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- PDB-2uvl: Human BIR3 domain of Baculoviral Inhibitor of Apoptosis Repeat- C... -

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Basic information

Entry
Database: PDB / ID: 2uvl
TitleHuman BIR3 domain of Baculoviral Inhibitor of Apoptosis Repeat- Containing 3 (BIRC3)
ComponentsBACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 3
KeywordsMETAL BINDING PROTEIN / CHROMOSOMAL REARRANGEMENT / METAL-BINDING PROTEIN / POLYMORPHISM / METAL-BINDING / FOCAL ADHESION / ZINC / APOPTOSIS / ZINC-FINGER / ZINC FINGER
Function / homology
Function and homology information


regulation of cysteine-type endopeptidase activity / regulation of RIG-I signaling pathway / 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 / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway / regulation of innate immune response ...regulation of cysteine-type endopeptidase activity / regulation of RIG-I signaling pathway / 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 / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway / regulation of innate immune response / non-canonical NF-kappaB signal transduction / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of inflammatory response / transferase activity / spermatogenesis / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / regulation of cell cycle / Ub-specific processing proteases / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / 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 ...: / 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 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsMoche, M. / Lehtio, L. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Moche, M. / Lehtio, L. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Upsten, M. / Van Den Berg, S. / Weigelt, J. / Nordlund, P.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structures of Bir Domains from Human Naip and Ciap2.
Authors: Herman, M.D. / Moche, M. / Flodin, S. / Welin, M. / Tresaugues, L. / Johansson, I. / Nilsson, M. / Nordlund, P. / Nyman, T.
History
DepositionMar 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 4, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 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_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_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 3
B: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4645
Polymers22,2412
Non-polymers2233
Water1,856103
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-4 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.410, 53.720, 85.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 3 / HUMAN BACULOVIRAL IAP REPEAT-CONTAINING 3 / INHIBITOR OF APOPTOSIS PROTEIN 1 / HIAP1 / HIAP-1 / C- ...HUMAN BACULOVIRAL IAP REPEAT-CONTAINING 3 / INHIBITOR OF APOPTOSIS PROTEIN 1 / HIAP1 / HIAP-1 / C-IAP2 / TNFR2-TRAF-SIGNALING COMPLEX PROTEIN 1 / IAP HOMOLOG C / APOPTOSIS INHIBITOR 2 / API2 / RING FINGER PROTEIN 49


Mass: 11120.550 Da / Num. of mol.: 2 / Fragment: BIR3 DOMAIN, RESIDUES 244-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13489
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.43 Å3/Da / Density % sol: 49.04 %
Crystal growDetails: 16% PEG 8000 40MM KPO4 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97845
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2006 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 18069 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.9 / % possible all: 81.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0032refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OXN

1oxn


Resolution: 1.91→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.488 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 925 5.1 %RANDOM
Rwork0.202 ---
obs0.204 17150 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.06 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.91→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 8 103 1656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221612
X-RAY DIFFRACTIONr_bond_other_d0.0010.021116
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.9072184
X-RAY DIFFRACTIONr_angle_other_deg0.83932675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0465191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22323.09584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29715252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6881512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02381
X-RAY DIFFRACTIONr_nbd_refined0.2050.2335
X-RAY DIFFRACTIONr_nbd_other0.190.21144
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2815
X-RAY DIFFRACTIONr_nbtor_other0.0830.2787
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.60321224
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.86731531
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3574819
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1675653
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 69
Rwork0.271 1051

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