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- PDB-5vi6: Crystal structure of histone deacetylase 8 in complex with trapoxin A -

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Basic information

Entry
Database: PDB / ID: 5vi6
TitleCrystal structure of histone deacetylase 8 in complex with trapoxin A
Components
  • Histone deacetylase 8
  • Trapoxin A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HDAC / epigenetics / natural product inhibitor / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex ...histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / Hsp70 protein binding / epigenetic regulation of gene expression / HDACs deacetylate histones / Hsp90 protein binding / regulation of protein stability / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Separation of Sister Chromatids / chromatin organization / DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Histone deacetylase / Histone deacetylase domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Trapoxin A / 1,4-DIETHYLENE DIOXIDE / : / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Helicoma ambiens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.237 Å
AuthorsPorter, N.J. / 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: ACS Chem. Biol. / Year: 2017
Title: Binding of the Microbial Cyclic Tetrapeptide Trapoxin A to the Class I Histone Deacetylase HDAC8.
Authors: Porter, N.J. / Christianson, D.W.
History
DepositionApr 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_entity_src_syn / pdbx_molecule_features / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_keywords / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_fragment / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 2.1Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 2.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.3Oct 4, 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 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 8
B: Trapoxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,74117
Polymers41,8012
Non-polymers94015
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-13 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.980, 50.980, 116.517
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Histone deacetylase 8 / HD8


Mass: 41161.777 Da / Num. of mol.: 1 / Fragment: residues 8-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BY41, histone deacetylase
#2: Protein/peptide Trapoxin A / (3S / 6S / 9S / 15aR)-6 / 9-dibenzyl-3-{6 / 6-dihydroxy-6-[(2S)-oxiran-2-yl]hexyl}octahydro-2H- ...(3S / 6S / 9S / 15aR)-6 / 9-dibenzyl-3-{6 / 6-dihydroxy-6-[(2S)-oxiran-2-yl]hexyl}octahydro-2H-pyrido[1 / 2-a][1 / 4 / 7 / 10]tetraazacyclododecine-1 / 4 / 7 / 10(3H / 12H)-tetrone


Type: Cyclic peptide / Class: Inhibitor / Mass: 638.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Helicoma ambiens (fungus) / References: Trapoxin A

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Non-polymers , 5 types, 392 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 35% dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.237→44.15 Å / Num. obs: 95873 / % possible obs: 99.1 % / Redundancy: 4.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.035 / Net I/σ(I): 13.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EWF

3ewf


Resolution: 1.237→41.286 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 13.23
RfactorNum. reflection% reflection
Rfree0.1433 4939 5.15 %
Rwork0.1213 --
obs0.1224 95812 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.237→41.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 100 377 3215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093099
X-RAY DIFFRACTIONf_angle_d1.0334215
X-RAY DIFFRACTIONf_dihedral_angle_d22.331130
X-RAY DIFFRACTIONf_chiral_restr0.081451
X-RAY DIFFRACTIONf_plane_restr0.008550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.237-1.2510.24741620.22233048X-RAY DIFFRACTION100
1.251-1.26580.26061360.21183045X-RAY DIFFRACTION100
1.2658-1.28120.25071700.1943123X-RAY DIFFRACTION100
1.2812-1.29740.2251960.18833008X-RAY DIFFRACTION100
1.2974-1.31450.1941600.18023046X-RAY DIFFRACTION100
1.3145-1.33250.20282020.16312947X-RAY DIFFRACTION99
1.3325-1.35150.1821550.15972937X-RAY DIFFRACTION95
1.3515-1.37170.18541590.14983027X-RAY DIFFRACTION98
1.3717-1.39320.17991780.13953031X-RAY DIFFRACTION100
1.3932-1.4160.19251820.13553082X-RAY DIFFRACTION100
1.416-1.44040.16711640.13153001X-RAY DIFFRACTION100
1.4404-1.46660.15051500.12123063X-RAY DIFFRACTION100
1.4666-1.49480.14341760.10753052X-RAY DIFFRACTION99
1.4948-1.52530.12491700.10042993X-RAY DIFFRACTION99
1.5253-1.55850.12581220.09993013X-RAY DIFFRACTION97
1.5585-1.59480.15241760.10182886X-RAY DIFFRACTION94
1.5948-1.63460.13351700.09843058X-RAY DIFFRACTION100
1.6346-1.67880.12721790.09423026X-RAY DIFFRACTION100
1.6788-1.72820.11921420.09513074X-RAY DIFFRACTION100
1.7282-1.7840.13721500.09683095X-RAY DIFFRACTION100
1.784-1.84780.13691400.10323060X-RAY DIFFRACTION100
1.8478-1.92180.1171500.10243034X-RAY DIFFRACTION99
1.9218-2.00920.11741970.10732902X-RAY DIFFRACTION96
2.0092-2.11520.13981400.10663114X-RAY DIFFRACTION100
2.1152-2.24770.13732020.11072985X-RAY DIFFRACTION100
2.2477-2.42120.12671600.10773074X-RAY DIFFRACTION100
2.4212-2.66480.13861600.11643055X-RAY DIFFRACTION100
2.6648-3.05030.14421580.12452990X-RAY DIFFRACTION98
3.0503-3.84260.12491550.1263082X-RAY DIFFRACTION100
3.8426-41.30850.14441780.13413022X-RAY DIFFRACTION100

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