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- PDB-1g73: CRYSTAL STRUCTURE OF SMAC BOUND TO XIAP-BIR3 DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1g73
TitleCRYSTAL STRUCTURE OF SMAC BOUND TO XIAP-BIR3 DOMAIN
Components
  • INHIBITORS OF APOPTOSIS-LIKE PROTEIN ILP
  • SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES
KeywordsAPOPTOSIS/APOPTOSIS INHIBITOR / helix bundle / zinc-binding domain / APOPTOSIS-APOPTOSIS INHIBITOR COMPLEX
Function / homology
Function and homology information


endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / regulation of BMP signaling pathway / copper ion homeostasis / Release of apoptotic factors from the mitochondria / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway ...endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / regulation of BMP signaling pathway / copper ion homeostasis / Release of apoptotic factors from the mitochondria / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / CD40 receptor complex / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / intrinsic apoptotic signaling pathway in response to oxidative stress / cysteine-type endopeptidase inhibitor activity / regulation of innate immune response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein K63-linked ubiquitination / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon production / protein serine/threonine kinase binding / Regulation of PTEN localization / intrinsic apoptotic signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of necroptotic cell death / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / regulation of cell population proliferation / regulation of inflammatory response / regulation of apoptotic process / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / positive regulation of apoptotic process / apoptotic process / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Smac/DIABLO-like superfamily / Smac/DIABLO protein / Second Mitochondria-derived Activator of Caspases / 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. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Smac/DIABLO-like superfamily / Smac/DIABLO protein / Second Mitochondria-derived Activator of Caspases / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Zinc finger RING-type profile. / Zinc finger, RING-type / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase XIAP / Diablo IAP-binding mitochondrial protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsWu, G. / Chai, J. / Suber, T.L. / Wu, J.-W. / Shi, Y.
CitationJournal: Nature / Year: 2000
Title: Structural basis of IAP recognition by Smac/DIABLO.
Authors: Wu, G. / Chai, J. / Suber, T.L. / Wu, J.W. / Du, C. / Wang, X. / Shi, Y.
History
DepositionNov 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.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_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
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SMAC (CHAIN A OR B) IS A HOMODIMER. ONE MISSENSE MUTATION WAS INTRODUCED SO THAT CHAIN A AND B NO LONGER FORMS A BIOLOGICALLY RELEVANT DIMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES
B: SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES
C: INHIBITORS OF APOPTOSIS-LIKE PROTEIN ILP
D: INHIBITORS OF APOPTOSIS-LIKE PROTEIN ILP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2126
Polymers64,0824
Non-polymers1312
Water00
1
A: SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES
C: INHIBITORS OF APOPTOSIS-LIKE PROTEIN ILP


Theoretical massNumber of molelcules
Total (without water)32,0412
Polymers32,0412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES
D: INHIBITORS OF APOPTOSIS-LIKE PROTEIN ILP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1724
Polymers32,0412
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.1, 52.9, 67.1
Angle α, β, γ (deg.)100.0, 104.1, 94.0
Int Tables number1
Space group name H-MP1

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Components

#1: Protein SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES / SMAC/DIABLO


Mass: 18115.334 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-162 / Mutation: F33D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAC / Plasmid: PET15-B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9NR28
#2: Protein INHIBITORS OF APOPTOSIS-LIKE PROTEIN ILP / IAP-LIKE PROTEIN ILP


Mass: 13925.435 Da / Num. of mol.: 2 / Fragment: BIR3 DOMAIN (RESIDUES 238-358)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET15-B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P98170
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Citrate, pH5.5 5% PEG4000 10% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Temperature: 23 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
2100 mMcitrate1reservoir
35 %PEG40001reservoir
410 %isopropanol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONNSLS X4A21.1
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEJul 1, 2000mirrors
FUJI2IMAGE PLATESep 13, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.11
ReflectionResolution: 2→20 Å / Num. all: 42559 / Num. obs: 40346 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 35
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.2 / Num. unique all: 3747 / Rsym value: 0.27 / % possible all: 88.5

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1895 -random
Rwork0.227 ---
all0.227 42559 --
obs0.227 40345 94.8 %-
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4008 0 2 0 4010
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d1.395
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.362 175 -
Rwork0.343 --
obs-3728 88 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30 Å2
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.362 / Rfactor Rwork: 0.343

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