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- PDB-2i3i: Structure of an ML-IAP/XIAP chimera bound to a peptidomimetic -

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Basic information

Entry
Database: PDB / ID: 2i3i
TitleStructure of an ML-IAP/XIAP chimera bound to a peptidomimetic
ComponentsBaculoviral IAP repeat-containing protein 7
KeywordsINHIBITOR/APOPTOSIS / ZINC BINDING / PEPTIDE COMPLEX / APOPTOSIS INHIBITION / PEPTIDOMIMETIC / SMALL MOLECULE / DRUG DESIGN / INHIBITOR-APOPTOSIS COMPLEX
Function / homology
Function and homology information


regulation of natural killer cell apoptotic process / Regulation of MITF-M-dependent genes involved in apoptosis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / lens development in camera-type eye / cysteine-type endopeptidase inhibitor activity / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of protein ubiquitination / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity ...regulation of natural killer cell apoptotic process / Regulation of MITF-M-dependent genes involved in apoptosis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / lens development in camera-type eye / cysteine-type endopeptidase inhibitor activity / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of protein ubiquitination / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of apoptotic process / regulation of cell cycle / protein ubiquitination / apoptotic process / centrosome / negative regulation of apoptotic process / enzyme binding / Golgi apparatus / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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
Chem-618 / : / Baculoviral IAP repeat-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsFairbrother, W.J. / Franklin, M.C.
Citation
Journal: Acs Chem.Biol. / Year: 2006
Title: Design, synthesis, and biological activity of a potent Smac mimetic that sensitizes cancer cells to apoptosis by antagonizing IAPs.
Authors: Zobel, K. / Wang, L. / Varfolomeev, E. / Franklin, M.C. / Elliott, L.O. / Wallweber, H.J. / Okawa, D.C. / Flygare, J.A. / Vucic, D. / Fairbrother, W.J. / Deshayes, K.
#1: 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. / Das, K. / Eckelman, B.P. / Shin, H. / Elliott, L.O. / Deshayes, K. / Salvesen, G.S. / Fairbrother, W.J.
#2: 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.
History
DepositionAug 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
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

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 7
B: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,42010
Polymers29,9552
Non-polymers1,4648
Water2,432135
1
A: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5403
Polymers14,9781
Non-polymers5622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8807
Polymers14,9781
Non-polymers9026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.356, 87.356, 73.196
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 , 1 types, 2 molecules AB

#1: Protein Baculoviral IAP repeat-containing protein 7 / Kidney inhibitor of apoptosis protein / KIAP / Melanoma inhibitor of apoptosis protein / ML-IAP / Livin


Mass: 14977.567 Da / Num. of mol.: 2 / Fragment: ML-IAP residues 63-172
Mutation: RESIDUES 150, 160-168, AND 172 REPLACED WITH XIAP-BIR3 HOMOLOGUES
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 6 types, 143 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-618 / (3R,6R,9AR)-2,2-DIMETHYL-6-[(N-METHYL-L-ALANYL)AMINO]-N-(3-METHYL-1-PHENYL-1H-PYRAZOL-5-YL)-5-OXO-2,3,5,6,9,9A-HEXAHYDRO[1,3]THIAZOLO[3,2-A]AZEPINE-3-CARBOXAMIDE


Mass: 496.625 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H32N6O3S
#4: Chemical ChemComp-LI / LITHIUM ION


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


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


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


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Lithium sulfate, PEG 3350, Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 21, 2005 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 13116 / Num. obs: 13095 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.169 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1277 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345345data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1.3 A structure of the ML-IAP/XIAP protein bound to a different peptidomimetic, with the ligand and surrounding waters removed

Resolution: 2.3→24.34 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.803 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22385 644 4.9 %RANDOM
Rwork0.18783 ---
all0.189 13116 --
obs0.18954 12395 99.71 %-
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: 1.897 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2---0.8 Å20 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 95 135 1724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211660
X-RAY DIFFRACTIONr_bond_other_d0.0010.021401
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9872247
X-RAY DIFFRACTIONr_angle_other_deg0.82733256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0365183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89223.03879
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71715223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.587158
X-RAY DIFFRACTIONr_chiral_restr0.0770.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
X-RAY DIFFRACTIONr_nbd_refined0.2180.2344
X-RAY DIFFRACTIONr_nbd_other0.1820.21363
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2787
X-RAY DIFFRACTIONr_nbtor_other0.0830.2803
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.297
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.213
X-RAY DIFFRACTIONr_mcbond_it0.4632.51181
X-RAY DIFFRACTIONr_mcbond_other0.0512.5380
X-RAY DIFFRACTIONr_mcangle_it0.61151464
X-RAY DIFFRACTIONr_scbond_it0.5282.5904
X-RAY DIFFRACTIONr_scangle_it0.8495783
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 52 -
Rwork0.223 883 -
obs--100 %
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)
13.3511-1.6301-0.46873.9084-0.0932.54760.07470.2339-0.0061-0.3263-0.1114-0.02760.03630.00520.0367-0.15620.00790.0077-0.16170.0018-0.18184.866568.170622.224
21.6325-0.87080.49134.302-1.70732.63940.0534-0.2011-0.0560.21940.02430.075-0.0804-0.0373-0.0777-0.1523-0.03080.0138-0.1874-0.0042-0.188377.931459.74750.1759
33.00560.55429.27280.10221.709828.60780.25480.9836-0.6483-1.1625-0.16550.5867-0.1137-1.0681-0.08930.04530.0661-0.1426-0.0319-0.0352-0.018879.297562.430514.3987
42.95555.4224-0.016316.5146-8.70411.4592-0.4995-0.24470.11250.4578-0.33511.49192.1493-0.32620.8346-0.181-0.06390.0580.0099-0.00210.081668.040455.136748.5896
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA78 - 16739 - 128
2X-RAY DIFFRACTION1AC10011
3X-RAY DIFFRACTION2BB78 - 17139 - 132
4X-RAY DIFFRACTION2BD10011
5X-RAY DIFFRACTION3AF5011
6X-RAY DIFFRACTION4BG5011

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