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- PDB-8fzk: Dimeric human importin alpha subunit -

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Basic information

Entry
Database: PDB / ID: 8fzk
TitleDimeric human importin alpha subunit
ComponentsImportin subunit alpha-1
KeywordsTRANSPORT PROTEIN / importin / karyopherin / nuclear 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 / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear import signal receptor activity / CaMK IV-mediated phosphorylation of CREB / 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 / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear import signal receptor activity / CaMK IV-mediated phosphorylation of CREB / nuclear localization sequence binding / DNA metabolic process / NLS-bearing protein import into nucleus / positive regulation of type I interferon production / ISG15 antiviral mechanism / histone deacetylase binding / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / host cell / 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 / cytoplasm / 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-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDonnelly, C.M. / Stewart, M. / Forwood, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Dimeric human importin alpha subunit
Authors: Donnelly, C.M. / Stewart, M. / Forwood, J.K.
History
DepositionJan 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 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-1
B: Importin subunit alpha-1
C: Importin subunit alpha-1
D: Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,3896
Polymers199,1704
Non-polymers2202
Water7,891438
1
A: Importin subunit alpha-1
B: Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7803
Polymers99,5852
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Importin subunit alpha-1
D: Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6093
Polymers99,5852
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.107, 90.838, 94.603
Angle α, β, γ (deg.)103.190, 90.370, 97.390
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 49792.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA2, RCH1, SRP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52292
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 14% PEG 8000, 0.2M Magnesium chloride, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→29.91 Å / Num. obs: 92088 / % possible obs: 98.039 % / Redundancy: 3.5 % / Biso Wilson estimate: 34.72 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06758 / Rpim(I) all: 0.04155 / Net I/σ(I): 21.41
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.5274 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 8992 / CC1/2: 0.757

