[English] 日本語
Yorodumi
- PDB-1oy7: Structure and Function Analysis of Peptide Antagonists of Melanom... -

+
Open data


ID or keywords:

Loading...

-
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 / lens development in camera-type eye / cysteine-type endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / 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 natural killer cell apoptotic process / lens development in camera-type eye / cysteine-type endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / 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 / protein ubiquitination / regulation of cell cycle / centrosome / apoptotic process / negative regulation of apoptotic process / Golgi apparatus / enzyme binding / nucleoplasm / metal ion binding / 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 / Zinc finger RING-type signature. ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Polyethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more