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- PDB-4j48: Crystal structure of XIAP-BIR2 domain with AMRV bound -

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Basic information

Entry
Database: PDB / ID: 4j48
TitleCrystal structure of XIAP-BIR2 domain with AMRV bound
Components
  • E3 ubiquitin-protein ligase XIAP
  • PEPTIDE (ALA-MET-ARG-VAL)
KeywordsAPOPTOSIS / IAP / XIAP / CASPASE / SMAC
Function / homology
Function and homology information


copper ion homeostasis / inhibition of cysteine-type endopeptidase activity involved in apoptotic process / regulation of BMP signaling pathway / positive regulation of protein linear polyubiquitination / regulation of nucleotide-binding oligomerization domain containing signaling pathway / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / SMAC (DIABLO) binds to IAPs ...copper ion homeostasis / inhibition of cysteine-type endopeptidase activity involved in apoptotic process / regulation of BMP signaling pathway / positive regulation of protein linear polyubiquitination / regulation of nucleotide-binding oligomerization domain containing signaling pathway / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / SMAC (DIABLO) binds to IAPs / RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / regulation of innate immune response / Regulation of PTEN localization / positive regulation of protein ubiquitination / TNFR1-induced NFkappaB signaling pathway / Regulation of TNFR1 signaling / Deactivation of the beta-catenin transactivating complex / RING-type E3 ubiquitin transferase / spindle microtubule / Regulation of necroptotic cell death / Wnt signaling pathway / ubiquitin protein ligase activity / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / neuron apoptotic process / regulation of cell population proliferation / regulation of inflammatory response / regulation of cell cycle / cellular response to DNA damage stimulus / negative regulation of apoptotic process / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
XIAP/BIRC8, UBA domain / BIR repeat. / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / BIR repeat / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Inhibitor of Apoptosis domain / Death-like domain superfamily / Ring finger ...XIAP/BIRC8, UBA domain / BIR repeat. / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / BIR repeat / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Inhibitor of Apoptosis domain / 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)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsGosu, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The structure of XIAP BIR2: understanding the selectivity of the BIR domains.
Authors: Lukacs, C. / Belunis, C. / Crowther, R. / Danho, W. / Gao, L. / Goggin, B. / Janson, C.A. / Li, S. / Remiszewski, S. / Schutt, A. / Thakur, M.K. / Singh, S.K. / Swaminathan, S. / Pandey, R. ...Authors: Lukacs, C. / Belunis, C. / Crowther, R. / Danho, W. / Gao, L. / Goggin, B. / Janson, C.A. / Li, S. / Remiszewski, S. / Schutt, A. / Thakur, M.K. / Singh, S.K. / Swaminathan, S. / Pandey, R. / Tyagi, R. / Gosu, R. / Kamath, A.V. / Kuglstatter, A.
History
DepositionFeb 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release

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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
C: E3 ubiquitin-protein ligase XIAP
B: PEPTIDE (ALA-MET-ARG-VAL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6687
Polymers20,3493
Non-polymers3194
Water1,18966
1
A: E3 ubiquitin-protein ligase XIAP
B: PEPTIDE (ALA-MET-ARG-VAL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5744
Polymers10,4132
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-20 kcal/mol
Surface area5400 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0943
Polymers9,9361
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)74.805, 74.805, 109.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ACB

#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 / X-linked inhibitor of apoptosis protein / X-linked IAP


Mass: 9936.131 Da / Num. of mol.: 2 / Fragment: XIAP-BIR2 RESIDUES 152-236 / Mutation: C202A, C213G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: API3, BIRC4, IAP3, U32974, XIAP / Plasmid: Pet28A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)PLYSS
References: UniProt: P98170, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide PEPTIDE (ALA-MET-ARG-VAL)


Mass: 476.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)

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Non-polymers , 4 types, 70 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.88 Å3/Da / Density % sol: 34.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.7-1.9 M ammonium sulfate, 125 mM bis-tris propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 9105 / % possible obs: 97 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 1.9 / % possible all: 80.11

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4J3Y
Resolution: 2.1→32.7 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.552 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25335 428 4.7 %RANDOM
Rwork0.18291 ---
obs0.18605 8677 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.348 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 13 66 1416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191390
X-RAY DIFFRACTIONr_bond_other_d0.0010.021241
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9221878
X-RAY DIFFRACTIONr_angle_other_deg0.88732839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2165161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.18722.23776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26915207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8291514
X-RAY DIFFRACTIONr_chiral_restr0.0990.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02383
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8922.188652
X-RAY DIFFRACTIONr_mcbond_other1.8552.183651
X-RAY DIFFRACTIONr_mcangle_it2.8853.26811
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4222.532737
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 27 -
Rwork0.263 481 -
obs--76.28 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.5229-0.25890.86590.8919-0.32030.7062-0.11570.2015-0.02860.0560.06030.0088-0.02670.06220.05530.0298-0.02020.02260.0361-0.01130.0254-34.599-17.6121-16.0379
23.6349-0.94-2.3612.96441.39444.52790.0358-0.15610.1079-0.0296-0.005-0.2247-0.1260.4454-0.03080.0097-0.02420.00640.07650.00550.0437-7.9931-18.09-12.2847
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A151 - 234
2X-RAY DIFFRACTION2C159 - 234

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