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- PDB-4x3g: Crystal structure of SIAH1 SINA domain in complex with a USP19 peptide -

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Basic information

Entry
Database: PDB / ID: 4x3g
TitleCrystal structure of SIAH1 SINA domain in complex with a USP19 peptide
Components
  • E3 ubiquitin-protein ligase SIAH1
  • Ubiquitin carboxyl-terminal hydrolase 19
KeywordsLIGASE / UBIQUITIN-PROTEIN LIGASE / HYDROLASE / UBIQUITIN SPECIFIC PROTEASE / PROTEIN-PEPTIDE COMPLEX / SGC
Function / homology
Function and homology information


regulation of ERAD pathway / positive regulation of cell cycle process / negative regulation of skeletal muscle tissue development / Netrin-1 signaling / regulation of cellular response to hypoxia / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / protein deubiquitination / canonical Wnt signaling pathway / anatomical structure morphogenesis ...regulation of ERAD pathway / positive regulation of cell cycle process / negative regulation of skeletal muscle tissue development / Netrin-1 signaling / regulation of cellular response to hypoxia / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / protein deubiquitination / canonical Wnt signaling pathway / anatomical structure morphogenesis / : / positive regulation of intrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / axon guidance / Hsp90 protein binding / protein catabolic process / RING-type E3 ubiquitin transferase / regulation of protein stability / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / amyloid fibril formation / protein stabilization / protein ubiquitination / Ub-specific processing proteases / cell cycle / positive regulation of apoptotic process / Amyloid fiber formation / apoptotic process / endoplasmic reticulum membrane / zinc ion binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Linker region of USP19 deubiquitinase / : / Sina, zinc finger / E3 ubiquitin-protein ligase sina/sinah, RING finger / 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. / CS domain ...Linker region of USP19 deubiquitinase / : / Sina, zinc finger / E3 ubiquitin-protein ligase sina/sinah, RING finger / 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. / 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 / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / HSP20-like chaperone / TRAF-like / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Papain-like cysteine peptidase superfamily / 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
Ubiquitin carboxyl-terminal hydrolase 19 / E3 ubiquitin-protein ligase SIAH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsWalker, J.R. / Dong, A. / Zhang, Q. / Huang, X. / Li, Y. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal structure of SIAH1 SINA domain in complex with a USP19 peptide
Authors: Walker, J.R. / Dong, A. / Zhang, Q. / Huang, X. / Li, Y. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Tong, Y. / Structural Genomics Consortium (SGC)
History
DepositionNov 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Derived calculations / Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: E3 ubiquitin-protein ligase SIAH1
C: Ubiquitin carboxyl-terminal hydrolase 19
D: Ubiquitin carboxyl-terminal hydrolase 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5878
Polymers46,3254
Non-polymers2624
Water1,00956
1
A: E3 ubiquitin-protein ligase SIAH1
C: Ubiquitin carboxyl-terminal hydrolase 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2934
Polymers23,1632
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-13 kcal/mol
Surface area11050 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase SIAH1
D: Ubiquitin carboxyl-terminal hydrolase 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2934
Polymers23,1632
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-18 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.343, 88.092, 59.590
Angle α, β, γ (deg.)90.000, 103.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 21651.742 Da / Num. of mol.: 2 / Fragment: SINA DOMAIN, RESIDUES 91-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIAH1, HUMSIAH / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): V2R-pRARE2
References: UniProt: Q8IUQ4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Ubiquitin carboxyl-terminal hydrolase 19 / Deubiquitinating enzyme 19 / Ubiquitin thioesterase 19 / Ubiquitin-specific-processing protease 19 ...Deubiquitinating enzyme 19 / Ubiquitin thioesterase 19 / Ubiquitin-specific-processing protease 19 / Zinc finger MYND domain-containing protein 9


