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- PDB-3ceg: Crystal structure of the UBC domain of baculoviral IAP repeat-con... -

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Basic information

Entry
Database: PDB / ID: 3ceg
TitleCrystal structure of the UBC domain of baculoviral IAP repeat-containing protein 6
ComponentsBaculoviral IAP repeat-containing protein 6
KeywordsLIGASE / APOPTOSIS / PROTEASE INHIBITOR / THIOL PROTEASE INHIBITOR / UBL CONJUGATION PATHWAY / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


labyrinthine layer development / (E3-independent) E2 ubiquitin-conjugating enzyme / ALK mutants bind TKIs / Flemming body / ubiquitin conjugating enzyme activity / microtubule organizing center / cysteine-type endopeptidase inhibitor activity / regulation of cytokinesis / negative regulation of extrinsic apoptotic signaling pathway / trans-Golgi network ...labyrinthine layer development / (E3-independent) E2 ubiquitin-conjugating enzyme / ALK mutants bind TKIs / Flemming body / ubiquitin conjugating enzyme activity / microtubule organizing center / cysteine-type endopeptidase inhibitor activity / regulation of cytokinesis / negative regulation of extrinsic apoptotic signaling pathway / trans-Golgi network / spindle pole / ubiquitin-protein transferase activity / Signaling by ALK fusions and activated point mutants / regulation of cell population proliferation / midbody / cell population proliferation / protein phosphorylation / endosome / protein ubiquitination / cell division / positive regulation of cell population proliferation / apoptotic process / centrosome / negative regulation of apoptotic process / metal ion binding / nucleus / membrane / cytosol
Similarity search - Function
Baculoviral IAP repeat-containing protein 6 / Baculoviral IAP repeat-containing protein 6 / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme ...Baculoviral IAP repeat-containing protein 6 / Baculoviral IAP repeat-containing protein 6 / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.008 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Mol Cell Proteomics / Year: 2012
Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.
Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S.
History
DepositionFeb 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 6
B: Baculoviral IAP repeat-containing protein 6


Theoretical massNumber of molelcules
Total (without water)74,1112
Polymers74,1112
Non-polymers00
Water5,675315
1
A: Baculoviral IAP repeat-containing protein 6


Theoretical massNumber of molelcules
Total (without water)37,0561
Polymers37,0561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Baculoviral IAP repeat-containing protein 6


Theoretical massNumber of molelcules
Total (without water)37,0561
Polymers37,0561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.199, 97.815, 129.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Baculoviral IAP repeat-containing protein 6 / Ubiquitin-conjugating BIR domain enzyme apollon


Mass: 37055.660 Da / Num. of mol.: 2 / Fragment: UBC domain: Residues 4470-4792
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC6, KIAA1289 / Plasmid: pET28-MHL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NR09, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 298 K / pH: 10
Details: 11 % PEG 8000, 0.1 M Gycine buffer pH 10.0, 0.001 M DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97942
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2008 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 62447 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.114 / Net I/σ(I): 18.623
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.585 / Rsym value: 0.637 / % possible all: 70.1

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.008→44.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.118 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25248 3127 5 %RANDOM
Rwork0.21089 ---
obs0.21295 59243 92.92 %-
all-62371 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.563 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2---0.35 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.008→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 0 315 4894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224755
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.9526462
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1465591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.89624.484223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11615783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7481525
X-RAY DIFFRACTIONr_chiral_restr0.0860.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023667
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.22273
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23309
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2330
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8233049
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5244785
X-RAY DIFFRACTIONr_scbond_it3.47251960
X-RAY DIFFRACTIONr_scangle_it4.71671677
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.008→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 170 -
Rwork0.353 3111 -
obs--67.1 %

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