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- PDB-1xb1: The Structure of the BIR domain of IAP-like protein 2 -

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Basic information

Entry
Database: PDB / ID: 1xb1
TitleThe Structure of the BIR domain of IAP-like protein 2
Components
  • Baculoviral IAP repeat-containing protein 8
  • Diablo homolog, mitochondrial
KeywordsAPOPTOSIS / IAP / caspase inhibition / SMAC / Diabolo
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 / 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 / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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)79,96535
Polymers78,46112
Non-polymers1,50423
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10510 Å2
ΔGint-571 kcal/mol
Surface area30820 Å2
MethodPISA
2
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

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)159,93070
Polymers156,92224
Non-polymers3,00946
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area28340 Å2
ΔGint-1405 kcal/mol
Surface area54320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.689, 88.689, 191.355
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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.: 23 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 5% PEG3000, 100mM Na 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 22931 / % possible obs: 92.9 % / Redundancy: 3 % / Rsym value: 0.071
Reflection shellResolution: 2.7→2.8 Å / Rsym value: 0.374 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40.23 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1661581.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1111 4.9 %RANDOM
Rwork0.232 ---
obs0.232 22904 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.4149 Å2 / ksol: 0.363543 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.73 Å27.04 Å20 Å2
2--6.73 Å20 Å2
3----13.45 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 23 188 5005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 171 4.5 %
Rwork0.298 3624 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

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