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- PDB-3wpt: Crystal structure of closed dimer of human importin-alpha1 (Rch1) -

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Basic information

Entry
Database: PDB / ID: 3wpt
TitleCrystal structure of closed dimer of human importin-alpha1 (Rch1)
ComponentsImportin subunit alpha-1
KeywordsTRANSPORT PROTEIN / Arm repeat / All Alpha protein / Armadillo repeat / Closed dimer / Nuclear transport / importin-beta / NLS-carring proteins
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
DI(HYDROXYETHYL)ETHER / Importin subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.629 Å
AuthorsMiyatake, H. / Sanjoh, A. / Matsuda, G. / Tatsumi, Y. / Dohmae, N. / Aida, Y.
CitationJournal: To be Published
Title: Crystal structure of closed dimer of human importin-alpha1 (Rch1)
Authors: Miyatake, H.
History
DepositionJan 17, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-1
B: Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,35119
Polymers91,5472
Non-polymers1,80417
Water3,585199
1
A: Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,94112
Polymers45,7731
Non-polymers1,16711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4107
Polymers45,7731
Non-polymers6376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.299, 139.299, 141.288
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-1 / / Rch1 / Karyopherin subunit alpha-2 / RAG cohort protein 1 / SRP1-alpha


Mass: 45773.355 Da / Num. of mol.: 2 / Fragment: UNP residues 75-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA2, RCH1, SRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52292
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 3.74 Å3/Da / Density % sol: 67.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 50MM MES, 100MM AMMONIUM SULFATE, 10MM MGCL, 15-20%(w/v) PEG8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2008 / Details: Mirror
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.629→46.51 Å / Num. obs: 40635 / % possible obs: 96.96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 48.38 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 31.83
Reflection shellResolution: 2.629→2.723 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 4.86 / Num. unique all: 3701 / Rsym value: 0.391 / % possible all: 90.25

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JDQ

2jdq


Resolution: 2.629→46.505 Å / FOM work R set: 0.8636 / SU ML: 0.3 / σ(F): 1.49 / σ(I): 0 / Phase error: 20.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2001 4.93 %RANDOM
Rwork0.1896 ---
obs0.191 40606 96.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.17 Å2 / Biso mean: 55.14 Å2 / Biso min: 23.91 Å2
Refinement stepCycle: LAST / Resolution: 2.629→46.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6428 0 119 199 6746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036646
X-RAY DIFFRACTIONf_angle_d0.7819015
X-RAY DIFFRACTIONf_chiral_restr0.0291087
X-RAY DIFFRACTIONf_plane_restr0.0031141
X-RAY DIFFRACTIONf_dihedral_angle_d15.0092444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6292-2.69490.31291120.2922510262289
2.6949-2.76780.27711120.23942616272893
2.7678-2.84920.25421320.2372656278895
2.8492-2.94120.28291400.23072699283996
2.9412-3.04630.25171540.22212675282996
3.0463-3.16820.26381410.21452732287397
3.1682-3.31240.25611490.22372775292498
3.3124-3.48690.23271450.21732753289898
3.4869-3.70530.2351410.19562796293799
3.7053-3.99130.18591570.16372780293798
3.9913-4.39270.19921550.1522831298699
4.3927-5.02760.15341570.148428563013100
5.0276-6.33170.24461580.200628993057100
6.3317-46.51250.18081480.16923029317798
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)
13.10970.322-0.71462.9057-0.58692.72330.1261-0.6255-0.35150.3622-0.3663-0.47830.39990.160.18630.5551-0.0704-0.07360.48280.1080.378754.567180.680871.8318
21.93771.16361.98951.2491.74232.74240.0601-0.27330.14020.074-0.08610.0743-0.0296-0.07880.02110.3606-0.00980.03410.3780.07240.387931.022879.166649.5661
31.9985-0.51460.35083.796-0.56471.563-0.08860.1141-0.2555-0.18980.14630.34290.3295-0.2416-0.06460.3745-0.06080.03430.37180.03770.41616.7553.15429.0895
43.17020.0103-0.96621.21220.71411.63660.1011-0.11660.1631-0.0662-0.1018-0.115-0.27170.1668-0.00910.4177-0.0340.04950.32130.10110.353719.545648.38753.5381
53.53991.82520.01592.6239-0.60821.1763-0.0909-0.2367-0.39690.02490.0596-0.03010.0455-0.19780.00630.31180.01270.00630.34390.06570.374449.801654.167649.334
61.46-0.092-0.4643.92651.39621.28530.1148-0.1219-0.04220.09830.0373-0.5326-0.0950.1162-0.14110.32680.0286-0.02040.31910.05620.322266.519583.925850.9601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 75 THROUGH 175 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 176 THROUGH 362 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 363 THROUGH 496 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 75 THROUGH 202 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 203 THROUGH 348 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 349 THROUGH 497 )

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