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- PDB-6ki0: Crystal Structure of Human ASC-CARD -

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Basic information

Entry
Database: PDB / ID: 6ki0
TitleCrystal Structure of Human ASC-CARD
ComponentsMaltose/maltodextrin-binding periplasmic protein,Apoptosis-associated speck-like protein containing a CARD
KeywordsIMMUNE SYSTEM / Death domain fold
Function / homology
Function and homology information


Pyrin domain binding / NLRP6 inflammasome complex / myosin I binding / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / myeloid dendritic cell activation involved in immune response / regulation of intrinsic apoptotic signaling pathway / myeloid dendritic cell activation / IkappaB kinase complex / The AIM2 inflammasome / macropinocytosis ...Pyrin domain binding / NLRP6 inflammasome complex / myosin I binding / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / myeloid dendritic cell activation involved in immune response / regulation of intrinsic apoptotic signaling pathway / myeloid dendritic cell activation / IkappaB kinase complex / The AIM2 inflammasome / macropinocytosis / AIM2 inflammasome complex / icosanoid biosynthetic process / interleukin-6 receptor binding / NLRP1 inflammasome complex / canonical inflammasome complex / NLRP3 inflammasome complex assembly / positive regulation of adaptive immune response / BMP receptor binding / NLRP3 inflammasome complex / negative regulation of protein serine/threonine kinase activity / negative regulation of interferon-beta production / CLEC7A/inflammasome pathway / positive regulation of cysteine-type endopeptidase activity / regulation of tumor necrosis factor-mediated signaling pathway / osmosensory signaling pathway / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of macrophage cytokine production / pattern recognition receptor signaling pathway / positive regulation of actin filament polymerization / detection of maltose stimulus / negative regulation of NF-kappaB transcription factor activity / maltose transport complex / tropomyosin binding / positive regulation of activated T cell proliferation / pyroptotic inflammatory response / carbohydrate transport / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of release of cytochrome c from mitochondria / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-10 production / The NLRP3 inflammasome / intrinsic apoptotic signaling pathway by p53 class mediator / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / negative regulation of cytokine production involved in inflammatory response / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of T cell migration / cellular response to interleukin-1 / Purinergic signaling in leishmaniasis infection / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of chemokine production / negative regulation of canonical NF-kappaB signal transduction / positive regulation of phagocytosis / positive regulation of defense response to virus by host / tumor necrosis factor-mediated signaling pathway / activation of innate immune response / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / positive regulation of interleukin-1 beta production / regulation of autophagy / positive regulation of interleukin-8 production / positive regulation of JNK cascade / regulation of protein stability / protein homooligomerization / positive regulation of DNA-binding transcription factor activity / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / activation of cysteine-type endopeptidase activity involved in apoptotic process / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / azurophil granule lumen / positive regulation of type II interferon production / positive regulation of T cell activation / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / outer membrane-bounded periplasmic space / cellular response to lipopolysaccharide / secretory granule lumen / defense response to Gram-negative bacterium / microtubule / defense response to virus / protease binding / transmembrane transporter binding / periplasmic space / positive regulation of ERK1 and ERK2 cascade / protein dimerization activity / defense response to Gram-positive bacterium / positive regulation of apoptotic process / Golgi membrane / innate immune response / neuronal cell body / apoptotic process / DNA damage response / Neutrophil degranulation / nucleolus / enzyme binding / endoplasmic reticulum
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-maltotriose / Maltose/maltodextrin-binding periplasmic protein / Apoptosis-associated speck-like protein containing a CARD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXu, Z.H. / Jin, T.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81872110 China
National Natural Science Foundation of China81272881 China
CitationJournal: Cell Death Dis / Year: 2021
Title: Homotypic CARD-CARD interaction is critical for the activation of NLRP1 inflammasome.
Authors: Xu, Z. / Zhou, Y. / Liu, M. / Ma, H. / Sun, L. / Zahid, A. / Chen, Y. / Zhou, R. / Cao, M. / Wu, D. / Zhao, W. / Li, B. / Jin, T.
History
DepositionJul 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 3, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_abbrev ..._chem_comp.pdbx_synonyms / _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 2.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,2787
Polymers102,9812
Non-polymers1,2975
Water4,846269
1
A: Maltose/maltodextrin-binding periplasmic protein,Apoptosis-associated speck-like protein containing a CARD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1874
Polymers51,4901
Non-polymers6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-17 kcal/mol
Surface area19130 Å2
MethodPISA
2
B: Maltose/maltodextrin-binding periplasmic protein,Apoptosis-associated speck-like protein containing a CARD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0913
Polymers51,4901
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.760, 56.020, 146.930
Angle α, β, γ (deg.)90.000, 106.580, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 1 through 458)
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 458 / Label seq-ID: 2 - 459

