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- PDB-1k2f: siah, Seven In Absentia Homolog -

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Basic information

Entry
Database: PDB / ID: 1k2f
Titlesiah, Seven In Absentia Homolog
Componentssiah-1A protein
KeywordsLIGASE / PROTEIN BINDING / beta-sandwich
Function / homology
Function and homology information


Antigen processing: Ubiquitination & Proteasome degradation / SCF ubiquitin ligase complex / male meiosis I / regulation of multicellular organism growth / canonical Wnt signaling pathway / post-embryonic development / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / disordered domain specific binding / ubiquitin protein ligase activity ...Antigen processing: Ubiquitination & Proteasome degradation / SCF ubiquitin ligase complex / male meiosis I / regulation of multicellular organism growth / canonical Wnt signaling pathway / post-embryonic development / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / disordered domain specific binding / ubiquitin protein ligase activity / neuron apoptotic process / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / protein ubiquitination / protein homodimerization activity / zinc ion binding / nucleus / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase SINA-like, animal / Seven-in-absentia protein, TRAF-like domain / : / Sina, TRAF-like domain / Sina, zinc finger / E3 ubiquitin-protein ligase sina/sinah, RING finger / Zinc finger, SIAH-type / Zinc finger SIAH-type profile. / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A ...E3 ubiquitin-protein ligase SINA-like, animal / Seven-in-absentia protein, TRAF-like domain / : / Sina, TRAF-like domain / Sina, zinc finger / E3 ubiquitin-protein ligase sina/sinah, RING finger / Zinc finger, SIAH-type / Zinc finger SIAH-type profile. / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / TRAF-like / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / E3 ubiquitin-protein ligase SIAH1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.6 Å
AuthorsPolekhina, G. / House, C.M. / Traficante, N. / Mackay, J.P. / Relaix, F. / Sassoon, D.A. / Parker, M.W. / Bowtell, D.D.L.
Citation
Journal: Nat.Struct.Biol. / Year: 2002
Title: Siah ubiquitin ligase is structurally related to TRAF and modulates TNF-alpha signaling.
Authors: Polekhina, G. / House, C.M. / Traficante, N. / Mackay, J.P. / Relaix, F. / Sassoon, D.A. / Parker, M.W. / Bowtell, D.D.
#1: Journal: DEVELOPMENT / Year: 1993
Title: Isolation and characterisation of murine homologues of the Drosophila seven inabsentia gene (sina)
Authors: Della, N.G. / Senior, P.V. / Bowtell, D.D.
History
DepositionSep 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_struct_conn_angle / struct_conn / struct_site
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_asym_id / _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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: siah-1A protein
B: siah-1A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,55212
Polymers42,8472
Non-polymers70510
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-42 kcal/mol
Surface area19710 Å2
MethodPISA
2
A: siah-1A protein
hetero molecules

B: siah-1A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,55212
Polymers42,8472
Non-polymers70510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area1970 Å2
ΔGint-75 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.474, 73.966, 80.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein siah-1A protein / seven in absentia 1A


Mass: 21423.533 Da / Num. of mol.: 2 / Fragment: C-terminal domain (residues 93-282)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pMalC2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61092
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: calcium chloride, ethanol, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMMES1reservoirpH6.5
220 mM1reservoirCaCl2
320 %(v/v)ethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 13, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 12661 / Num. obs: 12661 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 64.8 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 28
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 4.31 / Num. unique all: 1244 / Rsym value: 0.388 / % possible all: 99.4
Reflection
*PLUS

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1224 -RANDOM
Rwork0.2199 ---
all0.2265 12661 --
obs0.2265 12661 97.4 %-
Displacement parametersBiso mean: 56.7 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 22 65 3083
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 56.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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