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- PDB-5o6t: BIRC4 RING in complex with dimeric ubiquitin variant -

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Basic information

Entry
Database: PDB / ID: 5o6t
TitleBIRC4 RING in complex with dimeric ubiquitin variant
Components
  • E3 ubiquitin-protein ligase XIAP
  • Polyubiquitin-B
KeywordsLIGASE / E3 ring ligase / ubiquitin variant
Function / homology
Function and homology information


endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway ...endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / hypothalamus gonadotrophin-releasing hormone neuron development / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / female meiosis I / positive regulation of protein monoubiquitination / TNFR1-induced proapoptotic signaling / mitochondrion transport along microtubule / fat pad development / regulation of innate immune response / RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K63-linked ubiquitination / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of type I interferon production / negative regulation of tumor necrosis factor-mediated signaling pathway / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling
Similarity search - Function
XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) ...XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Death-like domain superfamily / Ring finger / Ubiquitin conserved site / Ubiquitin domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsGabrielsen, M. / Buetow, L. / Huang, D.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC596/A23278 United Kingdom
European Research Council647849 United Kingdom
CitationJournal: Mol. Cell / Year: 2017
Title: A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants.
Authors: Gabrielsen, M. / Buetow, L. / Nakasone, M.A. / Ahmed, S.F. / Sibbet, G.J. / Smith, B.O. / Zhang, W. / Sidhu, S.S. / Huang, D.T.
History
DepositionJun 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase XIAP
B: E3 ubiquitin-protein ligase XIAP
C: Polyubiquitin-B
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,60610
Polymers33,2214
Non-polymers3866
Water3,927218
1
A: E3 ubiquitin-protein ligase XIAP
B: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5248
Polymers15,1382
Non-polymers3866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-11 kcal/mol
Surface area7610 Å2
MethodPISA
2
C: Polyubiquitin-B
D: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)18,0832
Polymers18,0832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-25 kcal/mol
Surface area8590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.715, 69.972, 109.747
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 E3 ubiquitin-protein ligase XIAP / Baculoviral IAP repeat-containing protein 4 / IAP-like protein / hILP / Inhibitor of apoptosis ...Baculoviral IAP repeat-containing protein 4 / IAP-like protein / hILP / Inhibitor of apoptosis protein 3 / hIAP3 / RING-type E3 ubiquitin transferase XIAP / X-linked inhibitor of apoptosis protein / X-linked IAP


Mass: 7569.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XIAP, API3, BIRC4, IAP3 / Plasmid: pGEX4T.1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P98170, RING-type E3 ubiquitin transferase
#2: Protein Polyubiquitin-B


Mass: 9041.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A variant of ubiquitin identified from a phage-display library
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG47
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.06 Å3/Da / Density % sol: 40.41 % / Description: Rectangular cuboids
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 0.1 M NaHEPES pH 7.5, 1.4 M tri-Na citrate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.57→69.97 Å / Num. obs: 39227 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 20.57 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.042 / Net I/σ(I): 14.9
Reflection shellResolution: 1.57→1.577 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2 / Num. unique obs: 2560 / CC1/2: 0.663 / Rpim(I) all: 0.513 / % possible all: 96.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EB5, 1UBQ

3eb5

1ubq


Resolution: 1.57→43.18 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.076 / SU Rfree Blow DPI: 0.076 / SU Rfree Cruickshank DPI: 0.073
RfactorNum. reflection% reflectionSelection details
Rfree0.183 1950 4.98 %RANDOM
Rwork0.156 ---
obs0.158 39161 99.6 %-
Displacement parametersBiso mean: 29.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.2856 Å20 Å20 Å2
2--1.8939 Å20 Å2
3----3.1795 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: 1 / Resolution: 1.57→43.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 12 218 2432
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014741HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.158653HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1104SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes670HARMONIC5
X-RAY DIFFRACTIONt_it4741HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.34
X-RAY DIFFRACTIONt_other_torsion14.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion330SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5386SEMIHARMONIC4
LS refinement shellResolution: 1.57→1.61 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 128 4.68 %
Rwork0.2 2606 -
all0.202 2734 -
obs--95.35 %
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)
10.90170.0880.05631.10520.57690.9425-0.04250.0950.0744-0.11810.0491-0.0792-0.14260.0768-0.0067-0.0372-0.01360.0049-0.00070.0068-0.002843.368518.1291131.483
20.69470.12830.27341.031-0.67291.1972-0.03730.0631-0.0657-0.13740.03320.04690.1014-0.06660.0041-0.0352-0.0022-0.0086-0.0007-0.0015-0.00728.391818.7913131.263
31.4276-2.37420.00476.06680.03320.6984-0.0648-0.1336-0.03560.28440.19460.0706-0.0471-0.0317-0.1297-0.03110.01470.0312-0.04070.009-0.038333.946329.0331153.213
40.6619-0.8814-0.01374.1116-0.28260.5930.0152-0.01750.0330.27370.0330.00920.0726-0.0084-0.0482-0.01610.0089-0.027-0.0322-0.0025-0.040436.29997.7328153.331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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