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- PDB-3e4c: Procaspase-1 zymogen domain crystal structure -

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Basic information

Entry
Database: PDB / ID: 3e4c
TitleProcaspase-1 zymogen domain crystal structure
ComponentsCaspase-1
KeywordsHYDROLASE / ZYMOGEN / CASPASE-1 / INFLAMMASOME / ICE / CASPASE / IL-1B / PROCASPASE-1 / PROCASPASE / INNATE IMMUNITY / Apoptosis / Protease / Thiol protease
Function / homology
Function and homology information


caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / The IPAF inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / The IPAF inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing / canonical inflammasome complex / positive regulation of interleukin-18 production / NLRP3 inflammasome complex / CARD domain binding / caspase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / osmosensory signaling pathway / Interleukin-37 signaling / pattern recognition receptor signaling pathway / : / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / The NLRP3 inflammasome / protein autoprocessing / protein maturation / Pyroptosis / Purinergic signaling in leishmaniasis infection / positive regulation of interleukin-1 beta production / NOD1/2 Signaling Pathway / kinase binding / cellular response to type II interferon / positive regulation of inflammatory response / cellular response to mechanical stimulus / SARS-CoV-1 activates/modulates innate immune responses / regulation of inflammatory response / cellular response to lipopolysaccharide / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / microtubule / defense response to virus / endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / nucleolus / signal transduction / protein-containing complex / proteolysis / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. ...Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsElliott, J.M. / Rouge, L. / Wiesmann, C. / Scheer, J.M.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure of procaspase-1 zymogen domain reveals insight into inflammatory caspase autoactivation
Authors: Elliott, J.M. / Rouge, L. / Wiesmann, C. / Scheer, J.M.
History
DepositionAug 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 9, 2020Group: Database references / Derived calculations / Structure summary
Category: pdbx_struct_conn_angle / struct ...pdbx_struct_conn_angle / struct / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr3_auth_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.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caspase-1
B: Caspase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6193
Polymers67,5952
Non-polymers241
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.100, 58.004, 60.120
Angle α, β, γ (deg.)105.95, 119.60, 92.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Caspase-1 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta- ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta-converting enzyme / ICE / p45 / Caspase-1 subunit p20 / Caspase-1 subunit p10


Mass: 33797.402 Da / Num. of mol.: 2
Fragment: procaspase-1 zymogen domain (UNP residues 104-404)
Mutation: C285A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: HUMAN RNA ISOLATE / Gene: CASP1, IL1BC, IL1BCE / Plasmid: pST239 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P29466, caspase-1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 7.5
Details: 0.2 M MgCl2 20% PEG 3350, pH 7.5, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9779 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 16, 2007 / Details: mirrors
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 38407 / Num. obs: 37223 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.058 / Net I/σ(I): 11.2
Reflection shellResolution: 2.05→2.12 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.414 / % possible all: 87.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RWX

1rwx


Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 14.988 / SU ML: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.212 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.Residues 287:298 have poor electron density. The electron density for residues 291:298 can be explained by these residues stemming from ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.Residues 287:298 have poor electron density. The electron density for residues 291:298 can be explained by these residues stemming from either Chain A or from Chain B. To indicate this ambiguity, residues 287:298 of Chain A and Chain B have been modeled with an occupancy of 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1861 5 %RANDOM
Rwork0.2 ---
all0.204 38566 --
obs0.204 35359 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.783 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å22.51 Å20.5 Å2
2--3.46 Å23.81 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4286 0 1 136 4423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224374
X-RAY DIFFRACTIONr_bond_other_d0.0010.023938
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9555898
X-RAY DIFFRACTIONr_angle_other_deg0.80339212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8235536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08724.059202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.20715798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6911530
X-RAY DIFFRACTIONr_chiral_restr0.080.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02874
X-RAY DIFFRACTIONr_nbd_refined0.2130.2865
X-RAY DIFFRACTIONr_nbd_other0.1870.23901
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22054
X-RAY DIFFRACTIONr_nbtor_other0.0850.22467
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2174
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.022.53487
X-RAY DIFFRACTIONr_mcbond_other0.7142.51086
X-RAY DIFFRACTIONr_mcangle_it4.88354376
X-RAY DIFFRACTIONr_scbond_it3.672.51918
X-RAY DIFFRACTIONr_scangle_it5.08451522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.054→2.096 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.382 81 -
Rwork0.269 1729 -
obs--79.35 %
Refinement TLS params.Method: refined / Origin x: -1.9642 Å / Origin y: -8.793 Å / Origin z: -3.9975 Å
111213212223313233
T-0.1236 Å2-0.0048 Å2-0.0028 Å2--0.1502 Å2-0.0446 Å2---0.141 Å2
L2.1032 °2-0.2852 °2-0.1254 °2-1.7298 °2-0.9267 °2--2.1011 °2
S0.12 Å °-0.0326 Å °0.1129 Å °0.0355 Å °-0.0922 Å °0.0203 Å °0.104 Å °0.186 Å °-0.0279 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B405 - 472
2X-RAY DIFFRACTION1A405 - 473
3X-RAY DIFFRACTION1B1
4X-RAY DIFFRACTION1B128 - 404
5X-RAY DIFFRACTION1A126 - 404

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