[English] 日本語
Yorodumi
- PDB-5g0i: Crystal structure of Danio rerio HDAC6 CD1 and CD2 (linker cleave... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g0i
TitleCrystal structure of Danio rerio HDAC6 CD1 and CD2 (linker cleaved) in complex with Nexturastat A
ComponentsHDAC6
KeywordsCELL CYCLE / HISTONE / HISTONE DEACETYLASE
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 domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily ...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 domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NEXTURASTAT A / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMiyake, Y. / Keusch, J.J. / Wang, L. / Saito, M. / Hess, D. / Wang, X. / Melancon, B.J. / Helquist, P. / Gut, H. / Matthias, P.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural Insights Into Hdac6 Tubulin Deacetylation and its Selective Inhibition
Authors: Miyake, Y. / Keusch, J.J. / Wang, L. / Saito, M. / Hess, D. / Wang, X. / Melancon, B.J. / Helquist, P. / Gut, H. / Matthias, P.
History
DepositionMar 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HDAC6
B: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,79521
Polymers178,6952
Non-polymers2,10019
Water11,349630
1
A: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,41511
Polymers89,3481
Non-polymers1,06810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,38010
Polymers89,3481
Non-polymers1,0329
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.560, 52.830, 186.420
Angle α, β, γ (deg.)90.00, 108.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2148-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8189, 0.5739, -0.004035), (0.5733, -0.8184, -0.03993), (-0.02621, 0.03038, -0.9992)
Vector: -29.21, -46.92, 87.38)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein HDAC6


Mass: 89347.539 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN 1 AND 2, UNP RESIDUES 25-831
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Plasmid: POPINF / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: F8W4B7

-
Non-polymers , 6 types, 649 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.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-N4R / NEXTURASTAT A


Mass: 341.404 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H23N3O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growDetails: 23% PEG 3350, 0.1M KCL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 101593 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 45.35 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.3
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 0.9 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 5G0G AND 5G0H

5g0g

5g0h


Resolution: 1.99→45.58 Å / Cor.coef. Fo:Fc: 0.9596 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.165 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.137
Details: ADDUCT OF CYS581 COULD NOT BE IDENTIFIED AND HAS NOT BEEN MODELED. CHAIN A IS MORE ORDERED AND DISPLAYS HIGHER QUALITY ELECTRON DENSITY. NCS RESTRAINTS HAVE BEEN USED
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 5080 5 %RANDOM
Rwork0.1739 ---
obs0.1752 101593 98.19 %-
Displacement parametersBiso mean: 55.28 Å2
Baniso -1Baniso -2Baniso -3
1--3.0534 Å20 Å2-1.7433 Å2
2---5.1435 Å20 Å2
3---8.1969 Å2
Refine analyzeLuzzati coordinate error obs: 0.328 Å
Refinement stepCycle: LAST / Resolution: 1.99→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11227 0 121 630 11978
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111672HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0415831HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3983SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes262HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1793HARMONIC5
X-RAY DIFFRACTIONt_it11672HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion16.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1471SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13968SEMIHARMONIC4
LS refinement shellResolution: 1.99→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3407 323 5 %
Rwork0.3094 6138 -
all0.311 6461 -
obs--98.19 %
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)
10.86650.27990.28480.65510.31871.48490.0085-0.00730.02460.054-0.03320.06130.184-0.21590.0246-0.0144-0.02360.021-0.10950.0098-0.0351-18.7749-32.339459.2712
20.94560.12620.09810.91890.07561.6598-0.0224-0.01220.04890.08080.0171-0.09380.04260.3370.0053-0.08390.0063-0.0183-0.0740.0135-0.053414.7968-14.051371.2405
33.98241.0512-1.8080.9315-0.17611.1507-0.43471.50330.1712-0.25290.5260.16680.1752-0.7214-0.0913-0.2422-0.247-0.07210.27790.1089-0.3874-63.4868-33.544927.815
42.76730.2566-1.78810.8648-0.13712.6236-0.11690.6892-0.0637-0.31660.0885-0.17670.2432-0.50940.0284-0.1096-0.12140.08340.009-0.04-0.276-25.4408-29.848615.4213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|58 - 419}
2X-RAY DIFFRACTION2{A|442 - 801}
3X-RAY DIFFRACTION3{B|59 - 418}
4X-RAY DIFFRACTION4{B|442 - 801}

+
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