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- PDB-1tw6: Structure of an ML-IAP/XIAP chimera bound to a 9mer peptide deriv... -

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Basic information

Entry
Database: PDB / ID: 1tw6
TitleStructure of an ML-IAP/XIAP chimera bound to a 9mer peptide derived from Smac
Components
  • Baculoviral IAP repeat-containing protein 7
  • Diablo homolog, mitochondrial
KeywordsINHIBITOR/APOPTOSIS / ZINC BINDING / PEPTIDE COMPLEX / APOPTOSIS INHIBITION / INHIBITOR-APOPTOSIS COMPLEX
Function / homology
Function and homology information


regulation of natural killer cell apoptotic process / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / lens development in camera-type eye / intrinsic apoptotic signaling pathway in response to oxidative stress ...regulation of natural killer cell apoptotic process / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / lens development in camera-type eye / intrinsic apoptotic signaling pathway in response to oxidative stress / cysteine-type endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of tumor necrosis factor-mediated signaling pathway / intrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin protein ligase activity / regulation of cell population proliferation / neuron apoptotic process / regulation of apoptotic process / protein ubiquitination / regulation of cell cycle / positive regulation of apoptotic process / centrosome / apoptotic process / negative regulation of apoptotic process / Golgi apparatus / enzyme binding / mitochondrion / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Smac/DIABLO-like superfamily / Smac/DIABLO protein / Second Mitochondria-derived Activator of Caspases / 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 ...Smac/DIABLO-like superfamily / Smac/DIABLO protein / Second Mitochondria-derived Activator of Caspases / 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) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Baculoviral IAP repeat-containing protein 7 / Diablo IAP-binding mitochondrial protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.713 Å
AuthorsFranklin, M.C. / Vucic, D. / Wallweber, H.J.A. / Das, K. / Shin, H. / Elliott, L.O. / Kadkhodayan, S. / Deshayes, K. / Salvesen, G.S. / Fairbrother, W.J.
Citation
Journal: Biochem.J. / Year: 2005
Title: Engineering ML-IAP to produce an extraordinarily potent caspase 9 inhibitor: implications for Smac-dependent anti-apoptotic activity of ML-IAP
Authors: Vucic, D. / Franklin, M.C. / Wallweber, H.J.A. / Das, K. / Eckelman, B.P. / Shin, H. / Elliott, L.O. / Kadkhodayan, S. / Deshayes, K. / Salvesen, G.S. / Fairbrother, W.J.
#1: Journal: Biochemistry / Year: 2003
Title: Structure and Function Analysis of Peptide Antagonists of Melanoma Inhibitor of Apoptosis (ML-IAP)
Authors: Franklin, M.C. / Kadkhodayan, S. / Ackerly, H. / Alexandru, D. / Distefano, M.D. / Elliott, L.O. / Flygare, J.A. / Vucic, D. / Deshayes, K. / Fairbrother, W.J.
#2: Journal: Mol.Cell / Year: 2003
Title: Mechanism of XIAP-mediated inhibition of caspase-9
Authors: Shizoaki, E.N. / Chai, J. / Rigotti, D.J. / Riedl, S.J. / Li, P. / Srinivasula, S.M. / Alnemri, E.S. / Fairman, R. / Shi, Y.
History
DepositionJun 30, 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: Advisory / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE For entity 1 (chains A and B)residues 150, 160-168, and 172 replaced with XIAP-BIR3 homologues.

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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 7
B: Baculoviral IAP repeat-containing protein 7
C: Diablo homolog, mitochondrial
D: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,28110
Polymers31,8094
Non-polymers4716
Water3,981221
1
A: Baculoviral IAP repeat-containing protein 7
C: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9703
Polymers15,9052
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Baculoviral IAP repeat-containing protein 7
D: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3107
Polymers15,9052
Non-polymers4065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-9 kcal/mol
Surface area5980 Å2
MethodPISA
3
A: Baculoviral IAP repeat-containing protein 7
B: Baculoviral IAP repeat-containing protein 7
C: Diablo homolog, mitochondrial
D: Diablo homolog, mitochondrial
hetero molecules

A: Baculoviral IAP repeat-containing protein 7
B: Baculoviral IAP repeat-containing protein 7
C: Diablo homolog, mitochondrial
D: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,56120
Polymers63,6198
Non-polymers94212
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8090 Å2
ΔGint-52 kcal/mol
Surface area19140 Å2
MethodPISA
4
B: Baculoviral IAP repeat-containing protein 7
D: Diablo homolog, mitochondrial
hetero molecules

