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- PDB-3t6p: IAP antagonist-induced conformational change in cIAP1 promotes E3... -

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Basic information

Entry
Database: PDB / ID: 3t6p
TitleIAP antagonist-induced conformational change in cIAP1 promotes E3 ligase activation via dimerization
ComponentsBaculoviral IAP repeat-containing protein 2
KeywordsAPOPTOSIS / RING / BIR / CARD / UBA / E3 / ubiquitin ligase / SMAC/DIABLO / ubiquitin / caspase / IAP family / SMAC mimetic
Function / homology
Function and homology information


negative regulation of ripoptosome assembly involved in necroptotic process / FBXO family protein binding / positive regulation of protein monoubiquitination / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of protein K63-linked ubiquitination ...negative regulation of ripoptosome assembly involved in necroptotic process / FBXO family protein binding / positive regulation of protein monoubiquitination / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of protein K63-linked ubiquitination / CD40 receptor complex / XY body / negative regulation of necroptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / non-canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of reactive oxygen species metabolic process / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / necroptotic process / regulation of cell differentiation / canonical NF-kappaB signal transduction / response to cAMP / tumor necrosis factor-mediated signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / positive regulation of protein ubiquitination / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / placenta development / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / ubiquitin binding / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of cell population proliferation / protein-folding chaperone binding / transferase activity / regulation of inflammatory response / response to ethanol / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / response to hypoxia / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / Ub-specific processing proteases / regulation of cell cycle / apoptotic process / negative regulation of apoptotic process / protein-containing complex binding / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
BIRC2/BIRC3, 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. / Death Domain, Fas / Death Domain, Fas ...BIRC2/BIRC3, 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. / Death Domain, Fas / Death Domain, Fas / Ubiquitin-associated (UBA) domain / 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 / Helicase, Ruva Protein; domain 3 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.897 Å
AuthorsDueber, E.C. / Schoeffler, A.J. / Lingel, A. / Elliott, M. / Fedorova, A.V. / Giannetti, A.M. / Zobel, K. / Maurer, B. / Varfolomeev, E. / Wu, P. ...Dueber, E.C. / Schoeffler, A.J. / Lingel, A. / Elliott, M. / Fedorova, A.V. / Giannetti, A.M. / Zobel, K. / Maurer, B. / Varfolomeev, E. / Wu, P. / Wallweber, H. / Hymowitz, S. / Deshayes, K. / Vucic, D. / Fairbrother, W.J.
CitationJournal: Science / Year: 2011
Title: Antagonists induce a conformational change in cIAP1 that promotes autoubiquitination.
Authors: Dueber, E.C. / Schoeffler, A.J. / Lingel, A. / Elliott, J.M. / Fedorova, A.V. / Giannetti, A.M. / Zobel, K. / Maurer, B. / Varfolomeev, E. / Wu, P. / Wallweber, H.J. / Hymowitz, S.G. / ...Authors: Dueber, E.C. / Schoeffler, A.J. / Lingel, A. / Elliott, J.M. / Fedorova, A.V. / Giannetti, A.M. / Zobel, K. / Maurer, B. / Varfolomeev, E. / Wu, P. / Wallweber, H.J. / Hymowitz, S.G. / Deshayes, K. / Vucic, D. / Fairbrother, W.J.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4734
Polymers39,2771
Non-polymers1963
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.971, 85.432, 106.484
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Baculoviral IAP repeat-containing protein 2 / C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / IAP-2 / hIAP-2 / hIAP2 / RING finger ...C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / IAP-2 / hIAP-2 / hIAP2 / RING finger protein 48 / TNFR2-TRAF-signaling complex protein 2


Mass: 39277.156 Da / Num. of mol.: 1
Fragment: BIR3-RING, UNP residues 265-618 with a deletion of S363-D372
Mutation: F378Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: API1, BIRC2, IAP2, MIHB, RNF48 / Plasmid: pET52b / Production host: Escherichia coli (E. coli) / References: UniProt: Q13490
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 200 mM lithium chloride, 100 mM Tris pH 8, 20% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionRedundancy: 4.9 % / Av σ(I) over netI: 23.74 / Number: 164946 / Rmerge(I) obs: 0.081 / Χ2: 1.06 / D res high: 2.2 Å / D res low: 70 Å / Num. obs: 33419 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.747095.610.0561.0355.2
3.764.749810.0671.0485.1
3.293.7698.610.0691.0835.1
2.993.299910.081.0995
2.772.999910.0971.0425
2.612.7799.410.1171.0854.9
2.482.6199.310.141.0874.9
2.372.4899.410.1771.0884.8
2.282.3799.510.2161.0474.8
2.22.2899.610.2811.0184.6
ReflectionResolution: 1.897→50 Å / Num. obs: 27890 / % possible obs: 99.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.058 / Χ2: 1.044 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.897-1.974.80.53227291199.9
1.97-2.054.90.36427201.034198.6
2.05-2.144.90.26127161.064199
2.14-2.254.90.18527551.039199.3
2.25-2.394.90.14527651.035199.5
2.39-2.584.90.10927471.068199.7
2.58-2.844.90.08927991.044199.8
2.84-3.254.90.06928131.043199.8
3.25-4.094.80.04528541.0231100
4.09-504.50.03529921.093199.3

