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- PDB-7lf4: Structure of importin a3 bound to the p50- and p65-NLSs -

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Basic information

Entry
Database: PDB / ID: 7lf4
TitleStructure of importin a3 bound to the p50- and p65-NLSs
Components
  • Importin subunit alpha-3
  • Nuclear factor NF-kappa-B p105 subunit
  • Transcription factor p65
KeywordsPROTEIN TRANSPORT / NUCLEAR IMPORT / IMPORTIN ALPHA 3 / NLS / NF-kB / p50 / p65
Function / homology
Function and homology information


negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / negative regulation of cholesterol transport / positive regulation of hyaluronan biosynthetic process / antibacterial innate immune response / mammary gland involution / acetaldehyde metabolic process / prolactin signaling pathway / cellular response to interleukin-17 ...negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / negative regulation of cholesterol transport / positive regulation of hyaluronan biosynthetic process / antibacterial innate immune response / mammary gland involution / acetaldehyde metabolic process / prolactin signaling pathway / cellular response to interleukin-17 / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / dopamine secretion / positive regulation of Schwann cell differentiation / positive regulation of macrophage derived foam cell differentiation / positive regulation of lipid storage / cellular response to peptidoglycan / negative regulation of interleukin-12 production / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / NS1 Mediated Effects on Host Pathways / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / NLS-dependent protein nuclear import complex / negative regulation of protein sumoylation / cellular response to dsRNA / postsynapse to nucleus signaling pathway / defense response to tumor cell / nucleotide-binding oligomerization domain containing 2 signaling pathway / Interleukin-1 processing / cellular response to interleukin-6 / actinin binding / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to angiotensin / response to UV-B / vascular endothelial growth factor signaling pathway / interleukin-1-mediated signaling pathway / Regulation of NFE2L2 gene expression / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of protein metabolic process / nuclear import signal receptor activity / positive regulation of miRNA metabolic process / toll-like receptor 4 signaling pathway / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of T cell receptor signaling pathway / response to cobalamin / phosphate ion binding / non-canonical NF-kappaB signal transduction / cellular response to lipoteichoic acid / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / The NLRP3 inflammasome / general transcription initiation factor binding / Transcriptional Regulation by VENTX / hair follicle development / NF-kappaB binding / neuropeptide signaling pathway / positive regulation of transcription initiation by RNA polymerase II / positive regulation of vascular endothelial growth factor production / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / response to amino acid / cellular response to interleukin-1 / cellular defense response / Purinergic signaling in leishmaniasis infection / nuclear pore / JNK cascade / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / positive regulation of interleukin-12 production / NF-kB is activated and signals survival / CD209 (DC-SIGN) signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / negative regulation of angiogenesis / response to interleukin-1 / negative regulation of miRNA transcription / liver development / response to progesterone / response to organic substance / positive regulation of interleukin-1 beta production / response to cytokine / response to ischemia / positive regulation of interleukin-8 production / Dectin-1 mediated noncanonical NF-kB signaling / negative regulation of extrinsic apoptotic signaling pathway / Activation of NF-kappaB in B cells / transcription coregulator activity / peptide binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / B cell receptor signaling pathway / protein catabolic process
Similarity search - Function
: / Nuclear factor NF-kappa-B, p105 subunit / Transcription factor RelA (p65) / 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 ...: / Nuclear factor NF-kappa-B, p105 subunit / Transcription factor RelA (p65) / 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. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / 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 / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Armadillo-like helical / Immunoglobulin E-set / Armadillo-type fold / Immunoglobulin-like fold
Similarity search - Domain/homology
Importin subunit alpha-3 / Nuclear factor NF-kappa-B p105 subunit / Transcription factor p65
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsFlorio, T.J. / Lokareddy, R.K. / Cingolani, G.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122844 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA56036 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)OD017987 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)OD023479 United States
CitationJournal: Nat Commun / Year: 2022
Title: Differential recognition of canonical NF-kappa B dimers by Importin alpha 3.
Authors: Florio, T.J. / Lokareddy, R.K. / Yeggoni, D.P. / Sankhala, R.S. / Ott, C.A. / Gillilan, R.E. / Cingolani, G.
History
DepositionJan 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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-3
B: Nuclear factor NF-kappa-B p105 subunit
C: Importin subunit alpha-3
D: Transcription factor p65
F: Nuclear factor NF-kappa-B p105 subunit
E: Transcription factor p65


Theoretical massNumber of molelcules
Total (without water)125,2446
Polymers125,2446
Non-polymers00
Water0
1
A: Importin subunit alpha-3
B: Nuclear factor NF-kappa-B p105 subunit
E: Transcription factor p65


Theoretical massNumber of molelcules
Total (without water)62,6223
Polymers62,6223
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Importin subunit alpha-3
D: Transcription factor p65
F: Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)62,6223
Polymers62,6223
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.130, 117.130, 210.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 72 through 173 or resid 175 through 487))
21(chain C and (resid 72 through 173 or resid 175 through 487))
12chain B
22chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERVALVAL(chain A and (resid 72 through 173 or resid 175 through 487))AA72 - 17372 - 173
121GLUGLUSERSER(chain A and (resid 72 through 173 or resid 175 through 487))AA175 - 487175 - 487
211SERSERVALVAL(chain C and (resid 72 through 173 or resid 175 through 487))CC72 - 17372 - 173
221GLUGLUSERSER(chain C and (resid 72 through 173 or resid 175 through 487))CC175 - 487175 - 487
112GLUGLUPROPROchain BBB433 - 4434 - 14
212GLUGLUPROPROchain FFE433 - 4434 - 14

