[English] 日本語
Yorodumi
- PDB-5mmv: Crystal structure of human Caspase-1 with 2-((2-naphthoyl)-L-valy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mmv
TitleCrystal structure of human Caspase-1 with 2-((2-naphthoyl)-L-valyl)-4-hydroxy-N-((3S)-2-hydroxy-5-oxotetrahydrofuran-3-yl)-2-azabicyclo[2.2.2]octane-3-carboxamide (Compound 1)
Components(Caspase-1) x 2
KeywordsHYDROLASE / caspase-1 / nanomolar inhibitor / inflammatory diseases / sp3 hybridization
Function / homology
Function and homology information


caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing / canonical inflammasome complex / positive regulation of interleukin-18 production / NLRP3 inflammasome complex / caspase binding / CARD domain binding / osmosensory signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / Interleukin-37 signaling / pattern recognition receptor signaling pathway / : / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / cytokine binding / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / The NLRP3 inflammasome / protein maturation / Pyroptosis / Purinergic signaling in leishmaniasis infection / positive regulation of interleukin-1 beta production / NOD1/2 Signaling Pathway / cellular response to type II interferon / kinase binding / 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 / defense response to virus / endopeptidase activity / microtubule / defense response to bacterium / cysteine-type endopeptidase activity / nucleolus / apoptotic process / signal transduction / protein-containing complex / proteolysis / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Caspase recruitment domain / Caspase-like / 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 recruitment domain / Caspase-like / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-WE0 / Caspase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBrethon, A. / Chantalat, L. / Christin, O. / Clary, L. / Fournier, J.F. / Gastreich, M. / Harris, C. / Pascau, J. / Isabet, T. / Rodeschin, V. ...Brethon, A. / Chantalat, L. / Christin, O. / Clary, L. / Fournier, J.F. / Gastreich, M. / Harris, C. / Pascau, J. / Isabet, T. / Rodeschin, V. / Thoreau, E. / Roche, D.
CitationJournal: To Be Published
Title: Crystal structure of human Caspase-1 with 2-((2-naphthoyl)-L-valyl)-4-hydroxy-N-((3S)-2-hydroxy-5-oxotetrahydrofuran-3-yl)-2-azabicyclo[2.2.2]octane-3-carboxamide (Compound 1)
Authors: Brethon, A. / Chantalat, L. / Christin, O. / Clary, L. / Fournier, J.F. / Gastreich, M. / Harris, C. / Pascau, J. / Isabet, T. / Rodeschin, V. / Thoreau, E. / Roche, D.
History
DepositionDec 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,9173
Polymers30,3912
Non-polymers5261
Water2,162120
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-31 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.081, 63.081, 138.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-501-

HOH

-
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 / p45


Mass: 20001.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Production host: Escherichia coli (E. coli) / References: UniProt: P29466, caspase-1
#2: 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 / p45


Mass: 10389.950 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Production host: Escherichia coli (E. coli) / References: UniProt: P29466, caspase-1
#3: Chemical ChemComp-WE0 / (3~{S})-3-[[(3~{S})-2-[(2~{S})-3-methyl-2-(naphthalen-2-ylcarbonylamino)butanoyl]-4-oxidanyl-2-azabicyclo[2.2.2]octan-3-yl]carbonylamino]-4-oxidanyl-butanoic acid


Mass: 525.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H35N3O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.1 M HEPES (pH 7.4), 2 M (NH4)2SO4, and 25 mM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.989 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 15845 / % possible obs: 99.8 % / Redundancy: 13.7 % / Biso Wilson estimate: 43.68 Å2 / Net I/σ(I): 10.16
Reflection shellResolution: 2.15→2.23 Å / % possible all: 99.6

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
CNSrefinement
Cootmodel building
MOLREPphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→19.78 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.257 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.198
RfactorNum. reflection% reflectionSelection details
Rfree0.249 789 4.99 %RANDOM
Rwork0.197 ---
obs0.2 15819 99.8 %-
Displacement parametersBiso mean: 50.54 Å2
Baniso -1Baniso -2Baniso -3
1-2.8572 Å20 Å20 Å2
2--2.8572 Å20 Å2
3----5.7143 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 2.15→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 38 121 2168
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012101HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.142836HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d759SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes315HARMONIC5
X-RAY DIFFRACTIONt_it2101HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion17.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion279SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2497SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.268 161 5.76 %
Rwork0.208 2634 -
all0.212 2795 -
obs--99.68 %
Refinement TLS params.Method: refined / Origin x: -28.5754 Å / Origin y: 16.6506 Å / Origin z: 3.2729 Å
111213212223313233
T0.023 Å20.0035 Å2-0.0308 Å2-0.1191 Å20.0342 Å2---0.304 Å2
L1.3459 °2-0.2305 °20.7049 °2-1.3435 °2-0.8137 °2--2.66 °2
S0.1299 Å °-0.0026 Å °-0.1585 Å °-0.0486 Å °-0.0715 Å °0.0103 Å °0.371 Å °0.3417 Å °-0.0585 Å °
Refinement TLS groupSelection details: { *|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more