[English] 日本語
Yorodumi
- PDB-5efn: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5efn
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (H574A) in complex with histone H4 Lys6 tripeptide substrate
Components
  • Hdac6 protein
  • histone H4 tripeptide
KeywordsHYDROLASE
Function / homology
Function and homology information


: / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / potassium ion binding ...: / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / angiogenesis / negative regulation of transcription by RNA polymerase II / 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 / Histone deacetylase domain ...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
: / 7-AMINO-4-METHYL-CHROMEN-2-ONE / Hdac6 protein / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsHai, Y. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.
Authors: Hai, Y. / Christianson, D.W.
History
DepositionOct 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id
Revision 1.6Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Hdac6 protein
F: histone H4 tripeptide
A: Hdac6 protein
E: histone H4 tripeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,10215
Polymers81,2784
Non-polymers82411
Water11,422634
1
B: Hdac6 protein
F: histone H4 tripeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0828
Polymers40,6392
Non-polymers4436
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hdac6 protein
E: histone H4 tripeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0207
Polymers40,6392
Non-polymers3815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.997, 83.908, 86.903
Angle α, β, γ (deg.)90.00, 98.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules BAFE

#1: Protein Hdac6 protein / / histone deacetylase 6


Mass: 40218.418 Da / Num. of mol.: 2 / Fragment: catalytic domain 2 (UNP residues 288-646) / Mutation: H574A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli)
References: UniProt: A7YT55, UniProt: F8W4B7*PLUS, histone deacetylase
#2: Protein/peptide histone H4 tripeptide


Mass: 420.486 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 5 types, 645 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MCM / 7-AMINO-4-METHYL-CHROMEN-2-ONE / 7-AMINO-4-METHYLCOUMARIN


Mass: 175.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris, pH 6.5, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2015
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 70941 / % possible obs: 98.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 9.9
Reflection shellResolution: 1.8→1.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EEK

