- PDB-3uw4: Crystal structure of cIAP1 BIR3 bound to GDC0152 -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3uw4
Title
Crystal structure of cIAP1 BIR3 bound to GDC0152
Components
Baculoviral IAP repeat-containing protein 2, Baculoviral IAP repeat-containing protein 4
GDC0152
Keywords
Apoptosis Inhibitor / BIR domain
Function / homology
Function and homology information
negative regulation of ripoptosome assembly involved in necroptotic process / regulation of cysteine-type endopeptidase activity / FBXO family protein binding / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein linear polyubiquitination ...negative regulation of ripoptosome assembly involved in necroptotic process / regulation of cysteine-type endopeptidase activity / FBXO family protein binding / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / copper ion homeostasis / regulation of necroptotic process / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of protein K63-linked ubiquitination / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / CD40 receptor complex / XY body / negative regulation of necroptotic process / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / 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 / positive regulation of protein monoubiquitination / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / non-canonical NF-kappaB signal transduction / regulation of cell differentiation / necroptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein K63-linked ubiquitination / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon production / canonical NF-kappaB signal transduction / protein serine/threonine kinase binding / response to cAMP / tumor necrosis factor-mediated signaling pathway / Regulation of PTEN localization / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / positive regulation of protein ubiquitination / TNFR2 non-canonical NF-kB pathway / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / placenta development / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / regulation of cell population proliferation / protein-folding chaperone binding / transferase activity / regulation of inflammatory response / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / transcription coactivator activity / cell surface receptor signaling pathway / response to hypoxia / regulation of cell cycle / Ub-specific processing proteases / defense response to bacterium / apoptotic process / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function
BIRC2/BIRC3, UBA domain / 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 / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain ...BIRC2/BIRC3, UBA domain / 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 / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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
Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 1.81 Å3/Da / Density % sol: 32.4 %
Crystal grow
Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: Protein Solution (4mg/mL cIAP with 1 mM GDC-0152, 50 mM HEPES pH 7.2, 300 mM NaCl, 0.2 mM TCEP) was mixed with equal volumes of resevoir solution (0.1 M Tris-HCl pH 8.6, 0.5 M Magnesium ...Details: Protein Solution (4mg/mL cIAP with 1 mM GDC-0152, 50 mM HEPES pH 7.2, 300 mM NaCl, 0.2 mM TCEP) was mixed with equal volumes of resevoir solution (0.1 M Tris-HCl pH 8.6, 0.5 M Magnesium Formate)., VAPOR DIFFUSION, HANGING DROP, temperature 292K
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
Resolution: 1.79→31.36 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.83 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22113
736
9.8 %
RANDOM
Rwork
0.17706
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all
0.18134
7661
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obs
0.18134
7503
97.92 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 21.068 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.63 Å2
0 Å2
0 Å2
2-
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-0.98 Å2
-0 Å2
3-
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2.61 Å2
Refinement step
Cycle: LAST / Resolution: 1.79→31.36 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
746
0
2
53
801
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.02
780
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
3
X-RAY DIFFRACTION
r_angle_refined_deg
1.37
1.959
1053
X-RAY DIFFRACTION
r_angle_other_deg
1.023
3
9
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.15
5
86
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.199
23.077
39
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.072
15
112
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.882
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.089
0.2
99
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
618
LS refinement shell
Resolution: 1.79→1.827 Å / Total num. of bins used: 25
Rfactor
Num. reflection
% reflection
Rfree
0.296
40
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Rwork
0.209
325
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obs
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96.82 %
Refinement TLS params.
Method: refined / Origin x: -6.7745 Å / Origin y: 2.3651 Å / Origin z: -3.9479 Å
11
12
13
21
22
23
31
32
33
T
0.0282 Å2
-0.0062 Å2
0.0095 Å2
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0.0134 Å2
-0.0051 Å2
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0.009 Å2
L
2.2985 °2
-0.8087 °2
0.6958 °2
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1.496 °2
-0.6166 °2
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1.2721 °2
S
0.0037 Å °
0.0546 Å °
0.0889 Å °
0.0238 Å °
-0.0242 Å °
-0.0263 Å °
-0.0054 Å °
0.0322 Å °
0.0205 Å °
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