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- PDB-3eb6: Structure of the cIAP2 RING domain bound to UbcH5b -

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Basic information

Entry
Database: PDB / ID: 3eb6
TitleStructure of the cIAP2 RING domain bound to UbcH5b
Components
  • Baculoviral IAP repeat-containing protein 3
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsAPOPTOSIS / LIGASE / RING domain / E2 / Metal-binding / Zinc-finger / Ubl conjugation pathway
Function / homology
Function and homology information


regulation of cysteine-type endopeptidase activity / regulation of RIG-I signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / (E3-independent) E2 ubiquitin-conjugating enzyme / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / E2 ubiquitin-conjugating enzyme / RIPK1-mediated regulated necrosis ...regulation of cysteine-type endopeptidase activity / regulation of RIG-I signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / (E3-independent) E2 ubiquitin-conjugating enzyme / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / E2 ubiquitin-conjugating enzyme / RIPK1-mediated regulated necrosis / regulation of innate immune response / regulation of toll-like receptor signaling pathway / ubiquitin conjugating enzyme activity / non-canonical NF-kappaB signal transduction / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / RING-type E3 ubiquitin transferase / Regulation of necroptotic cell death / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of inflammatory response / transferase activity / spermatogenesis / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / regulation of cell cycle / Ub-specific processing proteases / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / protein-containing complex / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / BIRC2/3-like, UBA domain / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme ...: / BIRC2/3-like, UBA domain / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Death-like domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D2 / Baculoviral IAP repeat-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / Resolution: 3.4 Å
AuthorsMace, P.D. / Linke, K. / Schumacher, F.-R. / Smith, C.A. / Day, C.L.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structures of the cIAP2 RING Domain Reveal Conformational Changes Associated with Ubiquitin-conjugating Enzyme (E2) Recruitment.
Authors: Mace, P.D. / Linke, K. / Feltham, R. / Schumacher, F.R. / Smith, C.A. / Vaux, D.L. / Silke, J. / Day, C.L.
History
DepositionAug 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Baculoviral IAP repeat-containing protein 3
B: Ubiquitin-conjugating enzyme E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2694
Polymers25,1382
Non-polymers1312
Water0
1
A: Baculoviral IAP repeat-containing protein 3
B: Ubiquitin-conjugating enzyme E2 D2
hetero molecules

A: Baculoviral IAP repeat-containing protein 3
B: Ubiquitin-conjugating enzyme E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5388
Polymers50,2764
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/21
Unit cell
Length a, b, c (Å)137.226, 137.226, 111.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Baculoviral IAP repeat-containing protein 3 / Inhibitor of apoptosis protein 1 / HIAP-1 / HIAP1 / C-IAP2 / TNFR2-TRAF-signaling complex protein 1 ...Inhibitor of apoptosis protein 1 / HIAP-1 / HIAP1 / C-IAP2 / TNFR2-TRAF-signaling complex protein 1 / IAP homolog C / Apoptosis inhibitor 2 / API2 / RING finger protein 49


Mass: 8238.674 Da / Num. of mol.: 1 / Fragment: RING domain (RESIDUES 536 TO 604)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC3, API2, IAP1, MIHC, RNF49 / Plasmid: pGex6p3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13489
#2: Protein Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin-protein ligase D2 / Ubiquitin carrier protein D2 / Xubc4


Mass: 16899.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: ube2d2, ubc4 / Plasmid: pGex6p3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62840, ubiquitin-protein ligase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 6.05 Å3/Da / Density % sol: 79.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 3.3 M NaCl, 0.1 M HEPES, pH 7.3, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.401→58.521 Å / Num. all: 8950 / Num. obs: 8512 / % possible obs: 99.1 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 7.331
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.4-3.5870.8885312631.03299.6
3.58-3.871.5840412040.52199.4
3.8-4.0672.7785811240.28399.4
4.06-4.3975.3743510650.14299.7
4.39-4.816.97.868239870.09799.8
4.81-5.386.910.362409000.07199.5
5.38-6.216.811.854117930.0699.2
6.21-7.66.816.146576800.04498.6
7.6-10.756.818.535605260.02997.3
10.75-58.526.217.619123090.03293.1

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Processing

Software
NameVersionClassificationNB
SCALA3.2.21data scaling
REFMAC5.3.0037refinement
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementResolution: 3.4→58.52 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.884 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 48.459 / SU ML: 0.362 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.959 / ESU R Free: 0.494 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32 433 4.8 %RANDOM
Rwork0.281 ---
obs0.283 8512 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 123.11 Å2 / Biso mean: 102.875 Å2 / Biso min: 73.93 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å21.67 Å20 Å2
2--3.33 Å20 Å2
3----5 Å2
Refinement stepCycle: LAST / Resolution: 3.4→58.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1691 0 2 0 1693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221740
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9832361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8255211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54823.15173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.89115301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0321514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021310
X-RAY DIFFRACTIONr_nbd_refined0.240.2878
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21218
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.245
X-RAY DIFFRACTIONr_metal_ion_refined0.1960.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.224
X-RAY DIFFRACTIONr_mcbond_it0.251.51097
X-RAY DIFFRACTIONr_mcangle_it0.46821761
X-RAY DIFFRACTIONr_scbond_it0.7063717
X-RAY DIFFRACTIONr_scangle_it1.1294.5600
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.52 31 -
Rwork0.428 609 -
all-640 -
obs--99.84 %
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)
118.063-0.8516-3.859617.75985.723911.71750.350.8026-1.3207-0.1691-0.93361.35141.4768-1.27080.5837-0.40130.04560.2371-0.20210.245-0.091349.941-43.269-23.015
27.51311.0291-4.0154.5737-1.244913.55430.8172-0.58090.94271.039-0.4740.2024-0.42520.3926-0.3433-0.4161-0.19710.3855-0.56680.08030.045536.812-36.9740.545
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA541 - 60411 - 74
2X-RAY DIFFRACTION2BB0 - 1472 - 149

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