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- PDB-4ifp: X-ray Crystal Structure of Human NLRP1 CARD Domain -

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Basic information

Entry
Database: PDB / ID: 4ifp
TitleX-ray Crystal Structure of Human NLRP1 CARD Domain
ComponentsMaltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 1
KeywordsIMMUNE SYSTEM / Death fold superfamily / inflammasome / signal transduction / innate immune system
Function / homology
Function and homology information


NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / The NLRP1 inflammasome / self proteolysis / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor signaling pathway / pattern recognition receptor activity / cellular response to UV-B ...NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / The NLRP1 inflammasome / self proteolysis / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor signaling pathway / pattern recognition receptor activity / cellular response to UV-B / detection of maltose stimulus / maltose transport complex / pyroptotic inflammatory response / carbohydrate transport / cysteine-type endopeptidase activator activity involved in apoptotic process / response to muramyl dipeptide / antiviral innate immune response / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / signaling adaptor activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein homooligomerization / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / : / double-stranded RNA binding / peptidase activity / regulation of inflammatory response / outer membrane-bounded periplasmic space / double-stranded DNA binding / regulation of apoptotic process / neuron apoptotic process / defense response to virus / periplasmic space / defense response to bacterium / protein domain specific binding / apoptotic process / DNA damage response / nucleolus / enzyme binding / signal transduction / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
FIIND domain / Function to find / 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 / DAPIN domain profile. ...FIIND domain / Function to find / 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 / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Leucine Rich Repeat / 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 / Leucine-rich repeat profile. / Death-like domain superfamily / Leucine-rich repeat / Periplasmic binding protein-like II / Leucine-rich repeat domain superfamily / D-Maltodextrin-Binding Protein; domain 2 / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / MALONATE ION / Maltose/maltodextrin-binding periplasmic protein / NACHT, LRR and PYD domains-containing protein 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9948 Å
AuthorsJin, T. / Curry, J. / Smith, P. / Jiang, J. / Xiao, T.
CitationJournal: Proteins / Year: 2013
Title: Structure of the NLRP1 caspase recruitment domain suggests potential mechanisms for its association with procaspase-1.
Authors: Jin, T. / Curry, J. / Smith, P. / Jiang, J. / Xiao, T.S.
History
DepositionDec 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 1.3Nov 15, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _software.name
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.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 2.1Sep 20, 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,NACHT, LRR and PYD domains-containing protein 1
B: Maltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 1
C: Maltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,4239
Polymers155,0903
Non-polymers1,3336
Water27,7071538
1
A: Maltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1413
Polymers51,6971
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1413
Polymers51,6971
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Maltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1413
Polymers51,6971
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)187.011, 108.772, 121.266
Angle α, β, γ (deg.)90.00, 120.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 51696.559 Da / Num. of mol.: 3 / Fragment: NLRP1-CARD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Strain: K12
Gene: malE, b4034, JW3994, NLRP1, CARD7, DEFCAP, KIAA0926, NAC, NALP1
Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P0AEX9, UniProt: Q9C000
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1538 / 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: 3.41 Å3/Da / Density % sol: 63.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.4 M Malonate, 100 mM HEPES 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97 Å
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9948→50 Å / Num. all: 140326 / Num. obs: 139624 / % possible obs: 99.5 % / Observed criterion σ(F): 1.65 / Observed criterion σ(I): 2.72 / Redundancy: 4.2 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9948→2.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.72 / Num. unique all: 6953 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_1217)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VD8 and 3KAT

3vd8

3kat


Resolution: 1.9948→37.492 Å / SU ML: 0.19 / Cross valid method: Molprobity / σ(F): 1.34 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 7015 5.02 %random
Rwork0.1701 ---
obs0.1719 139608 98.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9948→37.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10713 0 90 1538 12341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711140
X-RAY DIFFRACTIONf_angle_d1.05515147
X-RAY DIFFRACTIONf_dihedral_angle_d13.6664070
X-RAY DIFFRACTIONf_chiral_restr0.0721674
X-RAY DIFFRACTIONf_plane_restr0.0041955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9948-2.01740.27382020.24313372X-RAY DIFFRACTION76
2.0174-2.04120.28512290.23884489X-RAY DIFFRACTION100
2.0412-2.06610.2842190.23074419X-RAY DIFFRACTION100
2.0661-2.09220.29582490.21924506X-RAY DIFFRACTION100
2.0922-2.11970.26082090.20954463X-RAY DIFFRACTION100
2.1197-2.14880.2431960.21254469X-RAY DIFFRACTION100
2.1488-2.17950.28032430.2054474X-RAY DIFFRACTION100
2.1795-2.2120.26762530.20314454X-RAY DIFFRACTION100
2.212-2.24660.23872560.19134463X-RAY DIFFRACTION100
2.2466-2.28340.24322400.18864415X-RAY DIFFRACTION100
2.2834-2.32270.2642630.19384459X-RAY DIFFRACTION100
2.3227-2.3650.23472420.18984436X-RAY DIFFRACTION100
2.365-2.41050.21062180.17714532X-RAY DIFFRACTION100
2.4105-2.45960.22522500.1794419X-RAY DIFFRACTION100
2.4596-2.51310.22522490.17264462X-RAY DIFFRACTION100
2.5131-2.57160.2432460.19234461X-RAY DIFFRACTION100
2.5716-2.63590.24962450.18844482X-RAY DIFFRACTION100
2.6359-2.70710.24442230.18834471X-RAY DIFFRACTION100
2.7071-2.78670.24012500.19414452X-RAY DIFFRACTION100
2.7867-2.87670.2522420.18824444X-RAY DIFFRACTION100
2.8767-2.97940.2252320.1964486X-RAY DIFFRACTION100
2.9794-3.09870.22222260.18214521X-RAY DIFFRACTION100
3.0987-3.23960.20662280.1794447X-RAY DIFFRACTION100
3.2396-3.41030.20222330.16574500X-RAY DIFFRACTION100
3.4103-3.62380.19852340.154500X-RAY DIFFRACTION100
3.6238-3.90330.18222390.14184489X-RAY DIFFRACTION100
3.9033-4.29570.15912410.13414496X-RAY DIFFRACTION100
4.2957-4.91610.12782150.12734538X-RAY DIFFRACTION100
4.9161-6.18920.1862430.15034493X-RAY DIFFRACTION100
6.1892-37.49830.17472000.1683981X-RAY DIFFRACTION86

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