[English] 日本語
Yorodumi
- PDB-3g76: Crystal structure of XIAP-BIR3 in complex with a bivalent compound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3g76
TitleCrystal structure of XIAP-BIR3 in complex with a bivalent compound
ComponentsBaculoviral IAP repeat-containing protein 4
KeywordsLIGASE / Apoptosis / IAP / SmacDIABLO / peptidomimetics / pro-apoptotic drugs / Cytoplasm / Metal-binding / Phosphoprotein / Polymorphism / Protease inhibitor / Thiol protease inhibitor / Ubl conjugation / Ubl conjugation pathway / Zinc / Zinc-finger
Function / homology
Function and homology information


regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Activation of caspases through apoptosome-mediated cleavage ...regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of innate immune response / cysteine-type endopeptidase inhibitor activity / protein K63-linked ubiquitination / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon production / Regulation of PTEN localization / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / protein serine/threonine kinase binding / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / Regulation of necroptotic cell death / RING-type E3 ubiquitin transferase / Regulation of PTEN stability and activity / Wnt signaling pathway / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / regulation of inflammatory response / regulation of apoptotic process / neuron apoptotic process / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / 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. ...XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / 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) / Death-like domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-CZ3 / E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCossu, F. / Milani, M. / Mastrangelo, E. / Bolognesi, M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural basis for bivalent smac-mimetics recognition in the IAP protein family
Authors: Cossu, F. / Milani, M. / Mastrangelo, E. / Vachette, P. / Servida, F. / Lecis, D. / Canevari, G. / Delia, D. / Drago, C. / Rizzo, V. / Manzoni, L. / Seneci, P. / Scolastico, C. / Bolognesi, M.
History
DepositionFeb 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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 / _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 4
B: Baculoviral IAP repeat-containing protein 4
C: Baculoviral IAP repeat-containing protein 4
D: Baculoviral IAP repeat-containing protein 4
E: Baculoviral IAP repeat-containing protein 4
F: Baculoviral IAP repeat-containing protein 4
G: Baculoviral IAP repeat-containing protein 4
H: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,25824
Polymers112,9818
Non-polymers8,27716
Water9,098505
1
A: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1573
Polymers14,1231
Non-polymers1,0352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1573
Polymers14,1231
Non-polymers1,0352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1573
Polymers14,1231
Non-polymers1,0352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1573
Polymers14,1231
Non-polymers1,0352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1573
Polymers14,1231
Non-polymers1,0352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1573
Polymers14,1231
Non-polymers1,0352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1573
Polymers14,1231
Non-polymers1,0352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1573
Polymers14,1231
Non-polymers1,0352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.077, 119.077, 105.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein
Baculoviral IAP repeat-containing protein 4 / E3 ubiquitin-protein ligase XIAP / Inhibitor of apoptosis protein 3 / X-linked inhibitor of ...E3 ubiquitin-protein ligase XIAP / Inhibitor of apoptosis protein 3 / X-linked inhibitor of apoptosis protein / X-linked IAP / IAP-like protein / HILP


Mass: 14122.637 Da / Num. of mol.: 8 / Fragment: BIR3 domain, UNP residues 241-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XIAP / Production host: Escherichia coli (E. coli)
References: UniProt: P98170, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CZ3 / 1,1'-{hexa-2,4-diyne-1,6-diylbis[oxy{(2S,3R)-2-[(N-methyl-L-alanyl)amino]-1-oxobutane-3,1-diyl}(2S)pyrrolidine-1,2-diylmethanediyl]}bis[5-(phenylsulfanyl)-1H-tetrazole]


Mass: 969.189 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C46H60N14O6S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 3.83 Å3/Da / Density % sol: 67.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 20% PEG MME 2000, 60mM sodium acetate tri-hydrate, 120mM Ammonium sulfate, 400mM sodium-potassium tartrate tetra-hydrate, pH 4.6, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2007
Details: Liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror
RadiationMonochromator: high resolution Si(311) cut and a lower resolution Si(111) cut
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 33440 / Redundancy: 3.6 % / Rmerge(I) obs: 0.101
Reflection shellHighest resolution: 3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4861

-
Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BIR3 DOMAIN FROM PDB ENTRY 3CLX

3clx


Resolution: 3→40 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.819 / Occupancy max: 1 / Occupancy min: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.613 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.311 1688 5.1 %RANDOM
Rwork0.231 31727 --
obs0.235 33415 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 172.64 Å2 / Biso mean: 72.888 Å2 / Biso min: 4.37 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å21.33 Å20 Å2
2--2.66 Å20 Å2
3----4 Å2
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6533 0 552 505 7590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227299
X-RAY DIFFRACTIONr_angle_refined_deg2.0422.0089889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9855794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39724.094342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.837151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5951528
X-RAY DIFFRACTIONr_chiral_restr0.1220.2956
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215680
X-RAY DIFFRACTIONr_mcbond_it4.6091.54018
X-RAY DIFFRACTIONr_mcangle_it7.38326403
X-RAY DIFFRACTIONr_scbond_it12.20433281
X-RAY DIFFRACTIONr_scangle_it16.964.53486
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 116 -
Rwork0.285 2325 -
obs-17810 99.92 %
Refinement TLS params.Method: refined / Origin x: 29.741 Å / Origin y: 17.166 Å / Origin z: 24.886 Å
111213212223313233
T0.0126 Å2-0.0198 Å20.0036 Å2-0.0686 Å20.0058 Å2---0.0087 Å2
L0.1024 °2-0.0481 °20.016 °2-0.0236 °20.0096 °2--0.3085 °2
S-0.0457 Å °-0.0632 Å °-0.0072 Å °-0.0088 Å °0.0166 Å °0.0022 Å °-0.0057 Å °0.0019 Å °0.029 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A200 - 600
2X-RAY DIFFRACTION1B200 - 600
3X-RAY DIFFRACTION1C200 - 600
4X-RAY DIFFRACTION1D200 - 600
5X-RAY DIFFRACTION1E200 - 600
6X-RAY DIFFRACTION1F200 - 600
7X-RAY DIFFRACTION1G200 - 600
8X-RAY DIFFRACTION1H200 - 600

+
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