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- PDB-8g8q: Monopartite p52 NLS in complex with Importin alpha 2 -

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Basic information

Entry
Database: PDB / ID: 8g8q
TitleMonopartite p52 NLS in complex with Importin alpha 2
Components
  • Importin subunit alpha-1
  • bacterial peptide
  • monopartite p52 NLS
KeywordsTRANSCRIPTION / Nuclear import / transcription factors / Nf-kB
Function / homology
Function and homology information


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 / nuclear import signal receptor activity / protein import into nucleus / cytoplasmic stress granule / host cell / DNA-binding transcription factor binding ...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 / nuclear import signal receptor activity / protein import into nucleus / cytoplasmic stress granule / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / 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-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTsimbslyuk, S. / Stewart, M. / Forwood, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Monopartite p52 NLS in complex with Importin alpha 2
Authors: Tsimbslyuk, S. / Stewart, M. / Forwood, J.K.
History
DepositionFeb 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details / struct / Item: _citation.title / _struct.title

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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: monopartite p52 NLS
C: bacterial peptide


Theoretical massNumber of molelcules
Total (without water)58,5953
Polymers58,5953
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.850, 88.755, 98.692
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Importin subunit alpha-1 / 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


Mass: 55268.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52293
#2: Protein/peptide monopartite p52 NLS


Mass: 2579.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RELB / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Protein/peptide bacterial peptide


Mass: 746.905 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.01M DTT, 0.1M sodium HEPES pH7.5, 0.8.5M sodium citrate

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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: Feb 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→33.84 Å / Num. obs: 22000 / % possible obs: 98.39 % / Redundancy: 5.7 % / Biso Wilson estimate: 52.28 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.3
Reflection shellResolution: 2.6→2.6 Å / Num. unique obs: 1053 / CC1/2: 0.636

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6bw0

6bw0


Resolution: 2.6→19.86 Å / SU ML: 0.3472 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.6852
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2099 974 5.08 %
Rwork0.1788 18182 -
obs0.1805 19156 88.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 0 31 3398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053442
X-RAY DIFFRACTIONf_angle_d0.78634679
X-RAY DIFFRACTIONf_chiral_restr0.0429560
X-RAY DIFFRACTIONf_plane_restr0.0064599
X-RAY DIFFRACTIONf_dihedral_angle_d13.10391279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.740.32591410.24852589X-RAY DIFFRACTION90.7
2.74-2.910.26231260.2152640X-RAY DIFFRACTION90.78
2.91-3.130.25561200.22632628X-RAY DIFFRACTION90.34
3.13-3.450.26531470.21332577X-RAY DIFFRACTION89.25
3.45-3.940.20071250.1792594X-RAY DIFFRACTION87.97
3.94-4.950.18121620.14822562X-RAY DIFFRACTION87.76
4.95-19.860.17511530.15282592X-RAY DIFFRACTION84.96
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)
10.0104912977980.00674094117744-0.003232745636190.00810097540522-0.004491940842080.00326930745461-0.360386165829-0.181685218465-0.09942198013690.0867650813123-0.185734549493-0.254329408170.1920441062630.3651011173450.5015224778341.161545490140.0127858417616-0.0286860740931.412652650390.01034336174781.371211962952.9348577215932.12928904288.02970353543
21.45167714134-0.5624698028230.08189352138452.472781255231.044699606080.7368246578950.08777565151680.00645179535453-0.07971285070960.0970873395297-0.01085668582570.114942608030.09090987093410.00230966667486-0.06127706536170.462756331558-0.0234080817404-0.009383103897970.406924690369-0.004590472808530.3786954055814.416751886985.17618535744-15.2690288029
31.80628129068-1.00038145219-1.075730941360.9601569340530.71873694021.566267778980.131409381052-0.103783140670.297670362986-0.08100461547750.0998875157781-0.256920238772-0.1344136060880.1110568942-0.1401186244780.480508677528-0.01012809695660.02363811727990.471841871038-0.0474337138610.669029644625-7.2693952114233.08373081661.29165153619
41.673947485580.357101014952-0.5572154293023.486720381660.8453137474352.541155396160.0206808058802-0.936425344625-0.003783998393720.9449388263050.211813632652-0.6028001254080.2146460861460.603644608969-0.2407802702550.673603204410.0372337570417-0.1354334611960.921465218818-0.1351071454730.628416500556-6.585125799639.204080607125.7754792724
53.391210836810.785424254980.1814822976564.855460704382.116400951533.03732629416-0.06020788648790.1420984927920.4733036652070.437101548965-0.508594710978-0.1162878578410.266484818776-0.4785064914810.506703946640.645638529299-0.004115913542650.05687704297740.5594302697640.09380851949340.668896397838-0.7291038960446.2717165211-6.4945230991
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 337 through 341 )CD337 - 3411 - 5
22chain 'A' and (resid 72 through 279 )AA72 - 2791 - 208
33chain 'A' and (resid 280 through 390 )AA280 - 390209 - 319
44chain 'A' and (resid 391 through 497 )AA391 - 497320 - 426
55chain 'B' and (resid 335 through 342 )BB335 - 3421 - 8

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