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- PDB-6gjw: Structure of XIAP-BIR1 domain in complex with an NF023 analog -

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Basic information

Entry
Database: PDB / ID: 6gjw
TitleStructure of XIAP-BIR1 domain in complex with an NF023 analog
ComponentsE3 ubiquitin-protein ligase XIAP
KeywordsAPOPTOSIS / BIR / NF-KB / XIAP / CANCER / DOCKING / INHIBITOR
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 / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat ...XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-F2H / E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSorrentino, L. / Cossu, F. / Malkoc, B. / Zaffaroni, M. / Milani, M. / Mastrangelo, E.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer Research17083 Italy
CitationJournal: Chemistryopen / Year: 2019
Title: Structure-Activity Relationship of NF023 Derivatives Binding to XIAP-BIR1.
Authors: Sorrentino, L. / Cossu, F. / Milani, M. / Malkoc, B. / Huang, W.C. / Tsay, S.C. / Ru Hwu, J. / Mastrangelo, E.
History
DepositionMay 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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
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: E3 ubiquitin-protein ligase XIAP
D: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,42610
Polymers49,4314
Non-polymers1,9956
Water3,081171
1
A: E3 ubiquitin-protein ligase XIAP
D: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7135
Polymers24,7152
Non-polymers9983
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase XIAP
C: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7135
Polymers24,7152
Non-polymers9983
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.500, 75.800, 70.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / 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: 12357.735 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XIAP, API3, BIRC4, IAP3 / Production host: Escherichia coli BL21 (bacteria)
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
#3: Chemical ChemComp-F2H / 4-[[3-[[3-[(4,8-disulfonatonaphthalen-1-yl)carbamoyl]phenyl]carbamoylamino]phenyl]carbonylamino]naphthalene-1,5-disulfonate


Mass: 866.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H22N4O15S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.02 Å3/Da / Density % sol: 39.07 % / Description: prismatic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 8% PEG 8000, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.968
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.89→33.33 Å / Num. all: 30098 / Num. obs: 114269 / % possible obs: 100 % / Redundancy: 7.117 % / Biso Wilson estimate: 30.873 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.123 / Χ2: 0.946 / Net I/σ(I): 11.59 / Num. measured all: 115299 / Scaling rejects: 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.89-1.947.2230.662.98494117811760.8270.71199.8
1.94-1.997.3070.6922.788374114611460.8130.745100
1.99-2.057.2710.5053.798078111111110.8860.544100
2.05-2.117.30.4134.617920108510850.9080.445100
2.11-2.187.3230.335.67704105210520.960.355100
2.18-2.267.2260.2827.127399102510240.9530.30499.9
2.26-2.347.2870.2487.5871499829810.970.26899.9
2.34-2.447.2940.1869.6869669559550.980.2100
2.44-2.557.2580.14911.9565909089080.9880.161100
2.55-2.677.2390.13612.9163058718710.9850.147100
2.67-2.827.1950.12414.4660948478470.9880.134100
2.82-2.997.190.10517.3555297697690.9930.113100
2.99-3.197.0670.08919.1153717607600.9950.096100
3.19-3.456.9940.08420.6948967007000.9940.091100
3.45-3.786.9070.07822.245176546540.9960.084100
3.78-4.226.7310.06723.8640055955950.9930.072100
4.22-4.886.6570.06823.9634755225220.9960.074100
4.88-5.976.5110.06423.5729954604600.9980.069100
5.97-8.456.2140.06623.2922623653640.9940.07299.7
8.45-33.335.3450.06422.0611762232200.9950.0798.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OXC

4oxc


Resolution: 1.9→33.33 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.882 / SU B: 0.007 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2889 1504 5 %RANDOM
Rwork0.239 ---
obs0.2415 28575 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.44 Å2 / Biso mean: 30.746 Å2 / Biso min: 12.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0 Å20.16 Å2
2--1.78 Å20 Å2
3----1.41 Å2
Refinement stepCycle: final / Resolution: 1.9→33.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 120 171 2759
Biso mean--36.92 34.64 -
Num. residues----312
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 110 -
Rwork0.401 2102 -
all-2212 -
obs--100 %

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