[English] 日本語
Yorodumi
- PDB-5k20: Caspase-7 S239E Phosphomimetic -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k20
TitleCaspase-7 S239E Phosphomimetic
Components
  • Caspase-7 large subunit
  • Caspase-7 small subunit
KeywordsHYDROLASE / protease / phosphomimetic / PAK2 / phosphorylation
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
Caspase-like / Rossmann fold - #1460 / 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-like / Rossmann fold - #1460 / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEron, S.J. / Hardy, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM080532 United States
CitationJournal: To Be Published
Title: PAK2 Phosphorylation Inhibits Caspase-7 by Two Divergent Mechanisms: Slowing Activation and Blocking Substrate Binding
Authors: Eron, S.J. / Hardy, J.A.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Caspase-7 large subunit
B: Caspase-7 small subunit
C: Caspase-7 large subunit
D: Caspase-7 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0487
Polymers70,9104
Non-polymers1383
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-82 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.757, 88.757, 185.141
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLNGLNAA57 - 19657 - 196
21THRTHRGLNGLNCC357 - 49657 - 196
12LYSLYSSERSERBB212 - 30214 - 104
22LYSLYSSERSERDD512 - 60214 - 104

NCS ensembles :
ID
1
2
Detailstetramer according to gel filtration, mass spectrometry, gel electroporesis, literature reports. This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This generates four chains from each monomer. The prodomain (residues 1-23) and the intersubunit linker (residues 199-206) are both released. Thus active, cleaved caspase-7 has two copies of the large subunit (residues 24-198) and two copies of the small subunit (residues 206-303).

-
Components

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


Mass: 22189.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This ...Details: This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This generates four chains from each monomer. The prodomain (residues 1-23) and the intersubunit linker (residues 199-206) are both released. Thus active, cleaved caspase-7 has two copies of the large subunit (residues 24-198) and two copies of the small subunit (residues 206-303). The large subunit of caspase-7 crystallized here consisted of residues 24-198.
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P55210, caspase-7
#2: Protein Caspase-7 small subunit / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3


Mass: 13265.836 Da / Num. of mol.: 2 / Mutation: S272E
Source method: isolated from a genetically manipulated source
Details: This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This ...Details: This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This generates four chains from each monomer. The prodomain (residues 1-23) and the intersubunit linker (residues 199-206) are both released. Thus active, cleaved caspase-7 has two copies of the large subunit (residues 24-198) and two copies of the small subunit (residues 206-303). The small subunit of caspase-7 crystallized here consisted of residues 206-303 (including a 6xHis tag).
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55210, caspase-7
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.07 Å3/Da / Density % sol: 59.87 % / Description: Rhomboids of 240 x 340 microns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.1 M Sodium Formate 100 mM Sodium Citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→76.98 Å / Num. obs: 43569 / % possible obs: 99.53 % / Redundancy: 10.9 % / Biso Wilson estimate: 66.3 Å2 / Rsym value: 0.076 / Net I/σ(I): 37.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 11 % / Mean I/σ(I) obs: 1.8 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALAdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IBF

3ibf


Resolution: 2.2→76.98 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 12.25 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.162
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 4298 9.9 %RANDOM
Rwork0.1912 ---
obs0.1948 39208 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 150.17 Å2 / Biso mean: 66.342 Å2 / Biso min: 40.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20.77 Å20 Å2
2--1.54 Å20 Å2
3----4.99 Å2
Refinement stepCycle: final / Resolution: 2.2→76.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 9 92 3835
Biso mean--68.7 57.58 -
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193804
X-RAY DIFFRACTIONr_bond_other_d0.0050.023579
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.9545117
X-RAY DIFFRACTIONr_angle_other_deg1.1538255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85324.324185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15415679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1191520
X-RAY DIFFRACTIONr_chiral_restr0.1010.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024306
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02898
X-RAY DIFFRACTIONr_mcbond_it3.3464.2921856
X-RAY DIFFRACTIONr_mcbond_other3.3564.2941857
X-RAY DIFFRACTIONr_mcangle_it4.4336.4172313
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A76060.14
12C76060.14
21B50330.09
22D50330.09
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 326 -
Rwork0.312 2862 -
all-3188 -
obs--99.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.20550.0181-0.13022.43910.68283.1275-0.04610.25740.2948-0.3340.065-0.0407-0.31710.1396-0.01890.2116-0.0852-0.03430.1348-0.01250.0681122.8256-26.6215179.6025
25.4323-0.9380.44734.43330.1513.8758-0.00810.2571-0.0619-0.09090.0889-0.42880.17780.5016-0.08080.1635-0.0345-0.01440.1566-0.04010.0593129.0836-27.3294192.1863
31.3798-0.6322-0.29983.3749-0.03561.9230.05360.1296-0.0379-0.12580.0413-0.03460.02630.0678-0.09490.0699-0.0286-0.01230.0765-0.0180.0136124.8821-6.1454205.4867
45.2692-0.99950.33374.2230.19814.3199-0.01340.14740.2634-0.0563-0.01410.4503-0.2123-0.47120.02750.1338-0.0365-0.01170.1105-0.0080.0958115.1274-14.0748200.0693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A57 - 196
2X-RAY DIFFRACTION2B212 - 303
3X-RAY DIFFRACTION3C357 - 496
4X-RAY DIFFRACTION4D511 - 603

+
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