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- PDB-3g76: Crystal structure of XIAP-BIR3 in complex with a bivalent compound -

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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 / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase inhibitor activity involved in apoptotic process ...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 / Activation of caspases through apoptosome-mediated cleavage / 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 / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of innate immune response / protein K63-linked ubiquitination / positive regulation of type I interferon production / negative regulation of tumor necrosis factor-mediated signaling pathway / cysteine-type endopeptidase inhibitor activity / protein serine/threonine kinase binding / Regulation of PTEN localization / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of JNK cascade / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / Regulation of necroptotic cell death / 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 / neuron apoptotic process / regulation of 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

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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 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

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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

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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: 3.83 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

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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

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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

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