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- PDB-3vd8: Crystal structure of human AIM2 PYD domain with MBP fusion -

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Basic information

Entry
Database: PDB / ID: 3vd8
TitleCrystal structure of human AIM2 PYD domain with MBP fusion
ComponentsMaltose-binding periplasmic protein, Interferon-inducible protein AIM2
KeywordsSUGAR BINDING PROTEIN / SIGNALING PROTEIN / MBP/PYD/DD / signal transduction / inflammasome
Function / homology
Function and homology information


pyroptosome complex assembly / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / cysteine-type endopeptidase activator activity / regulation of behavior / Cytosolic sensors of pathogen-associated DNA / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / pattern recognition receptor activity ...pyroptosome complex assembly / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / cysteine-type endopeptidase activator activity / regulation of behavior / Cytosolic sensors of pathogen-associated DNA / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / pattern recognition receptor activity / negative regulation of NF-kappaB transcription factor activity / pyroptotic inflammatory response / T cell homeostasis / carbohydrate transmembrane transporter activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / tumor necrosis factor-mediated signaling pathway / activation of innate immune response / positive regulation of interleukin-1 beta production / brain development / positive regulation of inflammatory response / neuron cellular homeostasis / cellular response to xenobiotic stimulus / positive regulation of NF-kappaB transcription factor activity / site of double-strand break / outer membrane-bounded periplasmic space / double-stranded DNA binding / defense response to virus / immune response / innate immune response / DNA damage response / mitochondrion / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / Death Domain, Fas / Death Domain, Fas / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain ...HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / Death Domain, Fas / Death Domain, Fas / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Death-like domain superfamily / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Nucleic acid-binding, OB-fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltotetraose / : / Interferon-inducible protein AIM2 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0685 Å
AuthorsJin, T.C. / Perry, A. / Smith, P. / Xiao, T.S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure of the Absent in Melanoma 2 (AIM2) Pyrin Domain Provides Insights into the Mechanisms of AIM2 Autoinhibition and Inflammasome Assembly.
Authors: Jin, T. / Perry, A. / Smith, P. / Jiang, J. / Xiao, T.S.
History
DepositionJan 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references / Structure summary
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _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_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_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_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein, Interferon-inducible protein AIM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,04510
Polymers53,9731
Non-polymers1,0719
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.599, 91.934, 100.281
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 Maltose-binding periplasmic protein, Interferon-inducible protein AIM2 / MBP / MMBP / Maltodextrin-binding protein / Absent in melanoma 2


Mass: 53973.414 Da / Num. of mol.: 1 / Fragment: PYD domain (UNP Residues 1-107) / Mutation: D82A, K83A, E172A, N173A, K239A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Strain: O157:H7 / Gene: AIM2, ECs5017, malE, MBP, Z5632 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEY0, UniProt: O14862
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% PEG3350, 0.1M Potassium Acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 7, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.068→50 Å / Num. all: 35519 / Num. obs: 35164 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Net I/σ(I): 12.36
Reflection shellResolution: 2.068→2.11 Å / Redundancy: 6 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2.24 / Num. unique all: 1704 / % possible all: 97

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_947)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OB4

3ob4


Resolution: 2.0685→38.887 Å / SU ML: 0.21 / σ(F): 0.82 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 1741 4.99 %random
Rwork0.1821 ---
obs0.1841 34906 98.33 %-
all-35519 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.696 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.233 Å20 Å20 Å2
2--0.1537 Å20 Å2
3---0.0793 Å2
Refinement stepCycle: LAST / Resolution: 2.0685→38.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 65 325 4020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033832
X-RAY DIFFRACTIONf_angle_d0.6945197
X-RAY DIFFRACTIONf_dihedral_angle_d11.3911400
X-RAY DIFFRACTIONf_chiral_restr0.05585
X-RAY DIFFRACTIONf_plane_restr0.003663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0685-2.12930.28121200.24572713X-RAY DIFFRACTION97
2.1293-2.1980.28381430.21872693X-RAY DIFFRACTION98
2.198-2.27660.25591390.20342713X-RAY DIFFRACTION98
2.2766-2.36770.2521500.19362741X-RAY DIFFRACTION98
2.3677-2.47550.23161270.18992753X-RAY DIFFRACTION99
2.4755-2.6060.23441530.19612757X-RAY DIFFRACTION99
2.606-2.76920.24041430.19812762X-RAY DIFFRACTION99
2.7692-2.98290.24461580.19632759X-RAY DIFFRACTION99
2.9829-3.2830.24461530.19362811X-RAY DIFFRACTION100
3.283-3.75770.19781410.15832809X-RAY DIFFRACTION100
3.7577-4.7330.18011700.14992838X-RAY DIFFRACTION100
4.733-38.89340.21871440.18732816X-RAY DIFFRACTION94

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