[English] 日本語
Yorodumi
- PDB-1tw6: Structure of an ML-IAP/XIAP chimera bound to a 9mer peptide deriv... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tw6
TitleStructure of an ML-IAP/XIAP chimera bound to a 9mer peptide derived from Smac
Components
  • Baculoviral IAP repeat-containing protein 7
  • Diablo homolog, mitochondrial
KeywordsINHIBITOR/APOPTOSIS / ZINC BINDING / PEPTIDE COMPLEX / APOPTOSIS INHIBITION / INHIBITOR-APOPTOSIS 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 / cysteine-type endopeptidase inhibitor activity / negative regulation of tumor necrosis factor-mediated signaling pathway / 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 / MOLECULAR REPLACEMENT / Resolution: 1.713 Å
AuthorsFranklin, M.C. / Vucic, D. / Wallweber, H.J.A. / Das, K. / Shin, H. / Elliott, L.O. / Kadkhodayan, S. / Deshayes, K. / Salvesen, G.S. / Fairbrother, W.J.
Citation
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.A. / Das, K. / Eckelman, B.P. / Shin, H. / Elliott, L.O. / Kadkhodayan, S. / Deshayes, K. / Salvesen, G.S. / Fairbrother, W.J.
#1: 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.
#2: Journal: Mol.Cell / Year: 2003
Title: Mechanism of XIAP-mediated inhibition of caspase-9
Authors: Shizoaki, E.N. / Chai, J. / Rigotti, D.J. / Riedl, S.J. / Li, P. / Srinivasula, S.M. / Alnemri, E.S. / Fairman, R. / Shi, Y.
History
DepositionJun 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...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: _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
Remark 999SEQUENCE For entity 1 (chains A and B)residues 150, 160-168, and 172 replaced with XIAP-BIR3 homologues.

-
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: Diablo homolog, mitochondrial
D: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,28110
Polymers31,8094
Non-polymers4716
Water3,981221
1
A: Baculoviral IAP repeat-containing protein 7
C: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9703
Polymers15,9052
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Baculoviral IAP repeat-containing protein 7
D: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3107
Polymers15,9052
Non-polymers4065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-9 kcal/mol
Surface area5980 Å2
MethodPISA
3
A: Baculoviral IAP repeat-containing protein 7
B: Baculoviral IAP repeat-containing protein 7
C: Diablo homolog, mitochondrial
D: Diablo homolog, mitochondrial
hetero molecules

A: Baculoviral IAP repeat-containing protein 7
B: Baculoviral IAP repeat-containing protein 7
C: Diablo homolog, mitochondrial
D: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,56120
Polymers63,6198
Non-polymers94212
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8090 Å2
ΔGint-52 kcal/mol
Surface area19140 Å2
MethodPISA
4
B: Baculoviral IAP repeat-containing protein 7
D: Diablo homolog, mitochondrial
hetero molecules

A: Baculoviral IAP repeat-containing protein 7
C: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,28110
Polymers31,8094
Non-polymers4716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2890 Å2
ΔGint-20 kcal/mol
Surface area10730 Å2
MethodPISA
5
A: Baculoviral IAP repeat-containing protein 7
C: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9703
Polymers15,9052
Non-polymers651
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation3_645-y+3/2,x-1/2,z+1/41
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area5750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.856, 87.856, 74.634
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Baculoviral IAP repeat-containing protein 7 / Kidney inhibitor of apoptosis protein / KIAP / Melanoma inhibitor of apoptosis protein / ML-IAP / ...Kidney inhibitor of apoptosis protein / KIAP / Melanoma inhibitor of apoptosis protein / ML-IAP / Livin / UNQ5800/PRO19607/PRO21344 / XIAP-BIR3 chimera


Mass: 14961.612 Da / Num. of mol.: 2 / Fragment: ML-IAP residues 63-172
Mutation: S150G, R160G, D161E, F162Y, V163I, H164N, S165N, V166I, Q167H, E168L, Q172L
Source method: isolated from a genetically manipulated source
Details: residues 150, 160-168, and 172 replaced with XIAP-BIR3 homologues
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
#2: Protein/peptide Diablo homolog, mitochondrial / Second mitochondria-derived activator of caspase / Smac protein / Direct IAP binding protein with low pI


Mass: 943.074 Da / Num. of mol.: 2 / Fragment: Smac residues 1-9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIABLO, SMAC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR28

-
Non-polymers , 5 types, 227 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#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.: 221 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: lithium sulfate, Bis-tris, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 9, 2003
RadiationMonochromator: Horizontal focus 5.05-degree asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. all: 32210 / Num. obs: 31742 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 21.4
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3165 / Rsym value: 0.664 / % possible all: 88.2

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OXN (without peptide)

1oxn


Resolution: 1.713→47.75 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.456 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17088 1578 5 %RANDOM 5%
Rwork0.15518 ---
all0.1559 32021 --
obs0.15595 31690 98.97 %-
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: 10.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.61 Å20 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.713→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 25 221 1808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211652
X-RAY DIFFRACTIONr_bond_other_d0.0020.021389
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.932227
X-RAY DIFFRACTIONr_angle_other_deg0.75833241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3185191
X-RAY DIFFRACTIONr_chiral_restr0.0660.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021823
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02369
X-RAY DIFFRACTIONr_nbd_refined0.2080.2328
X-RAY DIFFRACTIONr_nbd_other0.2270.21501
X-RAY DIFFRACTIONr_nbtor_other0.0810.2799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.226
X-RAY DIFFRACTIONr_mcbond_it1.3592.5972
X-RAY DIFFRACTIONr_mcangle_it2.19651544
X-RAY DIFFRACTIONr_scbond_it2.1472.5680
X-RAY DIFFRACTIONr_scangle_it3.4045683
LS refinement shellResolution: 1.713→1.757 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 115 -
Rwork0.234 1986 -
obs-1986 90.64 %
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)
12.382-0.56-0.3853.4685-0.25512.06660.05250.1639-0.0294-0.228-0.0844-0.10560.05240.0470.03190.01350.00660.01660.04130.00110.022585.335768.666522.8412
21.2097-0.55140.29563.5024-1.53181.96950.0121-0.0959-0.02130.1897-0.00620.0108-0.07660.0043-0.00590.0174-0.0070.01980.0136-0.0010.027178.638860.276450.4654
321.6498-4.0377-2.55074.95078.383333.72720.12751.2584-1.0395-0.248-0.50030.9764-0.234-1.36020.37290.14090.0565-0.00140.1206-0.02970.110979.895862.619615.16
412.403-2.5197-0.387523.37946.169134.07110.2840.9632-0.1537-1.2165-0.35410.820.2161-0.48030.07010.11580.01540.06580.10390.06430.249867.939955.475646.2878
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA78 - 16739 - 128
2X-RAY DIFFRACTION1AE1001
3X-RAY DIFFRACTION2BB78 - 16939 - 130
4X-RAY DIFFRACTION2BF1001
5X-RAY DIFFRACTION3CC1 - 41 - 4
6X-RAY DIFFRACTION4DD1 - 61 - 6

+
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