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- PDB-8g8r: RelB NLS in complex with Importin alpha 2 -

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Basic information

Entry
Database: PDB / ID: 8g8r
TitleRelB NLS in complex with Importin alpha 2
Components
  • Importin subunit alpha-1
  • Transcription factor RelB
KeywordsTRANSCRIPTION / Nuclear import / transcription factors / Nf-kB
Function / homology
Function and homology information


T-helper 1 cell differentiation / lymphocyte differentiation / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / myeloid dendritic cell differentiation / positive regulation of viral life cycle / negative regulation of interferon-beta production / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / cellular response to osmotic stress ...T-helper 1 cell differentiation / lymphocyte differentiation / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / myeloid dendritic cell differentiation / positive regulation of viral life cycle / negative regulation of interferon-beta production / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / cellular response to osmotic stress / NF-kappaB complex / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / non-canonical NF-kappaB signal transduction / antigen processing and presentation / canonical NF-kappaB signal transduction / host cell / transcription repressor complex / CD209 (DC-SIGN) signaling / NIK-->noncanonical NF-kB signaling / response to cytokine / Dectin-1 mediated noncanonical NF-kB signaling / circadian regulation of gene expression / cytoplasmic stress granule / protein import into nucleus / DNA-binding transcription factor binding / postsynaptic density / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / innate immune response / negative regulation of DNA-templated transcription / centrosome / glutamatergic synapse / synapse / chromatin / protein kinase binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Transcription factor RelB / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation domain / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain ...Transcription factor RelB / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation domain / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / 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 / ig-like, plexins, transcription factors / IPT domain / Armadillo/beta-catenin-like repeats / Armadillo / p53-like transcription factor, DNA-binding / Armadillo-like helical / Immunoglobulin E-set / Armadillo-type fold / Immunoglobulin-like fold
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Importin subunit alpha-1 / Transcription factor RelB
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
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

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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: Transcription factor RelB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2933
Polymers59,1392
Non-polymers1541
Water54030
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)78.465, 90.328, 99.501
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 Transcription factor RelB / I-Rel


Mass: 3870.531 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) / References: UniProt: Q01201
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.79 %
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, 2022
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: 88.74 % / Redundancy: 6.1 % / Biso Wilson estimate: 51.66 Å2 / CC1/2: 0.989 / Net I/σ(I): 6.9
Reflection shellResolution: 2.6→2.6 Å / Num. unique obs: 1053 / CC1/2: 0.841

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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→33.84 Å / SU ML: 0.2979 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5798
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2128 1053 4.79 %
Rwork0.1777 20947 -
obs0.1794 22000 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.84 Å2
Refinement stepCycle: LAST / Resolution: 2.6→33.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 8 30 3446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333498
X-RAY DIFFRACTIONf_angle_d0.60484751
X-RAY DIFFRACTIONf_chiral_restr0.0371567
X-RAY DIFFRACTIONf_plane_restr0.0052607
X-RAY DIFFRACTIONf_dihedral_angle_d13.54421302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.31021260.26682553X-RAY DIFFRACTION97.14
2.72-2.860.24681310.22832555X-RAY DIFFRACTION98.14
2.86-3.040.28311400.22022576X-RAY DIFFRACTION98.62
3.04-3.280.2561190.22152610X-RAY DIFFRACTION98.7
3.28-3.60.25061200.18132622X-RAY DIFFRACTION98.88
3.6-4.120.18181340.16012633X-RAY DIFFRACTION98.61
4.13-5.190.19141490.14242640X-RAY DIFFRACTION99.04
5.19-33.840.17961340.16382758X-RAY DIFFRACTION98.1
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)
12.64240097550.4212986838050.5703922752615.760211656021.331235813051.478992570410.22264805578-0.0800840444629-0.1471647055630.271770351162-0.165964509270.009233852489130.155536475827-0.140734689211-0.04365037283880.344009169579-0.0161766981589-0.02912136816310.352636014978-0.01076677538860.2338152498866.55833328491-2.93745150671-15.6868269607
21.36561571767-1.45768334886-1.483495856331.57715611541.549854158942.737279642310.133386709173-0.06901606667220.279355921943-0.1046589016660.063656775529-0.0663604821915-0.04352732615240.00841233252001-0.1832709749280.259852709966-0.045398558810.008383144115320.27916128962-0.0009276168499890.403070260461-4.1534945868128.0039342681-5.46954714239
31.418668322470.7240430861320.07074735462811.76661010710.7551286636723.242976184020.0828244287221-0.9162154637710.2564811255380.7188537928050.270971516763-0.4007234478140.1686569875870.554130369036-0.2248678101180.6206066145250.0463517066673-0.1062387545020.818017713978-0.1789136235960.566676397429-6.6295944996339.239247195426.0330905105
42.10752734764-0.1886950242930.5547649208012.44748480797-4.154713697467.09323881265-0.556811643507-0.1878478191910.9264320229070.379848926109-0.371333442890.06032626873240.7646632534630.05018476600160.910028695350.5995012663750.113464005841-0.03956457560070.542905787527-0.2126977632830.6616202529692.8646804982432.8225832977.53005553019
54.09170566222.647699211194.71985675331.716400518683.049262868335.46518069215-0.07073179662940.117481450865-0.5724506765080.1230512484840.390014744463-0.6524142356610.1172093557220.366717628673-0.1063317104181.258984354570.162864675167-0.1241849921540.981983166504-0.1943521586651.340799276222.2745499909921.06834259277.72724051742
65.603943869631.72953559647-0.03477617290642.937863331983.226910649695.48954001868-0.208120025833-0.2105411549840.618147605260.893665028953-0.2382819125551.44654628349-0.0647878274076-0.3706248902660.3251037060820.5838137667290.05636731187290.06751686445760.6487780367670.02648516172040.623366848213-2.652922459984.86633269219-8.54128175391
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 72 through 202 )AA72 - 2021 - 131
22chain 'A' and (resid 203 through 390 )AA203 - 390132 - 319
33chain 'A' and (resid 391 through 497 )AA391 - 497320 - 426
44chain 'B' and (resid 408 through 412 )BC408 - 4121 - 5
55chain 'B' and (resid 413 through 429 )BC413 - 4296 - 10
66chain 'B' and (resid 430 through 438 )BC430 - 43811 - 19

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