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- PDB-9g0l: Crystal structure of the RING-ZnF1 fragment of SIAH1 -

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Basic information

Entry
Database: PDB / ID: 9g0l
TitleCrystal structure of the RING-ZnF1 fragment of SIAH1
ComponentsE3 ubiquitin-protein ligase SIAH1
KeywordsTRANSFERASE / E3 ubiquitin-protein ligase / Apoptosis / Metal-binding
Function / homology
Function and homology information


Netrin-1 signaling / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / anatomical structure morphogenesis / canonical Wnt signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / axon guidance / protein catabolic process / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity ...Netrin-1 signaling / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / anatomical structure morphogenesis / canonical Wnt signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / axon guidance / protein catabolic process / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / ubiquitin-dependent protein catabolic process / neuron apoptotic process / spermatogenesis / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / positive regulation of apoptotic process / Amyloid fiber formation / apoptotic process / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
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. / TRAF-like / Zinc finger RING-type 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. / TRAF-like / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase SIAH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCoste, F. / Suskiewicz, M.J.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Febs J. / Year: 2025
Title: RING dimerisation drives higher-order organisation of SINA/SIAH E3 ubiquitin ligases.
Authors: Coste, F. / Mishra, A. / Chapuis, C. / Mance, L. / Pukalo, Z. / Bigot, N. / Goffinont, S. / Gaudon, V. / Garnier, N. / Talhaoui, I. / Castaing, B. / Huet, S. / Suskiewicz, M.J.
History
DepositionJul 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SIAH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1454
Polymers11,9491
Non-polymers1963
Water1,29772
1
A: E3 ubiquitin-protein ligase SIAH1
hetero molecules

A: E3 ubiquitin-protein ligase SIAH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2908
Polymers23,8982
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1600 Å2
ΔGint-16 kcal/mol
Surface area11040 Å2
Unit cell
Length a, b, c (Å)69.850, 69.850, 62.713
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein E3 ubiquitin-protein ligase SIAH1 / RING-type E3 ubiquitin transferase SIAH1 / Seven in absentia homolog 1 / Siah-1 / Siah-1a


Mass: 11948.755 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIAH1, HUMSIAH / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IUQ4, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MES-imidazole buffer, PEG550MME-20K, 1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→46.66 Å / Num. obs: 12780 / % possible obs: 100 % / Redundancy: 25.1 % / Biso Wilson estimate: 46.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Net I/σ(I): 17
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 27.3 % / Rmerge(I) obs: 2.909 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 804 / CC1/2: 0.669 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.66 Å / SU ML: 0.3412 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.5876
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2368 627 4.93 %
Rwork0.2022 12101 -
obs0.2038 12728 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.64 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms732 0 3 72 807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075749
X-RAY DIFFRACTIONf_angle_d1.04131020
X-RAY DIFFRACTIONf_chiral_restr0.0602116
X-RAY DIFFRACTIONf_plane_restr0.0097136
X-RAY DIFFRACTIONf_dihedral_angle_d6.2263103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.090.37221670.38252936X-RAY DIFFRACTION99.77
2.09-2.390.27371320.24222995X-RAY DIFFRACTION99.97
2.39-3.020.27711770.23452989X-RAY DIFFRACTION100
3.02-46.660.20151510.17373181X-RAY DIFFRACTION99.88
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)
16.41909794887-0.716201204909-6.56873261994.4288828356-0.7404352020289.81844959960.00665127065920.876040687638-0.9637463239980.03510310795510.1835437487761.023481032440.33974898019-1.48227726328-0.1088417407090.4460595276170.00639026827938-0.05421584436330.487974395251-0.001721494890320.6545960530686.4919675977910.3571437011-6.04143026628
24.122259913152.77979548541-0.7812088874567.313157148423.427769614986.09702503561-0.3110399866630.915150643756-0.0665933181869-1.60971400190.3479327487650.805547601332-0.3576854338540.0651446457462-0.0004336524459250.783697403146-0.024106635085-0.08384915518660.5433134219210.03500160301710.48384454402614.535669817515.2680356536-14.8781889863
34.158652076330.3330978543171.232918869477.19514690334-0.5397937184673.7555865181-0.1784744974420.434670065812-0.257311065322-0.5561838656750.02049173932290.00554069431097-0.0871025077362-0.00868189718350.1552641116820.4759206696240.01064887853870.05321267046380.40421534731-0.01335558676220.42685924317520.591138973520.0707348707-6.66778737992
47.130954492382.964168922691.484514294893.020896489863.39195520298.29807051492-0.531792364891.462819466880.18001131333-1.092699895110.433846796131-0.60253582289-0.1354991864040.9001219390870.02216234667450.614263861632-0.05480021086360.1053767786640.5884147361840.03394161543360.36885093357722.461766990324.6634967355-14.3774703278
55.990944521781.570723099631.603660665846.00489136857-0.7991612392244.419699051690.289461605307-0.0847843980388-0.541624098425-0.451615611612-0.17131038026-0.3559072903330.2155193910770.0841821569987-0.09900345371130.4043515607690.06222221871460.01551921866370.39372543052-0.03394919387120.3680916125620.679803295213.4912917484-2.1474567993
63.4354295399-0.0361863370497-0.1170207905384.807722877521.551834774225.91312574317-0.1608473077410.3103186164780.320800486887-0.595892726273-0.0523031440099-0.336459632486-0.4478052766580.1338618263590.220461600240.481208454804-0.0164377789567-0.05944296584060.3218279387530.01893743208190.50813916501314.08977200972.06743585686-16.4302809867
75.91661523844-1.838139296384.087011318029.365689392692.133347700828.77631500196-0.01461993009151.109868043430.150331056135-1.524943650170.303077573548-0.330198565602-0.813495729919-0.268210632462-0.36467559140.908336879473-0.0113965807949-0.002465483071160.5202444077920.04162381882460.57055896796613.5189347774-0.359179767176-26.6710112124
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 29 through 39 )29 - 391 - 11
22chain 'A' and (resid 40 through 49 )40 - 4912 - 21
33chain 'A' and (resid 50 through 62 )50 - 6222 - 34
44chain 'A' and (resid 63 through 78 )63 - 7835 - 50
55chain 'A' and (resid 79 through 93 )79 - 9351 - 65
66chain 'A' and (resid 94 through 120 )94 - 12066 - 92
77chain 'A' and (resid 121 through 125 )121 - 12593 - 97

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