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- PDB-2a25: Crystal structure of Siah1 SBD bound to the peptide EKPAAVVAPITTG... -

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Basic information

Entry
Database: PDB / ID: 2a25
TitleCrystal structure of Siah1 SBD bound to the peptide EKPAAVVAPITTG from SIP
Components
  • Calcyclin-binding protein peptide
  • Ubiquitin ligase SIAH1
KeywordsLIGASE / Protein-peptide complex
Function / homology
Function and homology information


Netrin-1 signaling / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / S100 protein binding / SCF ubiquitin ligase complex / nuclear envelope lumen / anatomical structure morphogenesis / canonical Wnt signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / tubulin binding ...Netrin-1 signaling / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / S100 protein binding / SCF ubiquitin ligase complex / nuclear envelope lumen / anatomical structure morphogenesis / canonical Wnt signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / tubulin binding / cellular response to leukemia inhibitory factor / axon guidance / RING-type E3 ubiquitin transferase / protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / heart development / nervous system development / ubiquitin-dependent protein catabolic process / spermatogenesis / neuron apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / amyloid fibril formation / protein ubiquitination / positive regulation of apoptotic process / Amyloid fiber formation / protein domain specific binding / ubiquitin protein ligase binding / apoptotic process / protein homodimerization activity / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Siah interacting protein, N-terminal / Calcyclin-binding protein, N-terminal / Calcyclin-binding Protein, CS domain / : / Siah interacting protein, N terminal / SGS domain / SGS domain / SGS domain profile. / E3 ubiquitin-protein ligase SINA-like, animal / Seven-in-absentia protein, TRAF-like domain ...Siah interacting protein, N-terminal / Calcyclin-binding protein, N-terminal / Calcyclin-binding Protein, CS domain / : / Siah interacting protein, N terminal / SGS domain / SGS domain / SGS domain profile. / 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. / CS domain / CS domain / CS domain profile. / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / HSP20-like chaperone / TRAF-like / Classic Zinc Finger / Double Stranded RNA Binding Domain / 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
E3 ubiquitin-protein ligase SIAH1 / Calcyclin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSantelli, E. / Leone, M. / Li, C. / Fukushima, T. / Preece, N.E. / Olson, A.J. / Ely, K.R. / Reed, J.C. / Pellecchia, M. / Liddington, R.C. / Matsuzawa, S.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Analysis of Siah1-Siah-interacting Protein Interactions and Insights into the Assembly of an E3 Ligase Multiprotein Complex
Authors: Santelli, E. / Leone, M. / Li, C. / Fukushima, T. / Preece, N.E. / Olson, A.J. / Ely, K.R. / Reed, J.C. / Pellecchia, M. / Liddington, R.C. / Matsuzawa, S.
History
DepositionJun 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ubiquitin ligase SIAH1
B: Calcyclin-binding protein peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0143
Polymers22,9482
Non-polymers651
Water1,802100
1
A: Ubiquitin ligase SIAH1
B: Calcyclin-binding protein peptide
hetero molecules

A: Ubiquitin ligase SIAH1
B: Calcyclin-binding protein peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0276
Polymers45,8974
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)47.635, 107.761, 78.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by the two fold axis: 1-x, y, 1/2-z

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Components

#1: Protein Ubiquitin ligase SIAH1 / Seven in absentia homolog 1 / Siah-1 / Siah-1a


Mass: 21693.820 Da / Num. of mol.: 1 / Fragment: Substrate binding domain (residues 90-282)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIAH1, HUMSIAH / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8IUQ4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Calcyclin-binding protein peptide / CacyBP / hCacyBP / Siah-interacting protein / S100A6-binding protein / PNAS-107


Mass: 1254.451 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide can be naturally found in Homo sapiens (human)
References: UniProt: Q9HB71
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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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: 2.94 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: sodium dihydrogen phospahte, di-potassium hydrogen phosphate, dithiothreithol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 10567 / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 3.9 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 27
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1k2f chain A

1k2f


Resolution: 2.2→29.11 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.472 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 524 5 %RANDOM
Rwork0.21342 ---
obs0.21529 10527 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.77 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20 Å2
2--1.36 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 1 100 1320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211249
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.9281683
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02927
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.2524
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0841.5771
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9621241
X-RAY DIFFRACTIONr_scbond_it3.423478
X-RAY DIFFRACTIONr_scangle_it5.1444.5442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.318 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.344 86
Rwork0.296 1392
Refinement TLS params.Method: refined / Origin x: 12.6082 Å / Origin y: 38.1424 Å / Origin z: 8.8587 Å
111213212223313233
T0.091 Å20.0131 Å20.0107 Å2-0.002 Å20.0049 Å2--0.1279 Å2
L8.057 °20.5473 °23.4563 °2-3.1063 °2-0.6595 °2--6.0939 °2
S-0.0056 Å °-0.2343 Å °-0.6125 Å °-0.2312 Å °0.1068 Å °-0.0205 Å °0.1452 Å °-0.3148 Å °-0.1012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA125 - 28236 - 193
2X-RAY DIFFRACTION1AC601
3X-RAY DIFFRACTION1BB59 - 672 - 10
4X-RAY DIFFRACTION1AD602 - 691

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