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- PDB-2vsl: Crystal Structure of XIAP BIR3 with a Bivalent Smac Mimetic -

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Basic information

Entry
Database: PDB / ID: 2vsl
TitleCrystal Structure of XIAP BIR3 with a Bivalent Smac Mimetic
Components
  • BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4
  • PEPTIDE (MAA-LYS-PRO-PHE)
KeywordsLIGASE / ZINC-FINGER / POLYMORPHISM / SMAC MIMETIC / METAL-BINDING / UBL CONJUGATION PATHWAY / THIOL PROTEASE INHIBITOR / PHOSPHOPROTEIN / UBL CONJUGATION / PROTEASE INHIBITOR / BIR3 / ZINC / XIAP / APOPTOSIS / CYTOPLASM / HYDROLASE 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
E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMeagher, J.L. / Stuckey, J.A.
CitationJournal: Biochemistry / Year: 2008
Title: Interaction of a Cyclic, Bivalent Smac Mimetic with the X-Linked Inhibitor of Apoptosis Protein.
Authors: Nikolovska-Coleska, Z. / Meagher, J.L. / Jiang, S. / Yang, C.Y. / Qiu, S. / Roller, P.P. / Stuckey, J.A. / Wang, S.
History
DepositionApr 24, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance

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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 4
B: PEPTIDE (MAA-LYS-PRO-PHE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1614
Polymers11,5662
Non-polymers1,5952
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-6 kcal/mol
Surface area5800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.478, 102.478, 65.218
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4 / XIAP / E3 UBIQUITIN-PROTEIN LIGASE XIAP / INHIBITOR OF APOPTOSIS PROTEIN 3 / X- LINKED INHIBITOR OF ...XIAP / E3 UBIQUITIN-PROTEIN LIGASE XIAP / INHIBITOR OF APOPTOSIS PROTEIN 3 / X- LINKED INHIBITOR OF APOPTOSIS PROTEIN / X-LINKED IAP / IAP-LIKE PROTEIN / HILP


Mass: 11089.397 Da / Num. of mol.: 1 / Fragment: BIR3 DOMAIN, RESIDUES 250-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P98170, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide PEPTIDE (MAA-LYS-PRO-PHE)


Mass: 476.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.46 Å3/Da / Density % sol: 64.2 % / Description: NONE
Crystal growpH: 7.5 / Details: 1.4 M NACL, 5% PEG 6000, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.96859
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 4, 2005
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 2.1→29.74 Å / Num. obs: 10431 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 20 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY SOLVED, UNPUBLISHED STRUCTURE

Resolution: 2.1→29.74 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1764553.24 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE B CHAIN IS A CYCLIC DIMERIC PEPTIDE WITH HALF OF IT IN THE ASYMMETRIC UNIT. THE FULL STRUCTURE IS GENERATED VIA CRYSTALLOGRAPHIC TWO-FOLD AXIS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1077 10.3 %RANDOM
Rwork0.218 ---
obs0.218 10423 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.4453 Å2 / ksol: 0.394327 e/Å3
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms817 0 6 60 883
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.552.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 176 10.4 %
Rwork0.244 1514 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ION.PARAMION.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3PEG.PARAMPEG.TOP
X-RAY DIFFRACTION4PROTEIN_REP.PARAMPROTEIN_REP.TOP.

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