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 1 through 458)AA
2chain BBB

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Apoptosis-associated speck-like protein containing a CARD / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / hASC / Caspase recruitment ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / hASC / Caspase recruitment domain-containing protein 5 / PYD and CARD domain-containing protein / Target of methylation-induced silencing 1


Mass: 51490.250 Da / Num. of mol.: 2 / Fragment: caspase recruitment domain / Mutation: D108A,K109A,E198A,N199A,K265A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, PYCARD, ASC, CARD5, TMS1 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEX9, UniProt: Q9ULZ3
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.42 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.80 M Ammonium Sulfate, 0.1 M HEPES 7.0

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Data collection

DiffractionMean temperature: 190 K / Ambient temp details: Liquid nitrogen steam / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 92520 / % possible obs: 99.2 % / Redundancy: 3.75 % / CC1/2: 0.998 / Rrim(I) all: 0.082 / Net I/σ(I): 12.21
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.78 % / Mean I/σ(I) obs: 1.76 / Num. unique obs: 14772 / CC1/2: 0.703 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VD8

3vd8


Resolution: 2→47.116 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.84
RfactorNum. reflection% reflection
Rfree0.2515 4616 5 %
Rwork0.2203 --
obs0.2218 92283 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.29 Å2 / Biso mean: 57.4627 Å2 / Biso min: 20.84 Å2
Refinement stepCycle: final / Resolution: 2→47.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7127 0 83 269 7479
Biso mean--54.24 46.82 -
Num. residues----917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057383
X-RAY DIFFRACTIONf_angle_d0.99410052
X-RAY DIFFRACTIONf_chiral_restr0.0521123
X-RAY DIFFRACTIONf_plane_restr0.0051284
X-RAY DIFFRACTIONf_dihedral_angle_d5.9734354
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4194X-RAY DIFFRACTION8.875TORSIONAL
12B4194X-RAY DIFFRACTION8.875TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02280.44631480.42772806295497
2.0228-2.04660.41711560.376629553111100
2.0466-2.07150.36521540.359929223076100
2.0715-2.09770.34121540.355729323086100
2.0977-2.12540.38371530.335628933046100
2.1254-2.15450.38231560.331929713127100
2.1545-2.18520.38331510.310128553006100
2.1852-2.21790.36491530.30862919307299
2.2179-2.25250.38981460.40582791293793
2.2525-2.28940.33981500.33242821297199
2.2894-2.32890.28151540.265929443098100
2.3289-2.37130.27891550.266429333088100
2.3713-2.41690.30861540.253629293083100
2.4169-2.46620.28731540.250929193073100
2.4662-2.51980.26941550.254929343089100
2.5198-2.57840.26781540.249129543108100
2.5784-2.64290.28231560.240829413097100
2.6429-2.71440.27631540.245329243078100
2.7144-2.79420.31221560.241929713127100
2.7942-2.88440.2911540.246129173071100
2.8844-2.98750.26741540.242229383092100
2.9875-3.10710.281560.233429523108100
3.1071-3.24850.25081540.231529313085100
3.2485-3.41970.2821550.22212952310799
3.4197-3.63390.25571530.19712920307399
3.6339-3.91430.1921540.18392925307998
3.9143-4.3080.20671580.17222988314699
4.308-4.93080.19971550.15922947310299
4.9308-6.210.20271580.18472996315499
6.21-47.1160.1971520.17822887303993

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