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- PDB-1oy7: Structure and Function Analysis of Peptide Antagonists of Melanom... -

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Basic information

Entry
Database: PDB / ID: 1oy7
TitleStructure and Function Analysis of Peptide Antagonists of Melanoma Inhibitor of Apoptosis (ML-IAP)
Components
  • AEVVAVKSE 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 / Regulation of MITF-M-dependent genes involved in apoptosis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / lens development in camera-type eye / negative regulation of tumor necrosis factor-mediated signaling pathway / cysteine-type endopeptidase inhibitor activity / 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 / negative regulation of tumor necrosis factor-mediated signaling pathway / cysteine-type endopeptidase inhibitor activity / 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 / cytoplasm / cytosol
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
Baculoviral IAP repeat-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 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: AEVVAVKSE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,33312
Polymers79,6796
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: AEVVAVKSE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7473
Polymers16,6812
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-3 kcal/mol
Surface area5810 Å2
MethodPISA
6
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 area2630 Å2
ΔGint-7 kcal/mol
Surface area10680 Å2
MethodPISA
7
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 area10890 Å2
MethodPISA
8
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
9
F: AEVVAVKSE peptide


  • defined by software
  • 932 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)9321
Polymers9321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.878, 83.878, 94.340
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 AEVVAVKSE peptide


Mass: 932.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED
#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: 3.1 Å3/Da / Density % sol: 60.05 %
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: SSRL / Beamline: BL1-5 / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 2, 2002 / Details: double crystal Si 111 monochromator
RadiationMonochromator: double crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 20337 / Num. obs: 20139 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 53.112 Å2 / Rmerge(I) obs: 0.141 / Rsym value: 0.141 / Net I/σ(I): 8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / Num. unique all: 2035 / Rsym value: 0.35 / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 99 % / Rmerge(I) obs: 0.137
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.6

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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: 2.7→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.017 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.737 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: refinement involved replacing the peptide in 1OXN and adjusting side chains and waters
RfactorNum. reflection% reflectionSelection details
Rfree0.21134 979 4.9 %copied from test set for 1OXN
Rwork0.15243 ---
all0.155 19324 --
obs0.1553 19096 98.82 %-
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: 44.175 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 27 403 4410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214154
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.9175623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1415493
X-RAY DIFFRACTIONr_chiral_restr0.0810.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023320
X-RAY DIFFRACTIONr_nbd_refined0.210.22093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2304
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.222
X-RAY DIFFRACTIONr_mcbond_it3.0572.52480
X-RAY DIFFRACTIONr_mcangle_it5.37953939
X-RAY DIFFRACTIONr_scbond_it3.9082.51674
X-RAY DIFFRACTIONr_scangle_it6.42151684
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 72 -
Rwork0.209 1376 -
obs-1376 99.2 %
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Num. reflection obs: 32692 / % reflection Rfree: 5 % / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.08

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