NCS ensembles :
ID
1
2

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Components

#1: Protein Importin subunit alpha-3 / / Importin alpha Q1 / Qip1 / Karyopherin subunit alpha-4


Mass: 57941.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA4, QIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00629
#2: Protein/peptide Nuclear factor NF-kappa-B p105 subunit / DNA-binding factor KBF1 / EBP-1 / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1


Mass: 1790.114 Da / Num. of mol.: 2
Fragment: Nuclear localization signal motif, residues 355-368
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P19838
#3: Protein/peptide Transcription factor p65 / Nuclear factor NF-kappa-B p65 subunit / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3


Mass: 2890.410 Da / Num. of mol.: 2
Fragment: Nuclear localization signal motif, residues 294-315
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206

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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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. obs: 34874 / % possible obs: 85.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 64.1 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.082 / Rsym value: 0.137 / Net I/σ(I): 6.3
Reflection shellResolution: 2.82→2.92 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1835 / CC1/2: 0.287 / Rpim(I) all: 0.712 / Rsym value: 0.853

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TBK

5tbk


Resolution: 2.85→14.98 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 2.15 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2377 1277 4.93 %
Rwork0.1966 24600 -
obs0.1987 25877 65.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 247.12 Å2 / Biso mean: 92.0714 Å2 / Biso min: 33.94 Å2
Refinement stepCycle: final / Resolution: 2.85→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6853 0 0 0 6853
Num. residues----881
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2496X-RAY DIFFRACTION4.654TORSIONAL
12C2496X-RAY DIFFRACTION4.654TORSIONAL
21B64X-RAY DIFFRACTION4.654TORSIONAL
22F64X-RAY DIFFRACTION4.654TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-2.960.3213400.3645986102624
2.96-3.10.383630.33481225128830
3.1-3.260.34331010.30911820192144
3.26-3.460.34351380.29832549268762
3.46-3.720.31651550.25723108326376
3.72-4.090.27531890.2153621381087
4.09-4.670.20041990.17753755395490
4.67-5.820.23471950.1853799399490
5.82-14.980.16731970.13013737393486
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)
10.74160.68230.87852.29640.29191.9012-0.106-0.26740.10140.5919-0.06270.9040.0444-0.41420.12820.93440.50670.04260.4103-0.16920.811340.08055.4335-37.5834
20.7123-0.7726-0.04471.22130.00950.2637-0.1327-0.1180.16020.12990.06960.0398-0.04790.00380.02140.78720.5391-0.18670.1241-0.14210.50159.8829-11.6951-45.6745
30.4039-0.2243-0.24520.6927-0.28260.9179-0.143-0.0666-0.4008-0.1412-0.07650.0750.7650.23940.00331.14920.6247-0.13930.44940.02590.564268.349-41.3105-40.316
40.22140.40590.11940.8266-0.01491.03880.01680.2655-0.2436-0.1207-0.04220.0140.1278-0.1325-0.00222.0022-0.1228-0.13320.89850.07521.373660.4111-61.2837-39.6364
53.8514-0.07150.36121.2401-0.66742.1166-0.1424-0.1142-0.25210.57930.099-0.10760.30440.16830.01711.12110.42650.03720.57930.08920.896150.1523-7.6381-32.9941
61.051-0.7598-0.39780.65440.35420.4125-0.17710.5466-0.357-0.33780.2328-0.89320.4131.3273-0.01710.95770.42930.13941.8078-0.09230.987691.5612-35.1345-75.8328
72.2689-0.23660.57431.89970.38252.6415-0.50090.0677-0.2269-0.37990.10870.25730.1349-0.57770.36760.7679-0.06840.03010.3652-0.01660.410548.6436-26.6932-78.238
80.56820.74471.1211.8141.47472.2124-0.2408-0.6063-0.48680.71420.02920.72840.6604-0.58430.22510.783-0.099-0.06150.9160.00520.720548.2082-32.3551-68.876
90.523-0.6448-0.50021.20570.63580.53140.0175-0.2489-0.27430.3-0.0472-0.11490.34390.18220.02661.4621-0.00120.08441.24480.07631.589157.756-36.3948-77.2989
100.7295-0.35311.16313.4908-0.68991.8588-0.24050.3829-0.2625-0.50240.0258-0.35370.12940.42450.21161.19990.14470.35621.5284-0.23821.151182.4846-34.3888-84.4848
114.26460.7692-0.80262.0284-2.0842.15050.19820.4853-0.4522-0.31-0.16110.31370.3949-0.5059-0.021.19690.2182-0.12320.82880.01740.673856.3737-36.0993-46.262
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 170 )A72 - 170
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 313 )A171 - 313
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 441 )A314 - 441
4X-RAY DIFFRACTION4chain 'A' and (resid 442 through 487 )A442 - 487
5X-RAY DIFFRACTION5chain 'B' and (resid 433 through 443 )B433 - 443
6X-RAY DIFFRACTION6chain 'C' and (resid 72 through 236 )C72 - 236
7X-RAY DIFFRACTION7chain 'C' and (resid 237 through 487 )C237 - 487
8X-RAY DIFFRACTION8chain 'D' and (resid 290 through 297 )D290 - 297
9X-RAY DIFFRACTION9chain 'D' and (resid 298 through 303 )D298 - 303
10X-RAY DIFFRACTION10chain 'F' and (resid 433 through 443 )F433 - 443
11X-RAY DIFFRACTION11chain 'E' and (resid 291 through 303 )E291 - 303

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