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- PDB-1xb0: Structure of the BIR domain of IAP-like protein 2 -

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Basic information

Entry
Database: PDB / ID: 1xb0
TitleStructure of the BIR domain of IAP-like protein 2
Components
  • Baculoviral IAP repeat-containing protein 8
  • Diablo homolog, mitochondrial
KeywordsAPOPTOSIS / SMAC / DIABLO / CASPASE INHIBITION / XIAP
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / intrinsic apoptotic signaling pathway in response to oxidative stress / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway ...Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / intrinsic apoptotic signaling pathway in response to oxidative stress / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / apoptotic signaling pathway / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / neuron apoptotic process / regulation of cell cycle / positive regulation of apoptotic process / apoptotic process / negative regulation of apoptotic process / mitochondrion / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Smac/DIABLO-like superfamily / Smac/DIABLO protein / Second Mitochondria-derived Activator of Caspases / 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. ...Smac/DIABLO-like superfamily / Smac/DIABLO protein / Second Mitochondria-derived Activator of Caspases / 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
Baculoviral IAP repeat-containing protein 8 / Diablo IAP-binding mitochondrial protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShin, H. / Renatus, M. / Eckelman, B.P. / Nunes, V.A. / Sampaio, C.A.M. / Salvesen, G.S.
CitationJournal: Biochem.J. / Year: 2005
Title: The BIR domain of IAP-like protein 2 is conformationally unstable: implications for caspase inhibition
Authors: Shin, H. / Renatus, M. / Eckelman, B.P. / Nunes, V.A. / Sampaio, C.A.M. / Salvesen, G.S.
History
DepositionAug 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Residues 253-261, of chains A-F, comprise an N-terminal fusion from A-F human XIAP

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 8
G: Diablo homolog, mitochondrial
B: Baculoviral IAP repeat-containing protein 8
H: Diablo homolog, mitochondrial
C: Baculoviral IAP repeat-containing protein 8
I: Diablo homolog, mitochondrial
D: Baculoviral IAP repeat-containing protein 8
J: Diablo homolog, mitochondrial
E: Baculoviral IAP repeat-containing protein 8
K: Diablo homolog, mitochondrial
F: Baculoviral IAP repeat-containing protein 8
L: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,03136
Polymers78,46112
Non-polymers1,57024
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.400, 86.400, 226.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Baculoviral IAP repeat-containing protein 8 / Inhibitor of apoptosis-like protein 2 / IAP-like protein 2 / ILP-2 / Testis-specific inhibitor of ...Inhibitor of apoptosis-like protein 2 / IAP-like protein 2 / ILP-2 / Testis-specific inhibitor of apoptosis / XILP2


Mass: 12349.910 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: XILP2: human ILP2 with an N-terminal fusion (residues 253-261 from human XIAP)
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC8, ILP2 / Plasmid: pet15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q96P09
#2: Protein/peptide
Diablo homolog, mitochondrial / Second mitochondria-derived activator of caspase / Smac protein / Direct IAP binding protein with low pI


Mass: 726.883 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: Q9NR28
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 5% PEG3000, 100mM sodium acetate, 100mM Zinc acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.984 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 44152 / % possible obs: 98.2 % / Redundancy: 5.9 % / Rsym value: 0.074
Reflection shellResolution: 2.2→2.27 Å / Rsym value: 0.382 / % possible all: 98.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1G73 (chain D)

1g73


Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 2196 -random
Rwork0.2225 ---
all-44603 --
obs-43968 98.7 %-
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 24 316 5158
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1

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