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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1oxn
TitleStructure and Function Analysis of Peptide Antagonists of Melanoma Inhibitor of Apoptosis (ML-IAP)
Components
  • AEAVPWKSE 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 / MAD / Resolution: 2.2 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 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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: AEAVPWKSE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,41812
Polymers79,7646
Non-polymers6536
Water7,224401
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: AEAVPWKSE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8323
Polymers16,7672
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-3 kcal/mol
Surface area5720 Å2
MethodPISA
6
E: Baculoviral IAP repeat-containing protein 7
F: AEAVPWKSE 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)80,41812
Polymers79,7646
Non-polymers6536
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation2_664-y+1,x-y+1,z-1/31
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-34 kcal/mol
Surface area23770 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: AEAVPWKSE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7888
Polymers48,2654
Non-polymers5234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-y+1,x-y+1,z-1/31
Buried area4290 Å2
ΔGint-17 kcal/mol
Surface area15130 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 area2030 Å2
ΔGint-4 kcal/mol
Surface area10670 Å2
MethodPISA
9
D: Baculoviral IAP repeat-containing protein 7
hetero molecules

E: Baculoviral IAP repeat-containing protein 7
F: AEAVPWKSE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9736
Polymers32,5163
Non-polymers4573
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-y+1,x-y+1,z-1/31
Buried area1950 Å2
ΔGint-12 kcal/mol
Surface area11300 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 area2630 Å2
ΔGint-7 kcal/mol
Surface area10440 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: AEAVPWKSE peptide


  • defined by software
  • 1.02 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,0171
Polymers1,0171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.770, 82.770, 93.170
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 AEAVPWKSE peptide


Mass: 1017.111 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.: 401 / 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: 2.99 Å3/Da / Density % sol: 58.5 %
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: BL9-2 / Wavelength: 1.2822, 1.2834, 1.1921
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 12, 2002 / Details: double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28221
21.28341
31.19211
ReflectionResolution: 2.2→30 Å / Num. all: 74935 / Num. obs: 73906 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 19.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 4.4 / Num. unique all: 7395 / Rsym value: 0.216 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 99.6 %

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.407 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 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 ...Details: 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
Rfree0.22502 1766 5 %RANDOM
Rwork0.16929 ---
all0.172 37860 --
obs0.17202 33874 95.16 %-
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: 36.119 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 27 401 4406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214152
X-RAY DIFFRACTIONr_angle_refined_deg1.0241.9175620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8585493
X-RAY DIFFRACTIONr_chiral_restr0.0720.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023320
X-RAY DIFFRACTIONr_nbd_refined0.2110.22412
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2406
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.229
X-RAY DIFFRACTIONr_mcbond_it3.0412.52480
X-RAY DIFFRACTIONr_mcangle_it5.08653937
X-RAY DIFFRACTIONr_scbond_it3.8172.51672
X-RAY DIFFRACTIONr_scangle_it5.76151683
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.288 138
Rwork0.265 2351
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. reflection obs: 71265 / % reflection Rfree: 5 % / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.169
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_deg1.02

+
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