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- PDB-2qra: Crystal structure of XIAP BIR1 domain (P21 form) -

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Basic information

Entry
Database: PDB / ID: 2qra
TitleCrystal structure of XIAP BIR1 domain (P21 form)
ComponentsBaculoviral IAP repeat-containing protein 4
KeywordsApoptosis / Signaling protein / Zinc binding
Function / homology
Function and homology information


regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Activation of caspases through apoptosome-mediated cleavage ...regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / 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 / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of innate immune response / cysteine-type endopeptidase inhibitor activity / protein K63-linked ubiquitination / 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 / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of JNK cascade / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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. ...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 / Zinc finger RING-type profile. / Zinc finger, RING-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHANOL / E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsLin, S.-C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of the BIR1 domain of XIAP in two crystal forms
Authors: Lin, S.C. / Huang, Y. / Lo, Y.C. / Lu, M. / Wu, H.
History
DepositionJul 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_auth_seq_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_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 1.4Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Baculoviral IAP repeat-containing protein 4
C: Baculoviral IAP repeat-containing protein 4
B: Baculoviral IAP repeat-containing protein 4
A: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,08514
Polymers49,5474
Non-polymers53810
Water1,17165
1
D: Baculoviral IAP repeat-containing protein 4
C: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0898
Polymers24,7742
Non-polymers3156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Baculoviral IAP repeat-containing protein 4
A: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9976
Polymers24,7742
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.563, 72.983, 68.904
Angle α, β, γ (deg.)90.000, 95.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Baculoviral IAP repeat-containing protein 4 / X-linked inhibitor of apoptosis / XIAP / Inhibitor of apoptosis protein 3 / X-linked IAP / IAP-like ...X-linked inhibitor of apoptosis / XIAP / Inhibitor of apoptosis protein 3 / X-linked IAP / IAP-like protein / HILP


Mass: 12386.801 Da / Num. of mol.: 4 / Fragment: BIR1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC4, API3, IAP3, XIAP / Plasmid: pET-28 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K-12 / References: UniProt: P98170
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 1.85 Å3/Da / Density % sol: 33.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% ethanol, 100mM sodium citrate, 200mM Li2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 12816 / % possible obs: 97.9 % / Redundancy: 3.46 % / Rmerge(I) obs: 0.041 / Χ2: 1.067 / Net I/σ(I): 33.5
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.540.0974761.12975.3
2.54-2.590.1046491.13499.8
2.59-2.640.0916651.03199.6
2.64-2.690.0916441.11499.5
2.69-2.750.0856451.08499.8
2.75-2.820.0786401.076100
2.82-2.890.076541.078100
2.89-2.960.0636461.05599.8
2.96-3.050.066591.06599.8
3.05-3.150.0526511.108100
3.15-3.260.0496411.04499.5
3.26-3.390.0456701.01999.9
3.39-3.550.0426341.02399.4
3.55-3.730.0396611.04397.9
3.73-3.970.0366241.02798.3
3.97-4.270.0346360.9696.8
4.27-4.70.0346571.08198.6
4.7-5.380.0336551.04999.1
5.38-6.760.0346551.11299.5
6.76-300.0316541.13495.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.671 / Packing: 0.559
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral98.1 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2POI

2poi


Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1267 10.1 %random
Rwork0.196 ---
obs-12283 97.6 %-
Solvent computationBsol: 42.148 Å2
Displacement parametersBiso mean: 46.255 Å2
Baniso -1Baniso -2Baniso -3
1--0.505 Å20 Å2-7.273 Å2
2--5.149 Å20 Å2
3----4.644 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 4 83 2595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.5-2.610.33621550.2599X-RAY DIFFRACTION1368
2.61-2.750.35761520.2694X-RAY DIFFRACTION1333
2.75-2.920.28561730.2276X-RAY DIFFRACTION1371
2.92-3.150.27441550.2266X-RAY DIFFRACTION1388
3.15-3.470.27991700.2178X-RAY DIFFRACTION1378
3.47-3.970.25211380.1944X-RAY DIFFRACTION1387
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4eoh.par

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