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- PDB-5h9m: Crystal structure of siah2 SBD domain -

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Basic information

Entry
Database: PDB / ID: 5h9m
TitleCrystal structure of siah2 SBD domain
ComponentsE3 ubiquitin-protein ligase SIAH2
KeywordsLIGASE / SBD / siah2 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of netrin-activated signaling pathway / protein catabolic process => GO:0030163 / Netrin-1 signaling / multicellular organism development / ubiquitin conjugating enzyme binding / small GTPase-mediated signal transduction / protein deubiquitination / regulation of protein ubiquitination / negative regulation of extrinsic apoptotic signaling pathway / RING-type E3 ubiquitin transferase ...negative regulation of netrin-activated signaling pathway / protein catabolic process => GO:0030163 / Netrin-1 signaling / multicellular organism development / ubiquitin conjugating enzyme binding / small GTPase-mediated signal transduction / protein deubiquitination / regulation of protein ubiquitination / negative regulation of extrinsic apoptotic signaling pathway / RING-type E3 ubiquitin transferase / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of canonical Wnt signaling pathway / regulation of circadian rhythm / protein polyubiquitination / ubiquitin-protein transferase activity / transcription corepressor activity / rhythmic process / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / amyloid fibril formation / early endosome / Ub-specific processing proteases / neuron projection / cell cycle / Amyloid fiber formation / intracellular membrane-bounded organelle / neuronal cell body / apoptotic process / negative regulation of apoptotic process / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase SINA-like, animal / Seven-in-absentia protein, TRAF-like domain / Sina, TRAF-like domain / 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 ...E3 ubiquitin-protein ligase SINA-like, animal / Seven-in-absentia protein, TRAF-like domain / Sina, TRAF-like domain / 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
E3 ubiquitin-protein ligase SIAH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.761 Å
AuthorsDong, A. / Zhang, Q. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of siah2 SBD domain
Authors: Zhang, Q. / Dong, A. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
History
DepositionDec 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SIAH2
B: E3 ubiquitin-protein ligase SIAH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,60315
Polymers42,7592
Non-polymers84513
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-35 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.624, 68.753, 102.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein E3 ubiquitin-protein ligase SIAH2 / Seven in absentia homolog 2 / hSiah2


Mass: 21379.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIAH2 / Plasmid: pET28-MKH8SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL
References: UniProt: O43255, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 5 types, 319 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG8000, 0.2 M NaCl, 0.1 M Hepes pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.76→50.01 Å / Num. obs: 38381 / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.034 / Rrim(I) all: 0.106 / Χ2: 1.143 / Net I/av σ(I): 25.746 / Net I/σ(I): 7.2 / Num. measured all: 352371
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.796.50.87918940.720.3630.9540.68599.9
1.79-1.827.80.75118780.8280.2790.8020.696100
1.82-1.868.50.61619080.8940.2170.6540.737100
1.86-1.99.50.51918810.9340.1710.5470.771100
1.9-1.949.50.45118650.9460.1490.4760.786100
1.94-1.989.50.36619130.9610.1210.3860.81100
1.98-2.039.50.30218810.9720.10.3180.855100
2.03-2.099.50.26118950.9780.0860.2750.878100
2.09-2.159.50.22619100.9840.0750.2380.902100
2.15-2.229.50.18618960.990.0610.1960.916100
2.22-2.39.50.16919060.9910.0560.1780.941100
2.3-2.399.50.14618900.9930.0480.1540.957100
2.39-2.59.60.13319290.9940.0440.140.976100
2.5-2.639.60.11219130.9950.0370.1181.021100
2.63-2.799.60.09119090.9960.030.0961.115100
2.79-3.019.60.07719390.9970.0260.0811.257100
3.01-3.319.60.0719430.9980.0230.0741.698100
3.31-3.799.40.06519570.9980.0220.0692.384100
3.79-4.789.20.05219700.9990.0180.0552.14100
4.78-508.80.04821040.9990.0170.0511.97499.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
MOLREPphasing
ARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C9Z

4c9z


Resolution: 1.761→50.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.747 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22677 945 2.5 %RANDOM
Rwork0.17761 ---
obs0.17885 37374 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.803 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2--1.52 Å2-0 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.761→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 39 306 3280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193220
X-RAY DIFFRACTIONr_bond_other_d0.0020.022943
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9374394
X-RAY DIFFRACTIONr_angle_other_deg0.9323.0036766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.34623.643140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98715501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8691516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023754
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02778
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3812.0331617
X-RAY DIFFRACTIONr_mcbond_other1.3792.0321616
X-RAY DIFFRACTIONr_mcangle_it2.2243.0412051
X-RAY DIFFRACTIONr_mcangle_other2.2243.0412052
X-RAY DIFFRACTIONr_scbond_it1.8452.2411603
X-RAY DIFFRACTIONr_scbond_other1.8442.2421604
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9793.2732343
X-RAY DIFFRACTIONr_long_range_B_refined5.12117.2813697
X-RAY DIFFRACTIONr_long_range_B_other5.0317.1263651
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.761→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 65 -
Rwork0.256 2633 -
obs--96.08 %

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