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- PDB-4i7b: Siah1 bound to synthetic peptide (ACE)KLRPV(ABA)MVRPTVR -

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Basic information

Entry
Database: PDB / ID: 4i7b
TitleSiah1 bound to synthetic peptide (ACE)KLRPV(ABA)MVRPTVR
Components
  • E3 ubiquitin-protein ligase SIAH1
  • Protein phyllopod
KeywordsLIGASE/LIGASE INHIBITOR / Sina / beta sandwich / zinc finger / ubiquitin ligase / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


R1/R6 cell fate commitment / sensory organ boundary specification / enteroendocrine cell differentiation / R7 cell fate commitment / sensory organ precursor cell fate determination / sevenless signaling pathway / Netrin-1 signaling / sensory organ development / beta-catenin destruction complex / ubiquitin conjugating enzyme binding ...R1/R6 cell fate commitment / sensory organ boundary specification / enteroendocrine cell differentiation / R7 cell fate commitment / sensory organ precursor cell fate determination / sevenless signaling pathway / Netrin-1 signaling / sensory organ development / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / negative regulation of Notch signaling pathway / ubiquitin-like ligase-substrate adaptor activity / anatomical structure morphogenesis / canonical Wnt signaling pathway / proteasomal protein catabolic process / ubiquitin ligase complex / positive regulation of intrinsic apoptotic signaling pathway / Notch signaling pathway / visual perception / axon guidance / epidermal growth factor receptor signaling pathway / RING-type E3 ubiquitin transferase / negative regulation of canonical Wnt signaling pathway / protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / amyloid fibril formation / protein ubiquitination / positive regulation of apoptotic process / Amyloid fiber formation / apoptotic process / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Zinc finger, AD-type / Zinc-finger associated domain (zf-AD) / : / 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. ...Zinc finger, AD-type / Zinc-finger associated domain (zf-AD) / : / 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. / 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
modified protein phyllopod peptide BI-117E1 / Protein phyllopod / E3 ubiquitin-protein ligase SIAH1
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSantelli, E. / Stebbins, J.L. / Feng, Y. / De, S.K. / Purves, A. / Motamedchaboki, K. / Wu, B. / Ronai, Z.A. / Liddington, R.C. / Pellecchia, M.
CitationJournal: Chem.Biol. / Year: 2013
Title: Structure-based design of covalent siah inhibitors.
Authors: Stebbins, J.L. / Santelli, E. / Feng, Y. / De, S.K. / Purves, A. / Motamedchaboki, K. / Wu, B. / Ronai, Z.A. / Liddington, R.C. / Pellecchia, M.
History
DepositionNov 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Sep 20, 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_conn_angle / struct_conn / struct_ref_seq_dif / 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.ptnr2_auth_asym_id / _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.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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SIAH1
B: Protein phyllopod
C: E3 ubiquitin-protein ligase SIAH1
D: Protein phyllopod
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3488
Polymers47,0864
Non-polymers2624
Water25214
1
A: E3 ubiquitin-protein ligase SIAH1
B: Protein phyllopod
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6744
Polymers23,5432
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-8 kcal/mol
Surface area11320 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase SIAH1
D: Protein phyllopod
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6744
Polymers23,5432
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-11 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.745, 87.913, 59.884
Angle α, β, γ (deg.)90.00, 100.59, 90.00
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: 21976.094 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 90-282)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIAH1, HUMSIAH / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8IUQ4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Protein phyllopod


Type: Oligopeptide / Class: Inhibitor / Mass: 1566.998 Da / Num. of mol.: 2 / Fragment: Siah-binding peptide (UNP residues 113-125) / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
References: UniProt: Q27934, modified protein phyllopod peptide BI-117E1
#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


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG6000, 5% MPD, 100 mM HEPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 28, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 8152 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 25.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A25 CHAIN A

2a25


Resolution: 3→35.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.907 / SU B: 56.542 / SU ML: 0.457 / Isotropic thermal model: ISOTROPIC WITH TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.506 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26051 375 4.6 %RANDOM
Rwork0.18628 ---
obs0.18951 8126 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.818 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å2-2.11 Å2
2--1.99 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 3→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 4 14 3141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023195
X-RAY DIFFRACTIONr_bond_other_d0.0010.022140
X-RAY DIFFRACTIONr_angle_refined_deg0.9071.9424327
X-RAY DIFFRACTIONr_angle_other_deg0.89135217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0195392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5523.973146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57515535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2431518
X-RAY DIFFRACTIONr_chiral_restr0.0560.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02650
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 26 -
Rwork0.288 528 -
obs--95.85 %
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)
126.21338.87968.18547.6307-2.440713.4758-0.5399-0.8224-1.5320.56110.2823-0.90570.26830.32140.25760.91040.12620.12510.55750.02380.819937.55821.4628.902
220.11599.295911.95197.25968.589910.3948-0.148-0.3519-0.2635-0.85370.0774-0.0657-1.1474-0.24120.07061.4546-0.0431-0.05160.7599-0.05321.135412.561-49.40213.916
315.73753.28253.589715.05330.187311.6014-1.14020.77010.2207-0.33971.22780.22-0.3295-0.793-0.08760.55530.1160.17780.2990.19470.288716.78912.1780.629
44.99360.97420.29239.1466-1.32784.6248-0.1020.2899-0.0587-0.35710.33880.0724-0.2065-0.1541-0.23680.2090.13790.10480.2240.04440.085616.217-3.96310.567
526.4133-2.5189-0.0247.56213.63232.09920.6132-0.497-2.02150.5758-0.1124-1.25160.97730.0979-0.50091.67320.18740.11020.56940.25110.993332.009-40.59624.483
65.95930.49361.87319.0151-3.37288.5376-0.03210.08080.07110.3171-0.2767-0.69550.26350.02160.30880.14740.06530.09530.13060.12080.186227.933-21.85322.746
719.21532.0992-9.53398.4221.77015.707-0.48921.5730.5928-0.21270.420.72250.2735-0.80080.06920.1298-0.0642-0.04920.49250.02220.10186.0124-3.92387.0284
85.24864.6831.29974.22731.335715.73630.7766-0.1527-0.23420.7066-0.1349-0.40760.72780.5944-0.64170.14680.0049-0.15180.10450.10070.8237.0845-20.256828.7835
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A92 - 125
2X-RAY DIFFRACTION1A602
3X-RAY DIFFRACTION2C94 - 125
4X-RAY DIFFRACTION2C602
5X-RAY DIFFRACTION3A126 - 154
6X-RAY DIFFRACTION3A601
7X-RAY DIFFRACTION4A155 - 282
8X-RAY DIFFRACTION5C126 - 154
9X-RAY DIFFRACTION5C601
10X-RAY DIFFRACTION6C155 - 282
11X-RAY DIFFRACTION7B114 - 124
12X-RAY DIFFRACTION8D114 - 124

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