[English] 日本語
Yorodumi
- PDB-9eu0: Crystal structure of Danio rerio HDAC6 CD2 in complex with hydrol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9eu0
TitleCrystal structure of Danio rerio HDAC6 CD2 in complex with hydrolyzed DFMO-inhibitor (ITF7209)
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / HISTONE DEACETYLASE / COMPLEX WITH HYDRAZIDE / NON-HYDROXAMATE ZINC BINDING GROUP / MECHANISM-BASED INHIBITOR
Function / homology
Function and homology information


Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression ...Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression / angiogenesis / zinc ion binding
Similarity search - Function
Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / : / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsBebel, A. / Cellupica, E. / Stevenazzi, A. / Sandrone, G. / Vergani, B. / Caprini, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2024
Title: Mechanistic and Structural Insights on Difluoromethyl-1,3,4-oxadiazole Inhibitors of HDAC6.
Authors: Cellupica, E. / Gaiassi, A. / Rocchio, I. / Rovelli, G. / Pomarico, R. / Sandrone, G. / Caprini, G. / Cordella, P. / Cukier, C. / Fossati, G. / Marchini, M. / Bebel, A. / Airoldi, C. / ...Authors: Cellupica, E. / Gaiassi, A. / Rocchio, I. / Rovelli, G. / Pomarico, R. / Sandrone, G. / Caprini, G. / Cordella, P. / Cukier, C. / Fossati, G. / Marchini, M. / Bebel, A. / Airoldi, C. / Palmioli, A. / Stevenazzi, A. / Steinkuhler, C. / Vergani, B.
History
DepositionMar 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone deacetylase 6
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,92511
Polymers80,6852
Non-polymers1,2409
Water7,008389
1
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0826
Polymers40,3431
Non-polymers7395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8445
Polymers40,3431
Non-polymers5014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.71, 91.56, 96.13
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Histone deacetylase 6


Mass: 40342.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8W4B7

-
Non-polymers , 5 types, 398 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-A1H7I / ~{N}'-[2,2-bis(fluoranyl)ethanoyl]-5-[(4-~{tert}-butyl-1,2,3-triazol-1-yl)methyl]thiophene-2-carbohydrazide


Mass: 357.379 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H17F2N5O2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1% (w/v) nOctyl-b-D-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 21% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.86→48.065 Å / Num. obs: 56003 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.997 / Net I/σ(I): 8.67
Reflection shellResolution: 1.86→1.91 Å / Mean I/σ(I) obs: 1.82 / Num. unique obs: 4085 / CC1/2: 0.792 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→48.065 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.632 / SU ML: 0.104 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2215 2801 5.002 %
Rwork0.1765 53202 -
all0.179 --
obs-56003 99.863 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.725 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0 Å2
2--1.164 Å20 Å2
3----0.754 Å2
Refinement stepCycle: LAST / Resolution: 1.86→48.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5573 0 69 389 6031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125829
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165342
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.827918
X-RAY DIFFRACTIONr_angle_other_deg0.5711.74812286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7955721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.823565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04210931
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.52210271
X-RAY DIFFRACTIONr_chiral_restr0.0830.2857
X-RAY DIFFRACTIONr_chiral_restr_other0.0060.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021388
X-RAY DIFFRACTIONr_nbd_refined0.2540.21313
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.25238
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22868
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22906
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2373
X-RAY DIFFRACTIONr_metal_ion_refined0.1540.223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.216
X-RAY DIFFRACTIONr_nbd_other0.1980.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2290.211
X-RAY DIFFRACTIONr_mcbond_it2.2472.652875
X-RAY DIFFRACTIONr_mcbond_other2.2462.652875
X-RAY DIFFRACTIONr_mcangle_it3.1244.753599
X-RAY DIFFRACTIONr_mcangle_other3.1244.7513600
X-RAY DIFFRACTIONr_scbond_it3.2253.0672954
X-RAY DIFFRACTIONr_scbond_other3.2243.0652954
X-RAY DIFFRACTIONr_scangle_it4.8315.4864319
X-RAY DIFFRACTIONr_scangle_other4.8315.4884320
X-RAY DIFFRACTIONr_lrange_it6.25427.8336757
X-RAY DIFFRACTIONr_lrange_other6.25427.8376758
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.86-1.9080.3532040.338700.30241020.9160.93799.31740.283
1.908-1.960.2821990.26337710.26439740.9430.95499.89930.246
1.96-2.0170.281940.24537000.24738970.9540.96299.9230.225
2.017-2.0790.2671880.21535560.21737470.9570.97199.91990.196
2.079-2.1470.2741840.20534970.20836810.9510.9751000.186
2.147-2.2220.2461760.18733580.1935340.960.981000.169
2.222-2.3060.2211710.17632380.17834100.9720.98299.97070.159
2.306-2.40.2251650.17131460.17433140.9730.98299.90950.155
2.4-2.5060.2341580.17330030.17631610.970.9841000.159
2.506-2.6280.2151520.17128820.17330340.9770.9851000.16
2.628-2.770.2461450.17627570.1829030.9630.98399.96560.168
2.77-2.9380.2511360.17525860.17827230.9660.98399.96330.171
2.938-3.140.1921300.16924570.1725870.9780.9841000.169
3.14-3.390.2111210.16823100.1724310.970.9831000.175
3.39-3.7120.2041110.15421090.15622230.9770.98799.86510.168
3.712-4.1470.1961010.15419230.15620260.9780.98799.90130.174
4.147-4.7820.16900.13117110.13218080.9870.99199.61280.157
4.782-5.8420.165780.14514650.14615480.9880.9999.6770.174
5.842-8.2020.171610.15211660.15312280.9830.98899.91860.185
8.202-48.0650.261370.26970.2037450.9170.97698.52350.243

+
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