone deacetylase binding / host cell / nuclear membrane ...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 / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / positive regulation of type I interferon production / histone deacetylase binding / host cell / nuclear membrane / nucleoplasm / cytosol
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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Importin subunit alpha
Similarity search - Component
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHawker, J.E. / Roby, J.A. / Stewart, M. / Forwood, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Cavia porcellus (guinea pig) importin-alpha 1 in cargo-free state
Authors: Hawker, J.E. / Roby, J.A. / Stewart, M. / Forwood, J.K.
History
DepositionFeb 9, 2023Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 22, 2023ID: 7S1E
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha
B: Importin subunit alpha


Theoretical massNumber of molelcules
Total (without water)91,9272
Polymers91,9272
Non-polymers00
Water90150
1
A: Importin subunit alpha


Theoretical massNumber of molelcules
Total (without water)45,9641
Polymers45,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Importin subunit alpha


Theoretical massNumber of molelcules
Total (without water)45,9641
Polymers45,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)184.169, 184.169, 57.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Importin subunit alpha


Mass: 45963.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: Kpna2 / Production host: Escherichia coli (E. coli) / Strain (production host): pLYS / References: UniProt: H0VVB1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MgCl2.6H2O; 0.1 M Na+ HEPES; 15%(w/v); pH 7.0; PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.35→29.41 Å / Num. obs: 41876 / % possible obs: 99.85 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.027 / Net I/σ(I): 12.1
Reflection shellResolution: 2.35→2.44 Å / Rmerge(I) obs: 1.296 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 41860 / CC1/2: 0.78 / Rpim(I) all: 0.37

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PHASERphasing
Cootmodel building
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→19.98 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 2119 5.07 %
Rwork0.2148 --
obs0.216 41800 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6452 0 0 50 6502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026595
X-RAY DIFFRACTIONf_angle_d0.5699000
X-RAY DIFFRACTIONf_dihedral_angle_d11.0612406
X-RAY DIFFRACTIONf_chiral_restr0.0381096
X-RAY DIFFRACTIONf_plane_restr0.0031148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.37811200.32982634X-RAY DIFFRACTION100
2.4-2.460.27851540.3022551X-RAY DIFFRACTION100
2.46-2.530.33771330.29622611X-RAY DIFFRACTION100
2.53-2.610.34871230.27792634X-RAY DIFFRACTION100
2.61-2.690.29491180.27052616X-RAY DIFFRACTION100
2.69-2.790.26871620.27242592X-RAY DIFFRACTION100
2.79-2.90.28411490.26422630X-RAY DIFFRACTION100
2.9-3.030.27891270.27162634X-RAY DIFFRACTION100
3.03-3.190.29691430.2632624X-RAY DIFFRACTION100
3.19-3.390.33471530.26352632X-RAY DIFFRACTION100
3.39-3.650.28331430.24622623X-RAY DIFFRACTION100
3.65-4.010.19761440.19462663X-RAY DIFFRACTION100
4.01-4.580.20161560.17552663X-RAY DIFFRACTION100
4.58-5.750.23031450.18882725X-RAY DIFFRACTION100
5.75-19.980.18141490.17712849X-RAY DIFFRACTION100
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)
12.9421-0.7139-0.84581.76561.99832.9950.02460.1274-0.48290.0642-0.10270.1435-0.08960.19310.00010.6504-0.0933-0.05480.58530.06480.604152.069521.06298.8969
20.3387-0.10260.51552.4239-1.15270.35180.0009-0.04840.2163-0.191-0.15050.19320.1369-0.0457-0.00010.7008-0.06850.04810.4952-0.01210.514441.991654.471912.6216
30.84050.84720.5891.0668-0.02841.5157-0.2830.14630.5636-0.026-0.03540.70510.0539-0.2154-00.7107-0.0852-0.16790.56020.04480.795130.015673.2319-1.6101
40.4765-0.4577-0.1080.9881-0.66880.7634-0.4715-0.05110.9326-1.0610.07490.4362-1.62960.05-0.00061.1931-0.0882-0.36750.79930.14771.029923.358178.6179-11.9932
51.6638-0.17910.46611.6337-0.59353.6005-0.1068-0.04380.0710.1055-0.3412-0.37430.220.4488-0.00250.52970.04090.14280.63070.10680.6798.570568.051129.3199
63.7616-0.91180.61131.4283-0.85062.20140.0284-0.25220.305-0.13250.00210.18320.16620.05670.00070.49810.0244-0.03010.3715-0.06440.38558.247482.653615.324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 76 through 222 )
2X-RAY DIFFRACTION2chain 'A' and (resid 223 through 390 )
3X-RAY DIFFRACTION3chain 'A' and (resid 391 through 454 )
4X-RAY DIFFRACTION4chain 'A' and (resid 455 through 497 )
5X-RAY DIFFRACTION5chain 'B' and (resid 75 through 245 )
6X-RAY DIFFRACTION6chain 'B' and (resid 246 through 497 )

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