A: Baculoviral IAP repeat-containing protein 7
C: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,28110
Polymers31,8094
Non-polymers4716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2890 Å2
ΔGint-20 kcal/mol
Surface area10730 Å2
MethodPISA
5
A: Baculoviral IAP repeat-containing protein 7
C: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9703
Polymers15,9052
Non-polymers651
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation3_645-y+3/2,x-1/2,z+1/41
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area5750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.856, 87.856, 74.634
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Baculoviral IAP repeat-containing protein 7 / Kidney inhibitor of apoptosis protein / KIAP / Melanoma inhibitor of apoptosis protein / ML-IAP / ...Kidney inhibitor of apoptosis protein / KIAP / Melanoma inhibitor of apoptosis protein / ML-IAP / Livin / UNQ5800/PRO19607/PRO21344 / XIAP-BIR3 chimera


Mass: 14961.612 Da / Num. of mol.: 2 / Fragment: ML-IAP residues 63-172
Mutation: S150G, R160G, D161E, F162Y, V163I, H164N, S165N, V166I, Q167H, E168L, Q172L
Source method: isolated from a genetically manipulated source
Details: residues 150, 160-168, and 172 replaced with XIAP-BIR3 homologues
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC7 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96CA5
#2: Protein/peptide Diablo homolog, mitochondrial / / Second mitochondria-derived activator of caspase / Smac protein / Direct IAP binding protein with low pI


Mass: 943.074 Da / Num. of mol.: 2 / Fragment: Smac residues 1-9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIABLO, SMAC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR28

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Non-polymers , 5 types, 227 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: lithium sulfate, Bis-tris, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 9, 2003
RadiationMonochromator: Horizontal focus 5.05-degree asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. all: 32210 / Num. obs: 31742 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 21.4
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3165 / Rsym value: 0.664 / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OXN (without peptide)

1oxn


Resolution: 1.713→47.75 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.456 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17088 1578 5 %RANDOM 5%
Rwork0.15518 ---
all0.1559 32021 --
obs0.15595 31690 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.61 Å20 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.713→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 25 221 1808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211652
X-RAY DIFFRACTIONr_bond_other_d0.0020.021389
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.932227
X-RAY DIFFRACTIONr_angle_other_deg0.75833241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3185191
X-RAY DIFFRACTIONr_chiral_restr0.0660.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021823
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02369
X-RAY DIFFRACTIONr_nbd_refined0.2080.2328
X-RAY DIFFRACTIONr_nbd_other0.2270.21501
X-RAY DIFFRACTIONr_nbtor_other0.0810.2799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.226
X-RAY DIFFRACTIONr_mcbond_it1.3592.5972
X-RAY DIFFRACTIONr_mcangle_it2.19651544
X-RAY DIFFRACTIONr_scbond_it2.1472.5680
X-RAY DIFFRACTIONr_scangle_it3.4045683
LS refinement shellResolution: 1.713→1.757 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 115 -
Rwork0.234 1986 -
obs-1986 90.64 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.382-0.56-0.3853.4685-0.25512.06660.05250.1639-0.0294-0.228-0.0844-0.10560.05240.0470.03190.01350.00660.01660.04130.00110.022585.335768.666522.8412
21.2097-0.55140.29563.5024-1.53181.96950.0121-0.0959-0.02130.1897-0.00620.0108-0.07660.0043-0.00590.0174-0.0070.01980.0136-0.0010.027178.638860.276450.4654
321.6498-4.0377-2.55074.95078.383333.72720.12751.2584-1.0395-0.248-0.50030.9764-0.234-1.36020.37290.14090.0565-0.00140.1206-0.02970.110979.895862.619615.16
412.403-2.5197-0.387523.37946.169134.07110.2840.9632-0.1537-1.2165-0.35410.820.2161-0.48030.07010.11580.01540.06580.10390.06430.249867.939955.475646.2878
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA78 - 16739 - 128
2X-RAY DIFFRACTION1AE1001
3X-RAY DIFFRACTION2BB78 - 16939 - 130
4X-RAY DIFFRACTION2BF1001
5X-RAY DIFFRACTION3CC1 - 41 - 4
6X-RAY DIFFRACTION4DD1 - 61 - 6

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