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- PDB-4ca1: Crystal structure of Siah1 at 1.58 A resolution. -

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Basic information

Entry
Database: PDB / ID: 4ca1
TitleCrystal structure of Siah1 at 1.58 A resolution.
ComponentsE3 UBIQUITIN-PROTEIN LIGASE SIAH1
KeywordsLIGASE
Function / homology
Function and homology information


Netrin-1 signaling / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / canonical Wnt signaling pathway / anatomical structure morphogenesis / 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 / canonical Wnt signaling pathway / anatomical structure morphogenesis / 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 / 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
: / 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 ...: / 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
E3 ubiquitin-protein ligase SIAH1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsRimsa, V. / Eadsforth, T.C. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Two High-Resolution Structures of the Human E3 Ubiquitin Ligase Siah1.
Authors: Rimsa, V. / Eadsforth, T.C. / Hunter, W.N.
History
DepositionOct 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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_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: E3 UBIQUITIN-PROTEIN LIGASE SIAH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,79626
Polymers43,8422
Non-polymers1,95324
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-88.7 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.060, 104.120, 133.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2036-

HOH

21A-2042-

HOH

31A-2060-

HOH

41A-2124-

HOH

51A-2187-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE SIAH1 / SEVEN IN ABSENTIA HOMOLOG 1 / SIAH-1 / SIAH-1A


Mass: 21921.082 Da / Num. of mol.: 2
Fragment: TWO ZINC FINGERS AND SUBSTRATE BINDING DOMAIN, RESIDUES 91-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: Q8IUQ4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 5 types, 355 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.99 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growDetails: CRYSTALS GREW FROM EQUAL VOLUMES OF PROTEIN SOLUTION (15 MG ML-1 IN 15 MM TRIS-HCL PH7.5, 30 MM NACL AND 10 MM DTT) AND RESERVOIR SOLUTION (100 MM HEPES PH7.0, 1.45 LI2SO4).

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.58→52.06 Å / Num. obs: 72738 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.1
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C9Z

4c9z


Resolution: 1.58→52.11 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.677 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 199-201 IN CHAIN A AND RESIDUES 198-199 IN CHAIN B ARE DISORDERED AND WERE NOT MODELED IN.
RfactorNum. reflection% reflectionSelection details
Rfree0.18907 3666 5 %RANDOM
Rwork0.14075 ---
obs0.14315 69071 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.821 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.73 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.58→52.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 0 104 331 3410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193472
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3351.964741
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.06524.204157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89515586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8731518
X-RAY DIFFRACTIONr_chiral_restr0.1710.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212660
X-RAY DIFFRACTIONr_gen_planes_other
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr10.04333471
X-RAY DIFFRACTIONr_sphericity_free30.6335119
X-RAY DIFFRACTIONr_sphericity_bonded22.13153597
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 250 -
Rwork0.209 5081 -
obs--99.93 %
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)
11.98122.3438-1.1984.6831-3.73233.5348-0.0571-0.29790.2548-0.55140.23590.32050.6225-0.5178-0.17880.1637-0.10440.01260.2806-0.01440.073312.266-4.91314.13
20.54430.47990.24351.05910.2070.991-0.027-0.01230.0594-0.122-0.07280.0869-0.0844-0.02660.09980.0430.0035-0.00980.0582-0.01710.017131.67117.6711.512
31.22022.6493-0.72535.8746-1.56930.5491-0.07740.01480.0906-0.31940.00880.30040.0030.05450.06860.1782-0.0012-0.16440.1157-0.03440.332756.89555.88233.101
40.71740.52010.62520.80230.45050.9708-0.0975-0.08810.1069-0.0347-0.00070.0228-0.0166-0.08760.09830.02930.0123-0.01680.0934-0.04250.029442.50330.58233.82
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A91 - 134
2X-RAY DIFFRACTION2A135 - 282
3X-RAY DIFFRACTION3B91 - 140
4X-RAY DIFFRACTION4B141 - 282

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