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.91 Å / SU ML: 0.2753 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.5052
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2468 4586 4.98 %
Rwork0.2013 87462 -
obs0.2036 92048 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12826 0 13 438 13277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016113182
X-RAY DIFFRACTIONf_angle_d1.38718006
X-RAY DIFFRACTIONf_chiral_restr0.06182185
X-RAY DIFFRACTIONf_plane_restr0.01082311
X-RAY DIFFRACTIONf_dihedral_angle_d5.92031795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.32381390.26172746X-RAY DIFFRACTION94.1
2.12-2.150.31161410.24682887X-RAY DIFFRACTION95.61
2.15-2.180.30311550.23712918X-RAY DIFFRACTION96.45
2.18-2.20.28891550.23852842X-RAY DIFFRACTION97.62
2.2-2.230.28891470.2342898X-RAY DIFFRACTION97.47
2.23-2.260.30161480.23152923X-RAY DIFFRACTION97.37
2.26-2.290.31981430.21992904X-RAY DIFFRACTION97.72
2.29-2.330.27731660.2272907X-RAY DIFFRACTION97.87
2.33-2.370.30551460.22282924X-RAY DIFFRACTION97.74
2.37-2.40.25921480.22482904X-RAY DIFFRACTION97.73
2.4-2.450.27611510.21452865X-RAY DIFFRACTION98.05
2.45-2.490.28891500.21292968X-RAY DIFFRACTION98.17
2.49-2.540.27911510.20442932X-RAY DIFFRACTION98.06
2.54-2.590.25981710.1922865X-RAY DIFFRACTION98.09
2.59-2.650.21731590.20582973X-RAY DIFFRACTION98.12
2.65-2.710.24731330.20512879X-RAY DIFFRACTION98.01
2.71-2.770.27591610.20992944X-RAY DIFFRACTION98.1
2.77-2.850.25271480.21312890X-RAY DIFFRACTION98.35
2.85-2.930.30481720.2252959X-RAY DIFFRACTION98.24
2.93-3.030.27941600.21142881X-RAY DIFFRACTION98.16
3.03-3.140.26391760.20372951X-RAY DIFFRACTION98.74
3.14-3.260.26851580.21252903X-RAY DIFFRACTION98.68
3.26-3.410.261520.20862928X-RAY DIFFRACTION98.88
3.41-3.590.2141620.18912953X-RAY DIFFRACTION98.95
3.59-3.810.21791230.17542990X-RAY DIFFRACTION98.98
3.81-4.110.2151480.16892958X-RAY DIFFRACTION99.17
4.11-4.520.20171600.16722944X-RAY DIFFRACTION99.17
4.52-5.170.19371320.17762943X-RAY DIFFRACTION99.1
5.17-6.50.2631710.21922933X-RAY DIFFRACTION98.79
6.5-29.910.22291600.20882950X-RAY DIFFRACTION99.42
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)
12.976408086421.094910054540.7821406939032.464262234352.922541894743.545612086460.538180298873-1.452099627240.849431554250.509980472218-0.303632849022-0.257714699194-0.225692474652-0.124784383504-0.2480452165070.657266362635-0.2146399142980.1310766721151.08993330336-0.5395367147250.9043560976119.7008952082750.647561285930.7216318936
22.07975332899-0.991947861726-0.6039050345322.372231349921.168866395181.17954733665-0.0035434493511-0.3720472559160.229248724960.203530437050.006055711673390.000655234975407-0.03804608903320.037345055597-0.002199396146950.217526682406-0.0475002233833-0.01893800885570.284355848137-0.030838926860.19785913899713.030276925228.67683632037.82803847319
32.17539033189-0.3385390548820.1371319328882.00086235933-0.2817442885493.047346013350.0456309627878-0.0841696726296-0.8623476930080.354398883778-0.02790250081190.0084465830450.7725551261660.0593709742710.008498761158650.435379085159-0.0099974788079-0.02147713568930.227495594240.03638669418390.4931809096424.2164242761-5.342695376685.463377429
42.11967431974-1.10615177375-0.519177459973.254831220241.548716193681.52506096678-0.215358338208-0.435340297149-0.374514706280.4989375218960.2083984930240.3145591214990.409260346341-0.0787732973219-0.0193922764460.530948689749-0.00222115193020.07895444223490.4543748864120.1511019340960.34275469030515.33728433428.700003007127.5210411585
51.506742167490.6838614146940.5582893299063.19193367649-0.1746625122812.38487528269-0.128354393757-0.1078314725310.321805718707-0.2963012490150.175533917311-1.0241140307-0.1964368039190.257404307133-0.06581226825870.451219723379-0.05132291042010.1481137066830.558397384513-0.310265842481.0688230130833.127810815750.412904351625.2646678688
62.66166633832-0.548952900502-0.9134622182051.38316568356-0.08282274060491.951974866-0.05226559196280.225808669932-0.175592433137-0.1121208751740.0131745897487-0.0279759021360.0807408428799-0.0610303565180.02853398271270.184685705737-0.0507779674002-0.03492708059650.357165386974-0.03540108397380.277422173411-14.61041107281.29680659892-31.9298225924
71.349904478260.8498253430520.5643876005553.143649293271.077582736631.6662913646-0.08015294868960.2186196387610.0661002125437-0.1565735300650.001601375581930.00867040946821-0.162678012768-0.1774178196610.07719144640740.2126201844810.00950270777152-0.02624530521260.281624016284-0.005524497431340.176375298104-9.8727886655923.4747540802-11.0975374077
82.020197940580.057442847651-0.06085667352142.62204684729-0.8332499082482.611427668040.139766962870.05390383530330.40125749803-0.170267595628-0.183510443074-0.256103182437-0.729068130814-0.04844957430980.05428504581950.5326179361810.0338558562904-0.03674883140640.227785398081-0.007432746887450.364579123022-1.9272343240444.6915728559-8.06756815767
91.783266787190.249859136058-0.989454731851.49195458866-0.9110124443753.524865078470.293604934539-0.1412068151760.5472080641760.2695142601370.0586636667026-0.0693747963178-1.161842597960.0639066366193-0.2693196231290.9503550050510.0424159065946-0.01554847882960.3722430113050.04912619571050.648277287055-2.337917130460.4076095286-13.5779509789
101.702815946080.745485831714-0.8746249690772.901451819881.832781959192.435061057410.119128557294-0.1252805755080.107001110475-0.271463257717-0.3098562401960.0763472615158-0.405152457987-0.226848960530.2600332037590.6835815104580.196621278063-0.02009194987090.4981991015130.1224341619870.445451778056-15.432937213745.6503668765-30.9811631445
111.7508284876-0.0227554832629-0.5305069902082.48522725771-0.507789700822.217593793750.121504125382-0.01853009863440.0243460276190.0337350854241-0.01247645698910.0492074421447-0.2394206471320.0903218696991-0.0960987029810.175313688972-0.00332873204634-0.003760161280550.2843552286430.02135143880720.1579653512817.70253227527.75154426946-36.9289634708
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 79 through 175 )AA79 - 1751 - 97
22chain 'A' and (resid 176 through 363 )AA176 - 36398 - 285
33chain 'A' and (resid 364 through 497 )AA364 - 497286 - 419
44chain 'B' and (resid 76 through 322 )BB76 - 3221 - 247
55chain 'B' and (resid 323 through 497 )BB323 - 497248 - 422
66chain 'C' and (resid 76 through 245 )CC76 - 2451 - 170
77chain 'C' and (resid 246 through 363 )CC246 - 363171 - 288
88chain 'C' and (resid 364 through 433 )CC364 - 433289 - 358
99chain 'C' and (resid 434 through 497 )CC434 - 497359 - 422
1010chain 'D' and (resid 75 through 245 )DF75 - 2451 - 171
1111chain 'D' and (resid 246 through 498 )DF246 - 498172 - 424

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