[English] 日本語
Yorodumi
- PDB-7p2t: Tetartohedrally twinned crystal structure of Schistosoma mansoni ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p2t
TitleTetartohedrally twinned crystal structure of Schistosoma mansoni HDAC8 in complex with a tricyclic thieno[3,2-b]indole capped hydroxamate-based inhibitor, bromine derivative
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / SmHDAC8 / active-site / HDACi / histone-deacetilase inhibitor complex / tetartohedral / twinning
Function / homology
Function and homology information


histone deacetylase / histone deacetylase activity / heterochromatin formation / metal ion binding / nucleus
Similarity search - Function
: / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Chem-4VX / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSaccoccia, F. / Gemma, S. / Campiani, G. / Ruberti, G.
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structures of Schistosoma mansoni histone deacetylase 8 reveal a novel binding site for allosteric inhibitors.
Authors: Saccoccia, F. / Pozzetti, L. / Gimmelli, R. / Butini, S. / Guidi, A. / Papoff, G. / Giannaccari, M. / Brogi, S. / Scognamiglio, V. / Gemma, S. / Ruberti, G. / Campiani, G.
History
DepositionJul 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 28, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone deacetylase 8
B: Histone deacetylase 8
C: Histone deacetylase 8
D: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,21125
Polymers199,3374
Non-polymers2,87421
Water1,11762
1
A: Histone deacetylase 8
hetero molecules


  • defined by author&software
  • Evidence: Steady-state kinetics experiments confirmed that ligand behaved as a competitive inhibitor; fluorescence spectra - at equilibrium - confirmed the binding in the active site; all of the ...Evidence: Steady-state kinetics experiments confirmed that ligand behaved as a competitive inhibitor; fluorescence spectra - at equilibrium - confirmed the binding in the active site; all of the above experiments were confirmed by dedicated mutant form. More details will be released in related publication
  • 50.5 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)50,4635
Polymers49,8341
Non-polymers6294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5026
Polymers49,8341
Non-polymers6685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6247
Polymers49,8341
Non-polymers7906
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6217
Polymers49,8341
Non-polymers7876
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.205, 99.003, 178.585
Angle α, β, γ (deg.)90.000, 91.300, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Histone deacetylase 8


Mass: 49834.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: HDAC8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5H660

-
Non-polymers , 6 types, 83 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-4VX / 5-[[(2R)-7-bromanyl-2-phenyl-2,3-dihydrothieno[3,2-b]indol-4-yl]methyl]-N-oxidanyl-thiophene-2-carboxamide


Mass: 485.417 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H17BrN2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 20-22% PEG 3350, 200mM sodium/potassium tartrate / Temp details: cold room

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2020
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.48
11-K, -H, -L20.189
11K, H, -L30.171
11h,-k,-l40.16
ReflectionResolution: 2.3→178.539 Å / Num. all: 76754 / Num. obs: 76754 / % possible obs: 100 % / Redundancy: 6.5 % / Rpim(I) all: 0.087 / Rrim(I) all: 0.226 / Rsym value: 0.208 / Net I/av σ(I): 2.3 / Net I/σ(I): 4.6 / Num. measured all: 501220
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.426.21.3460.669613111620.5831.471.3461.2100
2.42-2.576.40.9790.867881105580.4161.0660.9791.7100
2.57-2.756.60.6571.26596099340.2740.7130.6572.5100
2.75-2.976.50.4581.65971192370.1940.4980.4583.4100
2.97-3.256.60.332.25630885170.1380.3580.334.9100
3.25-3.646.80.2412.65291277310.0980.260.2416.8100
3.64-4.26.60.1813.44521268180.0750.1960.1818.2100
4.2-5.146.70.163.93854157830.0660.1740.169.2100
5.14-7.276.50.1553.82933545000.0650.1680.1558.6100
7.27-48.0636.30.095.21574725140.0380.0980.099.699.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bz5

4bz5


Resolution: 2.3→48.063 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.294 --RANDOM
obs0.2794 73098 100 %-
Displacement parametersBiso max: 119.88 Å2 / Biso mean: 50.183 Å2 / Biso min: 20.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12722 0 147 62 12931

+
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