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.2 Å / D res low: 66.64 Å / FOM : 0.427 / FOM acentric: 0.479 / FOM centric: 0.171 / Reflection: 17676 / Reflection acentric: 14896 / Reflection centric: 2263
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.13-12.790.4320.5660.18818011664
7.48-9.130.4990.6290.16521115259
6.49-7.480.5930.6940.26925319360
5.81-6.490.5490.6460.21528922465
5.31-5.810.5420.6380.18330123761
4.91-5.310.510.5850.18333327160
4.6-4.910.430.5010.1336529668
4.34-4.60.4080.4680.11237631362
4.11-4.340.4260.4860.1340433764
3.92-4.110.4330.5010.08542735866
3.76-3.920.4260.4810.13244337468
3.61-3.760.4080.4610.11146139266
3.48-3.610.4560.5070.12146340260
3.36-3.480.4620.5160.15549842473
3.26-3.360.4440.4890.12851244863
3.16-3.260.4590.5010.17751945365
3.07-3.160.4770.5270.18154546969
2.99-3.070.4720.5220.14356349166
2.91-2.990.4790.5330.1554347064
2.84-2.910.4780.5270.15958951368
2.78-2.840.4510.4940.17159952167
2.72-2.780.4580.510.17460652066
2.66-2.720.4190.4690.19262552274
2.61-2.660.4430.4830.17563956164
2.55-2.610.430.4770.17463954767
2.51-2.550.4220.4660.17364455467
2.46-2.510.4230.4670.18667157666
2.42-2.460.3920.4350.16368258665
2.38-2.420.3860.4220.26266256553
2.34-2.380.3740.4220.16870258671
2.3-2.340.3670.4030.21272861968
2.27-2.30.3610.3970.23468958454
2.23-2.270.3130.3460.16670159466
2.2-2.230.3070.3410.21770857868

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.897→32.778 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8313 / SU ML: 0.25 / σ(F): 0 / Phase error: 23.29 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 1344 4.98 %Random
Rwork0.1907 ---
obs0.1928 26966 95.58 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.523 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 134.06 Å2 / Biso mean: 40.4696 Å2 / Biso min: 20.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.7496 Å20 Å2-0 Å2
2--6.1409 Å20 Å2
3----4.3913 Å2
Refinement stepCycle: LAST / Resolution: 1.897→32.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 3 184 2822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062705
X-RAY DIFFRACTIONf_angle_d0.9543652
X-RAY DIFFRACTIONf_chiral_restr0.068411
X-RAY DIFFRACTIONf_plane_restr0.004474
X-RAY DIFFRACTIONf_dihedral_angle_d13.4841052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8971-1.96490.33441120.26162081219380
1.9649-2.04360.28591240.23172411253591
2.0436-2.13660.2781340.19982492262694
2.1366-2.24920.24781310.19292549268096
2.2492-2.39010.28051310.19462573270497
2.3901-2.57460.26281380.20072623276199
2.5746-2.83350.27981380.20652638277699
2.8335-3.24320.24871420.208926872829100
3.2432-4.08490.21811440.19127262870100
4.0849-32.78310.18561500.16382842299299
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)
14.76411.2473-0.42581.7345-0.41623.2899-0.04930.201-0.0082-0.02720.10070.02170.0006-0.2131-00.1510.03120.01480.14350.00850.15725.219965.838179.3491
21.86220.96210.55151.5335-0.75461.81150.0794-0.175-0.2025-0.0854-0.0403-0.19620.19030.0482-00.3326-0.00880.01490.28820.01650.289720.41254.74592.6357
30.11530.17190.08080.24940.11860.0704-0.26020.7499-0.25660.0675-0.17240.81670.29480.2506-00.4997-0.0818-0.02260.3293-0.01640.34788.503641.603787.1574
40.16620.0966-0.15070.30870.06740.2265-0.0411-0.4145-0.4460.2259-0.15860.15850.2553-0.385900.31610.0276-0.00010.4461-0.0020.267316.893734.557770.6423
51.14920.58290.42661.75720.29121.26480.05670.1021-0.0493-0.2853-0.0399-0.00760.12220.0836-00.28760.03450.03580.2616-0.00910.270815.494639.929355.5717
60.4473-0.0595-0.28280.3443-0.22430.3795-0.21990.5967-0.437-0.4426-0.4712-0.6430.14380.759900.32110.08510.050.4510.01590.39828.397230.875259.3313
7-0.0002-0.0013-0.00010.03550.01970.00830.0551-0.14940.8678-0.4752-0.2534-0.665-0.30050.1321-00.4418-0.0260.01140.7501-0.00480.767532.018851.261963.017
82.2846-0.15850.49312.1861.92552.4135-0.1502-0.08430.1832-0.08680.00170.151-0.03630.062400.25020.00940.00210.2209-0.00440.252711.844154.395765.5001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 264:362)A264 - 362
2X-RAY DIFFRACTION2(chain A and resid 386:435)A386 - 435
3X-RAY DIFFRACTION3(chain A and resid 436:450)A436 - 450
4X-RAY DIFFRACTION4(chain A and resid 451:463)A451 - 463
5X-RAY DIFFRACTION5(chain A and resid 464:527)A464 - 527
6X-RAY DIFFRACTION6(chain A and resid 528:544)A528 - 544
7X-RAY DIFFRACTION7(chain A and resid 545:555)A545 - 555
8X-RAY DIFFRACTION8(chain A and resid 556:616)A556 - 616

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