[English] 日本語
Yorodumi
- PDB-6x8j: Caspase-7 in complex with ketomethylene inhibitor reveals tetrahe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x8j
TitleCaspase-7 in complex with ketomethylene inhibitor reveals tetrahedral adduct
Components
  • (Caspase-7) x 2
  • ketomethylene inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / tetrahedral / complex / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / striated muscle cell differentiation / cysteine-type peptidase activity / protein maturation / protein catabolic process / protein processing / fibrillar center / positive regulation of neuron apoptotic process / peptidase activity / heart development / cellular response to lipopolysaccharide / neuron apoptotic process / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Peptidase C14 family / 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 ...Peptidase C14 family / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å
AuthorsSolania, A. / Xu, J.H. / Wolan, D.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R21AI112796 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM118382 United States
CitationJournal: To Be Published
Title: Caspase-7 in complex with ketomethylene inhibitor reveals tetrahedral adduct
Authors: Solania, A. / Xu, J.H. / Wolan, D.W.
History
DepositionJun 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Caspase-7
C: Caspase-7
B: Caspase-7
D: Caspase-7
E: ketomethylene inhibitor
F: ketomethylene inhibitor


Theoretical massNumber of molelcules
Total (without water)71,9476
Polymers71,9476
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy, previous determined
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15440 Å2
ΔGint-93 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.629, 88.629, 186.449
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 57 through 145 or (resid 146...
21chain B
12(chain C and ((resid 212 and (name N or name...
22chain D
13chain E
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 57 through 145 or (resid 146...A57 - 145
121(chain A and (resid 57 through 145 or (resid 146...A146
131(chain A and (resid 57 through 145 or (resid 146...A57 - 196
141(chain A and (resid 57 through 145 or (resid 146...A57 - 196
151(chain A and (resid 57 through 145 or (resid 146...A57 - 196
161(chain A and (resid 57 through 145 or (resid 146...A57 - 196
211chain BB57 - 196
112(chain C and ((resid 212 and (name N or name...C212
122(chain C and ((resid 212 and (name N or name...C212 - 302
132(chain C and ((resid 212 and (name N or name...C212 - 302
142(chain C and ((resid 212 and (name N or name...C212 - 302
152(chain C and ((resid 212 and (name N or name...C212 - 302
212chain DD212 - 302
113chain EE303 - 307
213chain FF403 - 407

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Caspase-7 / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3


Mass: 22189.203 Da / Num. of mol.: 2 / Fragment: p20 (UNP residues 34-231)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7
#2: Protein Caspase-7 / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3


Mass: 13223.800 Da / Num. of mol.: 2 / Fragment: p11 (UNP residues 232-336)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7
#3: Protein/peptide ketomethylene inhibitor


Mass: 560.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 1:1 protein : 0.15 M sodium citrate, 1.4 M sodium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 30, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26677 / % possible obs: 99.8 % / Redundancy: 9.5 % / Biso Wilson estimate: 52.61 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.044 / Rrim(I) all: 0.139 / Net I/σ(I): 0.218
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 1.341 / Num. unique obs: 1273 / CC1/2: 0.876 / Rpim(I) all: 0.451 / Rrim(I) all: 1.417

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4JJ8

4jj8


Resolution: 2.604→39.841 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 1333 5.01 %
Rwork0.1829 25265 -
obs0.1844 26598 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.57 Å2 / Biso mean: 55.8225 Å2 / Biso min: 25.36 Å2
Refinement stepCycle: final / Resolution: 2.604→39.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 26 43 3737
Biso mean--65.2 49.49 -
Num. residues----470
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A844X-RAY DIFFRACTION0.91TORSIONAL
12B844X-RAY DIFFRACTION0.91TORSIONAL
21C548X-RAY DIFFRACTION0.91TORSIONAL
22D548X-RAY DIFFRACTION0.91TORSIONAL
31E30X-RAY DIFFRACTION0.91TORSIONAL
32F30X-RAY DIFFRACTION0.91TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6042-2.69720.30951240.2398246999
2.6972-2.80520.33081300.23852469100
2.8052-2.93280.23781370.22162485100
2.9328-3.08740.25031320.22112494100
3.0874-3.28070.27191080.21532541100
3.2807-3.53390.21361560.19062476100
3.5339-3.88930.17021360.16542532100
3.8893-4.45140.20221400.15372529100
4.4514-5.60580.16891330.16072579100
5.6058-39.8410.2081370.1812269199

+
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://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