5eek


Resolution: 1.804→12.338 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 3591 5.06 %
Rwork0.1622 --
obs0.1638 70899 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.804→12.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 0 44 634 6284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065919
X-RAY DIFFRACTIONf_angle_d1.0418063
X-RAY DIFFRACTIONf_dihedral_angle_d12.8462175
X-RAY DIFFRACTIONf_chiral_restr0.042874
X-RAY DIFFRACTIONf_plane_restr0.0051053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8044-1.8280.30841310.23832435X-RAY DIFFRACTION93
1.828-1.8530.25291390.22682596X-RAY DIFFRACTION100
1.853-1.87940.2311360.21772602X-RAY DIFFRACTION100
1.8794-1.90730.2341340.21712603X-RAY DIFFRACTION100
1.9073-1.9370.27831280.21692603X-RAY DIFFRACTION100
1.937-1.96870.25051140.19532659X-RAY DIFFRACTION100
1.9687-2.00250.22251470.1822576X-RAY DIFFRACTION100
2.0025-2.03870.20871440.17982617X-RAY DIFFRACTION100
2.0387-2.07770.23241510.18212566X-RAY DIFFRACTION100
2.0777-2.120.21881330.1692638X-RAY DIFFRACTION100
2.12-2.16580.20721270.16162585X-RAY DIFFRACTION100
2.1658-2.21590.1961320.16562601X-RAY DIFFRACTION100
2.2159-2.2710.23491680.17512599X-RAY DIFFRACTION100
2.271-2.3320.23371210.16582621X-RAY DIFFRACTION100
2.332-2.40010.1891530.16172599X-RAY DIFFRACTION99
2.4001-2.4770.20691370.15372574X-RAY DIFFRACTION100
2.477-2.56480.19481270.1572619X-RAY DIFFRACTION99
2.5648-2.66650.17861230.15642596X-RAY DIFFRACTION98
2.6665-2.78650.1941430.15822582X-RAY DIFFRACTION99
2.7865-2.93150.18841390.15472603X-RAY DIFFRACTION99
2.9315-3.11250.19551350.15942620X-RAY DIFFRACTION99
3.1125-3.34830.15921420.14612566X-RAY DIFFRACTION98
3.3483-3.67710.16911480.13662584X-RAY DIFFRACTION99
3.6771-4.19090.15431420.13112603X-RAY DIFFRACTION98
4.1909-5.21290.13081530.13252532X-RAY DIFFRACTION97
5.2129-12.33780.18721440.15622529X-RAY DIFFRACTION94
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)
12.15771.2126-1.36293.7065-2.08762.87720.0401-0.0328-0.00910.123-0.1155-0.4183-0.15130.2480.07810.0327-0.0007-0.0270.1082-0.03340.098617.11016.05856.7952
20.55610.1308-0.2040.63030.15740.9534-0.0128-0.0178-0.04270.01620.0221-0.13870.09320.1639-0.00220.04710.0292-0.0140.089-0.01490.112114.5218-1.73935.2238
34.675-0.5746-0.33590.96030.49761.71530.13040.50780.3853-0.102-0.1137-0.3992-0.1660.0914-0.02950.0897-0.00770.03130.13250.03510.172820.222311.511-7.9133
40.6348-0.2030.14191.4579-0.05440.52750.02790.0875-0.0153-0.06660.0080.05760.03540.019-0.03170.0353-0.00030.00180.0674-0.0080.06221.8784-0.8349-1.3336
50.9412-0.4586-0.33321.93910.6652.21050.0147-0.03180.00290.0352-0.07090.1593-0.0315-0.23320.04890.0092-0.0033-0.00410.10080.00620.1035-11.7546.35723.4904
61.14830.43730.27911.48830.09970.9962-0.029-0.065-0.00680.04530.01910.1289-0.0282-0.06920.01140.05170.00640.00520.07350.00110.0728-3.97141.30139.7658
70.5852-0.34330.15340.267-0.05250.4804-0.0011-0.0712-0.01130.08030.0290.1830.0003-0.1414-0.02810.0723-0.0040.00990.10460.00830.1334-10.47164.623310.6439
81.9996-6.7837-9.3291.9999-8.10372-0.141-0.1589-0.04350.44230.0068-0.0151.27360.25830.1350.8671-0.13420.04790.29290.1480.9525.74919.087-5.8177
93.6832-2.63620.07683.5213-0.29371.52110.10550.1341-0.1376-0.3111-0.09790.03190.14720.10660.00010.1068-0.02620.00190.1147-0.04430.066826.065117.504325.5459
101.16010.29820.39591.39230.71121.0847-0.07440.11820.0511-0.14240.1051-0.1442-0.15260.1858-0.01890.1168-0.02050.0270.1014-0.00060.071426.018925.126728.4319
113.0440.7317-2.24171.0195-0.38922.7965-0.0343-0.1535-0.4430.06570.0674-0.50420.32320.77390.01450.11720.0681-0.04570.2707-0.10170.273140.580511.80432.4006
120.6210.1587-0.0211.68170.29680.7985-0.0004-0.09830.00250.26360.0296-0.1015-0.0330.0765-0.02360.11260.0022-0.01360.0824-0.01320.056223.487324.29542.3984
131.85860.72340.57911.83340.36181.25930.0852-0.1459-0.08830.552-0.02470.27830.1158-0.181-0.01310.2247-0.01140.07390.12340.00180.072410.919715.938349.6315
140.6573-0.00070.10681.49110.31281.7440.001-0.06570.00980.2315-0.00850.28630.0634-0.24070.00310.10190.00160.03770.10060.00050.10239.020820.386741.9179
151.99996.59212.000222.00021.9999-0.63780.11191.0063-0.5918-0.1852-0.1309-0.9571-0.18570.82070.92990.11640.09090.3132-0.00260.876429.37064.330142.3922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 442 through 466 )
2X-RAY DIFFRACTION2chain 'B' and (resid 467 through 516 )
3X-RAY DIFFRACTION3chain 'B' and (resid 517 through 537 )
4X-RAY DIFFRACTION4chain 'B' and (resid 538 through 656 )
5X-RAY DIFFRACTION5chain 'B' and (resid 657 through 684 )
6X-RAY DIFFRACTION6chain 'B' and (resid 685 through 746 )
7X-RAY DIFFRACTION7chain 'B' and (resid 747 through 798 )
8X-RAY DIFFRACTION8chain 'F' and (resid 2 through 3 )
9X-RAY DIFFRACTION9chain 'A' and (resid 442 through 466 )
10X-RAY DIFFRACTION10chain 'A' and (resid 467 through 516 )
11X-RAY DIFFRACTION11chain 'A' and (resid 517 through 537 )
12X-RAY DIFFRACTION12chain 'A' and (resid 538 through 656 )
13X-RAY DIFFRACTION13chain 'A' and (resid 657 through 684 )
14X-RAY DIFFRACTION14chain 'A' and (resid 685 through 798 )
15X-RAY DIFFRACTION15chain 'E' and (resid 2 through 3 )

+
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