Mass: 1510.840 Da / Num. of mol.: 2 / Fragment: SIAH1 BINDING MOTIF (SBM), RESIDUES 461-474 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O94966, ubiquitinyl hydrolase 1
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: SIAH1 AT 17.6 MG/ML WAS MIXED WITH A TWO-FOLD EXCESS OF USP19 PEPTIDE ON ICE FOR 30 MIN. BEFORE SETTING UP FOR CRYSTALLIZATION. CRYSTALS WERE GROWN AT 298K USING THE SITTING DROP METHOD BY ...Details: SIAH1 AT 17.6 MG/ML WAS MIXED WITH A TWO-FOLD EXCESS OF USP19 PEPTIDE ON ICE FOR 30 MIN. BEFORE SETTING UP FOR CRYSTALLIZATION. CRYSTALS WERE GROWN AT 298K USING THE SITTING DROP METHOD BY MIXING 0.5 UL PROTEIN:PEPTIDE MIX WITH 0.5 UL WELL SOLUTION CONSISTING OF 20% PEG6000, 0.1 M BICINE PH 9.0. THE CRYSTALS WERE CRYOPROTECTED BY FIRST IMMERSION IN WELL SOLUTION MIXED WITH 15% (FINAL) ETHYLENE GLYCOL, THEN IMMERSION IN N-PARATONE.
PH range: 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 15818 / % possible obs: 90.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 67.92 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1.007 / Net I/av σ(I): 9.631 / Net I/σ(I): 6.2 / Num. measured all: 36140
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.33-2.371.50.445130.45658.9
2.37-2.411.70.4096590.4376.3
2.41-2.461.80.3527060.37582.1
2.46-2.5120.3347320.45284.2
2.51-2.562.10.3017700.49788.4
2.56-2.622.10.2697800.44491.8
2.62-2.692.20.2438230.52893.4
2.69-2.762.30.2398150.55295.1
2.76-2.842.40.28360.66296.4
2.84-2.942.40.1678530.71497.5
2.94-3.042.40.1478320.84698.5
3.04-3.162.50.1348510.97896.8
3.16-3.312.50.1258401.49597.6
3.31-3.482.50.0998341.67296.2
3.48-3.72.40.0948451.26695.8
3.7-3.982.50.0888431.37397.2
3.98-4.382.40.0788261.45395.6
4.38-5.022.50.0838441.40395
5.02-6.322.50.0878191.46694.5
6.32-502.40.0727971.20487.9

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Processing

Software
NameVersionClassification
HKL-3000data reduction
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I7B

4i7b


Resolution: 2.34→48.45 Å / Cor.coef. Fo:Fc: 0.9353 / Cor.coef. Fo:Fc free: 0.9303 / SU R Cruickshank DPI: 0.54 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.508 / SU Rfree Blow DPI: 0.265 / SU Rfree Cruickshank DPI: 0.271
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 780 4.94 %RANDOM
Rwork0.2218 ---
obs0.2233 15802 89.68 %-
Displacement parametersBiso max: 173.92 Å2 / Biso mean: 82.59 Å2 / Biso min: 31.82 Å2
Baniso -1Baniso -2Baniso -3
1-4.7768 Å20 Å2-1.8572 Å2
2---19.3544 Å20 Å2
3---14.5776 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: final / Resolution: 2.34→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 4 58 3141
Biso mean--92.57 69.86 -
Num. residues----399
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1068SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes464HARMONIC5
X-RAY DIFFRACTIONt_it3190HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion429SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3399SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3190HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4335HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion1.97
X-RAY DIFFRACTIONt_other_torsion18.94
LS refinement shellResolution: 2.34→2.5 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.27 99 4.56 %
Rwork0.2334 2074 -
all0.235 2173 -
obs--89.68 %
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)
12.53970.7306-0.11513.5326-0.92361.0883-0.08940.50330.1379-0.10220.3811-0.0983-0.0781-0.3051-0.2917-0.1890.08770.05540.20880.027-0.2221.11131.3498.9114
21.88541.09550.99533.7359-1.27972.9621-0.0252-0.1945-0.2247-0.38830.0574-0.43020.7702-0.6147-0.0322-0.1227-0.22420.06480.06580.0391-0.20694.6407-32.139620.7236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|91 - A|602 }A91 - 602
2X-RAY DIFFRACTION2{ B|93 - B|602 }B93 - 602

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