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Basic information

Entry
Database: PDB / ID: 1oxq
TitleStructure and Function Analysis of Peptide Antagonists of Melanoma Inhibitor of Apoptosis (ML-IAP)
Components
  • AVPIAQKSE (Smac) peptide
  • Baculoviral IAP repeat-containing protein 7
KeywordsAPOPTOSIS/peptide / zinc binding / peptide complex / apoptosis inhibition / APOPTOSIS-peptide complex
Function / homology
Function and homology information


regulation of natural killer cell apoptotic process / Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / Regulation of MITF-M-dependent genes involved in apoptosis / 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 / lens development in camera-type eye ...regulation of natural killer cell apoptotic process / Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / Regulation of MITF-M-dependent genes involved in apoptosis / 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 / lens development in camera-type eye / intrinsic apoptotic signaling pathway in response to oxidative stress / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of tumor necrosis factor-mediated signaling pathway / cysteine-type endopeptidase inhibitor activity / intrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / positive regulation of JNK cascade / apoptotic signaling pathway / RING-type E3 ubiquitin transferase / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of cell population proliferation / neuron apoptotic process / regulation of apoptotic process / regulation of cell cycle / protein ubiquitination / positive regulation of apoptotic process / apoptotic process / centrosome / negative regulation of apoptotic process / enzyme binding / Golgi apparatus / mitochondrion / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
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. ...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 / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsFranklin, M.C. / Kadkhodayan, S. / Ackerly, H. / Alexandru, D. / Distefano, M.D. / Elliott, L.O. / Flygare, J.A. / Vucic, D. / Deshayes, K. / Fairbrother, W.J.
Citation
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. / Mausisa, G. / Okawa, D.C. / Ong, D. / Vucic, D. / Deshayes, K. / Fairbrother, W.J.
#1: Journal: Curr.Biol. / Year: 2000
Title: ML-IAP, a novel inhibitor of apoptosis that is preferentially expressed in human melanomas
Authors: Vucic, D. / Stennicke, H.R. / Pisabarro, M.T. / Salvesen, G.S. / Dixit, V.M.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: SMAC negatively regulates the anti-apoptotic activity of melanoma inhibitor of apoptosis (ML-IAP)
Authors: Vucic, D. / Deshayes, K. / Ackerly, H. / Pisabarro, M.T. / Kadkhodayan, S. / Fairbrother, W.J. / Dixit, V.M.
History
DepositionApr 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / 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: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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

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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: Baculoviral IAP repeat-containing protein 7
D: Baculoviral IAP repeat-containing protein 7
E: Baculoviral IAP repeat-containing protein 7
F: AVPIAQKSE (Smac) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,34412
Polymers79,6906
Non-polymers6536
Water7,260403
1
A: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8152
Polymers15,7491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8152
Polymers15,7491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8152
Polymers15,7491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1413
Polymers15,7491
Non-polymers3922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Baculoviral IAP repeat-containing protein 7
F: AVPIAQKSE (Smac) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7583
Polymers16,6922
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-4 kcal/mol
Surface area5760 Å2
MethodPISA
6
E: Baculoviral IAP repeat-containing protein 7
F: AVPIAQKSE (Smac) peptide
hetero molecules

A: Baculoviral IAP repeat-containing protein 7
B: Baculoviral IAP repeat-containing protein 7
C: Baculoviral IAP repeat-containing protein 7
D: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,34412
Polymers79,6906
Non-polymers6536
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation2_664-y+1,x-y+1,z-1/31
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-37 kcal/mol
Surface area24000 Å2
MethodPISA
7
A: Baculoviral IAP repeat-containing protein 7
D: Baculoviral IAP repeat-containing protein 7
hetero molecules

E: Baculoviral IAP repeat-containing protein 7
F: AVPIAQKSE (Smac) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7148
Polymers48,1914
Non-polymers5234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-y+1,x-y+1,z-1/31
Buried area4320 Å2
ΔGint-18 kcal/mol
Surface area15290 Å2
MethodPISA
8
B: Baculoviral IAP repeat-containing protein 7
C: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6304
Polymers31,4992
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-4 kcal/mol
Surface area10710 Å2
MethodPISA
9
D: Baculoviral IAP repeat-containing protein 7
hetero molecules

E: Baculoviral IAP repeat-containing protein 7
F: AVPIAQKSE (Smac) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8996
Polymers32,4423
Non-polymers4573
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-y+1,x-y+1,z-1/31
Buried area1960 Å2
ΔGint-13 kcal/mol
Surface area11440 Å2
MethodPISA
10
A: Baculoviral IAP repeat-containing protein 7
D: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9565
Polymers31,4992
Non-polymers4573
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-7 kcal/mol
Surface area10530 Å2
MethodPISA
11
E: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8152
Polymers15,7491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
F: AVPIAQKSE (Smac) peptide


  • defined by software
  • 943 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)9431
Polymers9431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.189, 83.189, 93.612
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsEach of the five BIR domains in the asymmetric unit represents the biologically active monomer

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Components

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


Mass: 15749.411 Da / Num. of mol.: 5 / Fragment: BIR domain, residues 63-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC7 OR KIAP OR MLIAP OR LIVIN / 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 AVPIAQKSE (Smac) peptide


Mass: 943.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED / References: UniProt: Q9NR28*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 3.03 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: sodium acetate, PEG 300, DTT, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMMES1droppH6.5
220 mg/mlprotein1drop
350 mMsodium acetate1reservoirpH5.0
45 %(v/v)PEG3001reservoir
55 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1.2686 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 13, 2002
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2686 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 64496 / Num. obs: 62709 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 41.211 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 21.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.4 / Num. unique all: 6453 / Rsym value: 0.379 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1OXN

1oxn


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.872 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Refinement involved replacing the peptide in 1OXN and adjusting side chains and waters. The discrepancies between observed reflections and reflections used for refinement is due to merging ...Details: Refinement involved replacing the peptide in 1OXN and adjusting side chains and waters. The discrepancies between observed reflections and reflections used for refinement is due to merging of Bijvoet mates during refinement. Since the dataset was collected at the zinc anomalous edge, the Bijvoet mates are not identical and represent crystallographically unique reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.21827 1528 4.9 %copied from test set for 1OXN
Rwork0.16064 ---
all0.1634 30570 --
obs0.16345 29677 97.08 %-
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: 40.259 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3979 0 27 403 4409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214154
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.9185624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9765493
X-RAY DIFFRACTIONr_chiral_restr0.0740.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023320
X-RAY DIFFRACTIONr_nbd_refined0.2040.22252
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2381
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.219
X-RAY DIFFRACTIONr_mcbond_it3.1932.52481
X-RAY DIFFRACTIONr_mcangle_it5.34753942
X-RAY DIFFRACTIONr_scbond_it3.9942.51673
X-RAY DIFFRACTIONr_scangle_it6.08251682
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.273 117
Rwork0.221 2169
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. reflection obs: 59357 / % reflection Rfree: 5 % / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.07

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