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- PDB-4i7d: Siah1 bound to synthetic peptide (ACE)KLRPVAMVRP(PRK)VR -

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Basic information

Entry
Database: PDB / ID: 4i7d
TitleSiah1 bound to synthetic peptide (ACE)KLRPVAMVRP(PRK)VR
Components
  • E3 ubiquitin-protein ligase SIAH1
  • Protein phyllopod
KeywordsLIGASE/LIGASE INHIBITOR / Sina / beta sandwich / zinc finger / ubiquitin ligase / covalent inhibitor / 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 / canonical Wnt signaling pathway / anatomical structure morphogenesis / ubiquitin ligase complex / positive regulation of intrinsic apoptotic signaling pathway / Notch signaling pathway / visual perception / axon guidance / proteasomal protein catabolic process / protein catabolic process / negative regulation of canonical Wnt signaling pathway / RING-type E3 ubiquitin transferase / epidermal growth factor receptor signaling pathway / 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 / cell cycle / positive regulation of apoptotic process / Amyloid fiber formation / apoptotic process / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
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-117F7 / 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: 2.4 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 / pdbx_struct_special_symmetry / 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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: 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)47,6049
Polymers47,2244
Non-polymers3805
Water2,594144
1
A: E3 ubiquitin-protein ligase SIAH1
B: Protein phyllopod
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8615
Polymers23,6122
Non-polymers2493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-8 kcal/mol
Surface area11180 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase SIAH1
D: Protein phyllopod
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7434
Polymers23,6122
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-16 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.977, 160.977, 160.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

21A-730-

HOH

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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: HUMSIAH, SIAH1 / 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: 1636.103 Da / Num. of mol.: 2 / Fragment: Siah-binding peptide (UNP residues 113-125) / Mutation: T123(PRK) / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
References: UniProt: Q27934, modified protein phyllopod peptide BI-117F7
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.68 Å3/Da / Density % sol: 66.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 65% MPD, 100 mM bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2012 / Details: mirrors
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: 2.4→50 Å / Num. obs: 27179 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 22.2
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1344 / % possible all: 99.8

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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: 2.4→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 10.165 / SU ML: 0.117 / Isotropic thermal model: ISOTROPIC WITH TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20167 1390 5.1 %RANDOM
Rwork0.1714 ---
obs0.17296 27176 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.586 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 12 144 3336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193267
X-RAY DIFFRACTIONr_bond_other_d0.0010.022224
X-RAY DIFFRACTIONr_angle_refined_deg1.031.9554419
X-RAY DIFFRACTIONr_angle_other_deg0.7835418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2245398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49823.851148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04615551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9411520
X-RAY DIFFRACTIONr_chiral_restr0.0650.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02667
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 98 -
Rwork0.257 1770 -
obs--99.89 %
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)
12.03390.3427-0.09394.0761-0.68262.30730.11280.23510.0163-0.0362-0.0901-0.05610.2670.0665-0.02270.0906-0.01020.00060.09160.02940.0215-20.64520.90165.767
210.11326.34545.928215.2518.279514.30010.12780.4661-0.1154-0.3270.2126-0.4180.06450.5346-0.34040.1860.13250.05370.20280.1120.2232-11.59314.70763.775
32.3213-0.1985-0.66643.0671-0.85212.7247-0.0272-0.00090.0111-0.18450.10160.1939-0.1107-0.0204-0.07440.0582-0.0531-0.03030.10050.07260.0711-25.10442.86158.528
46.15152.79441.62883.51970.797415.59490.1204-0.35070.0901-0.02150.03150.4959-0.2415-0.6431-0.15190.17130.09180.00140.1220.09060.2959-33.76350.0261.685
513.3026-0.7974-5.66619.78042.00719.0476-0.14280.1523-1.70710.097-0.37420.59450.65580.0460.5170.4001-0.0219-0.04870.04530.00150.3744-25.4062.65471.224
65.88253.2008-0.4037.4790.07385.83930.3770.54520.57770.0023-0.18140.343-0.6449-0.0944-0.19570.20480.02280.0110.16250.14480.1806-23.84257.57845.879
711.7993-2.6691-3.7344.7581.67326.66250.37350.63740.9769-0.8026-0.0858-0.4723-0.8750.2005-0.28770.353-0.12160.06580.23750.0650.1407-47.7489.25879.468
825.2191-10.9747-11.90985.40937.131312.80460.06890.7801-1.15740.2111-0.39730.40950.5724-1.0730.32840.3788-0.0820.10890.3710.04160.3906-2.52249.82835.899
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A156 - 282
2X-RAY DIFFRACTION2B112 - 125
3X-RAY DIFFRACTION3C156 - 282
4X-RAY DIFFRACTION4D112 - 125
5X-RAY DIFFRACTION5A125 - 155
6X-RAY DIFFRACTION5A601
7X-RAY DIFFRACTION6C125 - 155
8X-RAY DIFFRACTION6C601
9X-RAY DIFFRACTION7A91 - 124
10X-RAY DIFFRACTION7A602
11X-RAY DIFFRACTION8C92 - 124
12X-RAY DIFFRACTION8C602

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