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- PDB-6y1j: 14-3-3 sigma in complex with IkappaBalpha pS63 peptide -

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Basic information

Entry
Database: PDB / ID: 6y1j
Title14-3-3 sigma in complex with IkappaBalpha pS63 peptide
Components
  • 14-3-3 protein sigma
  • NF-kappa-B inhibitor alpha
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 sigma / IkBa / Nf-kB
Function / homology
Function and homology information


I-kappaB/NF-kappaB complex / cytoplasmic sequestering of NF-kappaB / negative regulation of myeloid cell differentiation / nucleotide-binding oligomerization domain containing 1 signaling pathway / IkBA variant leads to EDA-ID / molecular sequestering activity / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / nucleotide-binding oligomerization domain containing 2 signaling pathway / transcription regulator inhibitor activity ...I-kappaB/NF-kappaB complex / cytoplasmic sequestering of NF-kappaB / negative regulation of myeloid cell differentiation / nucleotide-binding oligomerization domain containing 1 signaling pathway / IkBA variant leads to EDA-ID / molecular sequestering activity / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / nucleotide-binding oligomerization domain containing 2 signaling pathway / transcription regulator inhibitor activity / interleukin-1-mediated signaling pathway / cellular response to cold / nuclear localization sequence binding / toll-like receptor 4 signaling pathway / response to exogenous dsRNA / negative regulation of NF-kappaB transcription factor activity / regulation of epidermal cell division / protein kinase C inhibitor activity / negative regulation of Notch signaling pathway / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / positive regulation of cholesterol efflux / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / NF-kappaB binding / phosphoserine residue binding / positive regulation of transcription initiation by RNA polymerase II / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / canonical NF-kappaB signal transduction / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of canonical NF-kappaB signal transduction / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Notch signaling pathway / lipopolysaccharide-mediated signaling pathway / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / positive regulation of protein metabolic process / protein export from nucleus / negative regulation of innate immune response / NF-kB is activated and signals survival / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Activation of NF-kappaB in B cells / B cell receptor signaling pathway / negative regulation of protein kinase activity / TAK1-dependent IKK and NF-kappa-B activation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / CLEC7A (Dectin-1) signaling / positive regulation of inflammatory response / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / intrinsic apoptotic signaling pathway in response to DNA damage / Downstream TCR signaling / cellular response to tumor necrosis factor / regulation of cell population proliferation / positive regulation of cell growth / regulation of cell cycle / Ub-specific processing proteases / cadherin binding / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeats (many copies) / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein ...Ankyrin repeats (many copies) / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
NF-kappa-B inhibitor alpha / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.127 Å
AuthorsWolter, M. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission Netherlands
CitationJournal: Acs Omega / Year: 2020
Title: Interaction of an I kappa B alpha Peptide with 14-3-3.
Authors: Wolter, M. / Santo, D.L. / Herman, P. / Ballone, A. / Centorrino, F. / Obsil, T. / Ottmann, C.
History
DepositionFeb 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: NF-kappa-B inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,68813
Polymers29,9032
Non-polymers78511
Water6,017334
1
A: 14-3-3 protein sigma
P: NF-kappa-B inhibitor alpha
hetero molecules

A: 14-3-3 protein sigma
P: NF-kappa-B inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,37626
Polymers59,8064
Non-polymers1,56922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7610 Å2
ΔGint-95 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.460, 111.820, 62.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

21A-722-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 28226.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide NF-kappa-B inhibitor alpha / I-kappa-B-alpha / IkappaBalpha / Major histocompatibility complex enhancer-binding protein MAD3


Mass: 1676.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P25963

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Non-polymers , 5 types, 345 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.095 M Na-HEPES pH 7.1, 27% PEG400, 0.19 M Calcium chloride, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.127→45.492 Å / Num. obs: 108705 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 9.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.023 / Rrim(I) all: 0.07 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.13-1.158.60.6994586853380.8720.250.7432.7100
6.17-45.499.80.04173917560.9920.0140.04449.399.8

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4fr3

4fr3


Resolution: 1.127→45.492 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.36
RfactorNum. reflection% reflection
Rfree0.1833 5461 5.03 %
Rwork0.1695 --
obs0.1702 108654 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.59 Å2 / Biso mean: 14.9916 Å2 / Biso min: 2.28 Å2
Refinement stepCycle: final / Resolution: 1.127→45.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 102 334 2337
Biso mean--58.38 25.64 -
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072181
X-RAY DIFFRACTIONf_angle_d0.9712952
X-RAY DIFFRACTIONf_chiral_restr0.185311
X-RAY DIFFRACTIONf_plane_restr0.006392
X-RAY DIFFRACTIONf_dihedral_angle_d21.554846
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.127-1.13980.29891980.27653417
1.1398-1.15320.26631820.26963421
1.1532-1.16730.29711510.27063391
1.1673-1.18210.23341890.24733414
1.1821-1.19760.25411910.24643419
1.1976-1.2140.25361980.23323379
1.214-1.23140.23351760.2423402
1.2314-1.24970.25241780.21963408
1.2497-1.26930.22661750.22663416
1.2693-1.29010.20891870.20253434
1.2901-1.31230.20911900.19123394
1.3123-1.33620.2091770.18983449
1.3362-1.36190.20941720.18183408
1.3619-1.38970.20951920.18673379
1.3897-1.41990.19611880.17083425
1.4199-1.4530.17931890.16683408
1.453-1.48930.15371790.15413429
1.4893-1.52960.17391940.153409
1.5296-1.57460.16071500.15463462
1.5746-1.62540.17971840.15283437
1.6254-1.68350.15871660.15573442
1.6835-1.75090.16481890.15153434
1.7509-1.83060.171890.15493462
1.8306-1.92710.16571900.1583434
1.9271-2.04780.17541860.15183456
2.0478-2.2060.1621880.14633464
2.206-2.42790.1521580.14743508
2.4279-2.77920.16391790.15963499
2.7792-3.50130.17511860.15953525
3.5013-45.4920.18511900.16763668

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