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- PDB-5gpp: Crystal structure of zebrafish ASC PYD domain -

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Basic information

Entry
Database: PDB / ID: 5gpp
TitleCrystal structure of zebrafish ASC PYD domain
ComponentsMaltose-binding periplasmic protein,Apoptosis-associated speck-like protein containing a CARD
KeywordsIMMUNE SYSTEM / death fold / innate immune signaling pathway
Function / homology
Function and homology information


Formation of apoptosome / : / The NLRP1 inflammasome / Regulation of the apoptosome activity / Pyrin domain binding / NLRP6 inflammasome complex / Neutrophil degranulation / NLRP1 inflammasome complex / canonical inflammasome complex / NLRP3 inflammasome complex ...Formation of apoptosome / : / The NLRP1 inflammasome / Regulation of the apoptosome activity / Pyrin domain binding / NLRP6 inflammasome complex / Neutrophil degranulation / NLRP1 inflammasome complex / canonical inflammasome complex / NLRP3 inflammasome complex / pattern recognition receptor signaling pathway / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / carbohydrate transmembrane transporter activity / positive regulation of interleukin-1 beta production / positive regulation of inflammatory response / outer membrane-bounded periplasmic space / regulation of apoptotic process / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / cytoplasm
Similarity search - Function
CARD8/ASC/NALP1, CARD domain / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site ...CARD8/ASC/NALP1, CARD domain / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment 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
Similarity search - Domain/homology
alpha-maltose / ACETATE ION / Maltose/maltodextrin-binding periplasmic protein / Apoptosis-associated speck-like protein containing a CARD
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Danio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJin, T. / Li, Y.
CitationJournal: FEBS J. / Year: 2018
Title: Functional and structural characterization of zebrafish ASC.
Authors: Li, Y. / Huang, Y. / Cao, X. / Yin, X. / Jin, X. / Liu, S. / Jiang, J. / Jiang, W. / Xiao, T.S. / Zhou, R. / Cai, G. / Hu, B. / Jin, T.
History
DepositionAug 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_assembly_gen / struct_asym / struct_conn / 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.pdbx_formal_charge / _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.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Apoptosis-associated speck-like protein containing a CARD
B: Maltose-binding periplasmic protein,Apoptosis-associated speck-like protein containing a CARD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,21715
Polymers102,6982
Non-polymers1,51913
Water10,016556
1
A: Maltose-binding periplasmic protein,Apoptosis-associated speck-like protein containing a CARD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1208
Polymers51,3491
Non-polymers7717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area22170 Å2
MethodPISA
2
B: Maltose-binding periplasmic protein,Apoptosis-associated speck-like protein containing a CARD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0987
Polymers51,3491
Non-polymers7496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.310, 121.280, 176.870
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,Apoptosis-associated speck-like protein containing a CARD / MBP / MMBP / Maltodextrin-binding protein / PYD and CARD domain-containing protein


Mass: 51349.145 Da / Num. of mol.: 2 / Fragment: UNP residues 27-384,UNP residues 3-88 / Mutation: D83A,K84A,E173A,N174A,K240A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Danio rerio (zebrafish)
Strain: O157:H7 / Gene: malE, pycard
Production host: Bacteria Latreille et al. 1825 (Bacteria stick insect)
References: UniProt: P0AEY0, UniProt: Q9I9N6
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 20% PEG2000MME, 0.1 M NaAcO

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0331 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 493629 / % possible obs: 99.5 % / Redundancy: 6.5 % / Net I/σ(I): 15.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.255 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.34
RfactorNum. reflection% reflection
Rfree0.2517 3808 2.65 %
Rwork0.2013 --
obs0.2026 143867 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→47.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7116 0 95 556 7767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127388
X-RAY DIFFRACTIONf_angle_d1.08910024
X-RAY DIFFRACTIONf_dihedral_angle_d14.3274432
X-RAY DIFFRACTIONf_chiral_restr0.0561117
X-RAY DIFFRACTIONf_plane_restr0.0061297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9971-2.02240.42721310.43224634X-RAY DIFFRACTION89
2.0224-2.0490.37281450.36375278X-RAY DIFFRACTION100
2.049-2.07710.31511370.3265125X-RAY DIFFRACTION100
2.0771-2.10680.31751450.28965204X-RAY DIFFRACTION100
2.1068-2.13820.31511420.29025292X-RAY DIFFRACTION100
2.1382-2.17160.33251370.27695152X-RAY DIFFRACTION100
2.1716-2.20720.33341410.27125257X-RAY DIFFRACTION100
2.2072-2.24530.29251410.25845225X-RAY DIFFRACTION100
2.2453-2.28610.28651420.24975159X-RAY DIFFRACTION100
2.2861-2.33010.3251390.24815302X-RAY DIFFRACTION100
2.3301-2.37770.28371410.22765162X-RAY DIFFRACTION100
2.3777-2.42930.27691390.23125219X-RAY DIFFRACTION100
2.4293-2.48590.27831420.23035211X-RAY DIFFRACTION100
2.4859-2.5480.3231430.22395207X-RAY DIFFRACTION100
2.548-2.61690.32171400.22355195X-RAY DIFFRACTION100
2.6169-2.69390.32611450.22115298X-RAY DIFFRACTION100
2.6939-2.78080.26051420.21115116X-RAY DIFFRACTION100
2.7808-2.88020.26221450.21255252X-RAY DIFFRACTION100
2.8802-2.99550.2731400.21135205X-RAY DIFFRACTION100
2.9955-3.13180.25841390.21235171X-RAY DIFFRACTION100
3.1318-3.29690.26941440.20795230X-RAY DIFFRACTION100
3.2969-3.50340.23091380.19935201X-RAY DIFFRACTION100
3.5034-3.77380.21851450.17495215X-RAY DIFFRACTION100
3.7738-4.15340.21481380.15295154X-RAY DIFFRACTION99
4.1534-4.75390.19261450.14695219X-RAY DIFFRACTION99
4.7539-5.98750.23151320.1535193X-RAY DIFFRACTION99
5.9875-47.26810.17211500.16975183X-RAY DIFFRACTION99

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