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- PDB-8w59: Crystal structure of the RING domain of human XIAP treated with a... -

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Basic information

Entry
Database: PDB / ID: 8w59
TitleCrystal structure of the RING domain of human XIAP treated with arsenic trioxide
ComponentsE3 ubiquitin-protein ligase XIAP
KeywordsTRANSFERASE / RING domain / XIAP / As / LIGASE
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 / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TNFR1-induced proapoptotic signaling / regulation of innate immune response / RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity / 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 PTEN localization / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
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) / Death-like domain superfamily ...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) / Death-like domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.339 Å
AuthorsZhang, Q. / Sun, H. / Hu, X. / Wang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)R7070-18 Hong Kong
CitationJournal: To Be Published
Title: Crystal structure of the RING domain of human XIAP
Authors: Zhang, Q. / Sun, H.
History
DepositionAug 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 25, 2023Group: Structure summary / Category: audit_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,9777
Polymers14,6762
Non-polymers3025
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-17 kcal/mol
Surface area7620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.663, 49.080, 39.720
Angle α, β, γ (deg.)90.00, 97.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein E3 ubiquitin-protein ligase XIAP / Baculoviral IAP repeat-containing protein 4 / IAP-like protein / ILP / hILP / Inhibitor of ...Baculoviral IAP repeat-containing protein 4 / IAP-like protein / ILP / hILP / Inhibitor of apoptosis protein 3 / IAP-3 / hIAP-3 / hIAP3 / RING-type E3 ubiquitin transferase XIAP / X-linked inhibitor of apoptosis protein / X-linked IAP


Mass: 7337.820 Da / Num. of mol.: 2 / Fragment: RING domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XIAP, API3, BIRC4, IAP3 / Production host: Escherichia coli (E. coli)
References: UniProt: P98170, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 32% PEG 3350, 25% glycerol, 1 mM TCEP, 100mM Tri-HCl, pH 7.4, 3 mM arsenic trioxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.339→42.21 Å / Num. obs: 28779 / % possible obs: 94 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 0.217
Reflection shellResolution: 1.339→42.21 Å / Rmerge(I) obs: 0.323 / Num. unique obs: 1041

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Processing

Software
NameVersionClassification
PHENIXv1.0refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.339→30.711 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 25.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1475 5.13 %
Rwork0.2136 --
obs0.2147 28775 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.339→30.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 5 59 1041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005988
X-RAY DIFFRACTIONf_angle_d0.8591325
X-RAY DIFFRACTIONf_dihedral_angle_d4.011386
X-RAY DIFFRACTIONf_chiral_restr0.093159
X-RAY DIFFRACTIONf_plane_restr0.006165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.339-1.38220.2656870.26091772X-RAY DIFFRACTION67
1.3822-1.43160.28311200.24562196X-RAY DIFFRACTION84
1.4316-1.48890.24741470.23162530X-RAY DIFFRACTION96
1.4889-1.55670.24931570.22822622X-RAY DIFFRACTION100
1.5567-1.63870.25931350.20572609X-RAY DIFFRACTION99
1.6387-1.74140.23491260.22252624X-RAY DIFFRACTION99
1.7414-1.87580.25361260.22672613X-RAY DIFFRACTION98
1.8758-2.06460.22291470.20752632X-RAY DIFFRACTION100
2.0646-2.36320.21751280.20422634X-RAY DIFFRACTION99
2.3632-2.9770.23871490.22292602X-RAY DIFFRACTION98
2.977-30.7110.22181530.20022466X-RAY DIFFRACTION92

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