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- PDB-3m1d: Structure of BIR1 from cIAP1 -

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Basic information

Entry
Database: PDB / ID: 3m1d
TitleStructure of BIR1 from cIAP1
ComponentsBaculoviral IAP repeat-containing protein 2
KeywordsMETAL BINDING PROTEIN / BIR / IAP / Apoptosis / Zinc-finger
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 / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / positive regulation of protein K63-linked ubiquitination / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway ...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 / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / 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 / regulation of reactive oxygen species metabolic process / positive regulation of protein monoubiquitination / TNFR1-induced proapoptotic signaling / non-canonical NF-kappaB signal transduction / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway / regulation of innate immune response / regulation of cell differentiation / Apoptotic cleavage of cellular proteins / necroptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / response to cAMP / 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 / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / RING-type E3 ubiquitin transferase / placenta development / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of cell population proliferation / protein-folding chaperone binding / regulation of inflammatory response / transferase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of 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 / protein-containing complex binding / negative regulation of apoptotic process / apoptotic process / 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. / BIR repeat / Inhibitor of Apoptosis domain ...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. / 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
Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMace, P.D. / Day, C.L.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Asymmetric recruitment of cIAPs by TRAF2
Authors: Mace, P.D. / Smits, C. / Vaux, D.L. / Silke, J. / Day, C.L.
History
DepositionMar 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 2
B: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1274
Polymers18,9962
Non-polymers1312
Water1,56787
1
A: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5632
Polymers9,4981
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5632
Polymers9,4981
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.180, 59.180, 199.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-134-

HOH

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Components

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


Mass: 9497.891 Da / Num. of mol.: 2 / Fragment: BIR1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGex6p3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13490
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1% PEG 4000, 0.1M LiSO4, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 12496 / Num. obs: 12496 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 30.73 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.6
Reflection shellHighest resolution: 2 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 2.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2poi

2poi


Resolution: 2→19.399 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.854 / SU ML: 0.18 / σ(F): 1.38 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 606 4.86 %
Rwork0.1962 --
obs0.1979 12470 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.461 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 94.58 Å2 / Biso mean: 35.76 Å2 / Biso min: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.203 Å20 Å20 Å2
2---0.203 Å2-0 Å2
3---0.406 Å2
Refinement stepCycle: LAST / Resolution: 2→19.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 2 87 1325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061284
X-RAY DIFFRACTIONf_angle_d0.9331734
X-RAY DIFFRACTIONf_chiral_restr0.056181
X-RAY DIFFRACTIONf_plane_restr0.004219
X-RAY DIFFRACTIONf_dihedral_angle_d14.84458
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.2010.2821520.2328923044
2.201-2.520.271570.19328963053
2.52-3.1720.2331580.18529453103
3.172-19.40.211390.19331313270

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