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- PDB-3kat: Crystal Structure of the CARD domain of the human NLRP1 protein, ... -

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Basic information

Entry
Database: PDB / ID: 3kat
TitleCrystal Structure of the CARD domain of the human NLRP1 protein, Northeast Structural Genomics Consortium Target HR3486E
ComponentsNACHT, LRR and PYD domains-containing protein 1
KeywordsAPOPTOSIS / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Alternative splicing / ATP-binding / Cytoplasm / Leucine-rich repeat / Nucleotide-binding / Nucleus / Polymorphism
Function / homology
Function and homology information


NLRP1 inflammasome complex assembly / NLRP1 inflammasome complex / The NLRP1 inflammasome / NLRP3 inflammasome complex / self proteolysis / cysteine-type endopeptidase activator activity / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / cellular response to UV-B ...NLRP1 inflammasome complex assembly / NLRP1 inflammasome complex / The NLRP1 inflammasome / NLRP3 inflammasome complex / self proteolysis / cysteine-type endopeptidase activator activity / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / cellular response to UV-B / pattern recognition receptor activity / pyroptotic inflammatory response / response to muramyl dipeptide / signaling adaptor activity / antiviral innate immune response / activation of innate immune response / intrinsic apoptotic signaling pathway / positive regulation of interleukin-1 beta production / molecular condensate scaffold activity / protein homooligomerization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / positive regulation of inflammatory response / peptidase activity / double-stranded RNA binding / double-stranded DNA binding / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / defense response to virus / defense response to bacterium / inflammatory response / protein domain specific binding / apoptotic process / nucleolus / enzyme binding / signal transduction / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
FIIND domain / Function to find / UPA-FIIND domain / FIIND domain profile. / CARD8/ASC/NALP1, CARD domain / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain ...FIIND domain / Function to find / UPA-FIIND domain / FIIND domain profile. / CARD8/ASC/NALP1, CARD domain / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain / NACHT nucleoside triphosphatase / NACHT domain / DAPIN domain profile. / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Leucine Rich Repeat / Death-like domain superfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NACHT, LRR and PYD domains-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsForouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. ...Forouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target HR3486E
Authors: Forouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: NACHT, LRR and PYD domains-containing protein 1


Theoretical massNumber of molelcules
Total (without water)12,7331
Polymers12,7331
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NACHT, LRR and PYD domains-containing protein 1

A: NACHT, LRR and PYD domains-containing protein 1


Theoretical massNumber of molelcules
Total (without water)25,4662
Polymers25,4662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area690 Å2
ΔGint-9 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.708, 40.708, 160.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Detailslight scattering data suggest monomer.

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Components

#1: Protein NACHT, LRR and PYD domains-containing protein 1 / Death effector filament-forming ced-4-like apoptosis protein / Nucleotide-binding domain and ...Death effector filament-forming ced-4-like apoptosis protein / Nucleotide-binding domain and caspase recruitment domain / Caspase recruitment domain-containing protein 7


Mass: 12733.026 Da / Num. of mol.: 1 / Fragment: CARD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARD7, DEFCAP, KIAA0926, NAC, NALP1, NLRP1 / Plasmid: pET 14-15C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9C000
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 18% PEG3350 and 150 mM sodium formate., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97882 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97882 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 4726 / Num. obs: 3795 / % possible obs: 80.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 43.4 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.063 / Net I/σ(I): 18.01
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 3.79 / Num. unique all: 462 / Rsym value: 0.198 / % possible all: 54.9

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Processing

Software
NameVersionClassificationNB
CNS1.2 & XtalViewrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXthen SOLVE/RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 3.1→19.97 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 196886.016 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 176 4.7 %RANDOM
Rwork0.202 ---
obs-3749 80.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.595 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 58.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20 Å20 Å2
2--2.18 Å20 Å2
3----4.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms707 0 0 0 707
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_improper_angle_d0.66
LS refinement shellResolution: 3.1→3.21 Å / Rfactor Rfree error: 0.102 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.395 15 6 %
Rwork0.331 237 -
obs-252 53.8 %

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