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- PDB-3ewf: Crystal Structure Analysis of human HDAC8 H143A variant complexed... -

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Basic information

Entry
Database: PDB / ID: 3ewf
TitleCrystal Structure Analysis of human HDAC8 H143A variant complexed with substrate.
Components
  • Histone deacetylase 8
  • PEPTIDIC SUBSTRATE
KeywordsHYDROLASE / HDAC / metalloenzyme / acetylation / arginase fold / HDAC8 / histone deacetylase / substrate complex / Alternative splicing / Chromatin regulator / Nucleus / Repressor / Transcription / Transcription regulation
Function / homology
Function and homology information


histone decrotonylase activity / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / regulation of telomere maintenance ...histone decrotonylase activity / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / regulation of telomere maintenance / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / negative regulation of protein ubiquitination / Hsp70 protein binding / Resolution of Sister Chromatid Cohesion / 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 / heterochromatin formation / chromatin organization / DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / 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
: / 7-AMINO-4-METHYL-CHROMEN-2-ONE / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDowling, D.P. / Gantt, S.L. / Gattis, S.G. / Fierke, C.A. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2008
Title: Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors.
Authors: Dowling, D.P. / Gantt, S.L. / Gattis, S.G. / Fierke, C.A. / Christianson, D.W.
History
DepositionOct 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Author supporting evidence
Category: pdbx_struct_assembly_auth_evidence / pdbx_unobs_or_zero_occ_atoms
Revision 1.3Dec 30, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: audit_author / pdbx_entity_src_syn ...audit_author / pdbx_entity_src_syn / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.name / _pdbx_entity_src_syn.details ..._audit_author.name / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 20, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 8
B: Histone deacetylase 8
C: Histone deacetylase 8
D: Histone deacetylase 8
I: PEPTIDIC SUBSTRATE
J: PEPTIDIC SUBSTRATE
K: PEPTIDIC SUBSTRATE
L: PEPTIDIC SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,55726
Polymers175,1518
Non-polymers1,40618
Water5,386299
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15860 Å2
ΔGint-261 kcal/mol
Surface area49940 Å2
MethodPISA
2
A: Histone deacetylase 8
I: PEPTIDIC SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1727
Polymers43,7882
Non-polymers3845
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-41 kcal/mol
Surface area14900 Å2
MethodPISA
3
B: Histone deacetylase 8
J: PEPTIDIC SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1066
Polymers43,7882
Non-polymers3194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-61 kcal/mol
Surface area14770 Å2
MethodPISA
4
C: Histone deacetylase 8
K: PEPTIDIC SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1727
Polymers43,7882
Non-polymers3845
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-41 kcal/mol
Surface area14880 Å2
MethodPISA
5
D: Histone deacetylase 8
L: PEPTIDIC SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1066
Polymers43,7882
Non-polymers3194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-59 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.903, 91.844, 196.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE OCTAMER MENTIONED FOR BIOMOLECULE 1 IS BELIEVED TO BE A CRYSTALLOGRAPHIC ARTIFACT DUE TO LIGAND BINDING. IT CONSISTS OF FOUR HDAC8 MONOMERS, EACH COMPLEXED WITH AN ACETYLLYSINE SUBSTRATE PEPTIDE. THE DIMER QUATERNARY STRUCTURE OF BIOMOLECULES 2, 3, 4, AND 5 MENTIONED IN REMARK 350 ARE BETWEEN AN HDAC8 MONOMER AND ITS ACETYLLYSINE SUBSTRATE PEPTIDE. DYNAMIC LIGHT SCATTERING STUDIES HAVE INDICATED THAT HDAC8 EXISTS AS A MONOMER IN SOLUTION

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDIJKL

#1: Protein
Histone deacetylase 8 / HD8


Mass: 43107.875 Da / Num. of mol.: 4 / Mutation: H143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDA07, HDAC8, HDACL1 / Plasmid: pHD2-Xa-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BY41, histone deacetylase
#2: Protein/peptide
PEPTIDIC SUBSTRATE


Mass: 679.811 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 317 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-MCM / 7-AMINO-4-METHYL-CHROMEN-2-ONE / 7-AMINO-4-METHYLCOUMARIN


Mass: 175.184 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Reservoir solution: 50 mM Tris-HCl, 50 mM MgCl2, 150 mM KCl, 13% PEG 6000, 2 mM TCEP. Enzyme was incubated with 3.2 mM substrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.97926
SYNCHROTRONAPS 24-ID-E20.9792
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 10, 2008
ADSC QUANTUM 3152CCDJul 10, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.97921
ReflectionResolution: 2.5→50 Å / Num. all: 52790 / Num. obs: 52790 / % possible obs: 99.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.8 / % possible all: 95.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2V5W

2v5w


Resolution: 2.5→49.15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 21579.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4032 8.2 %RANDOM
Rwork0.198 ---
obs0.198 49380 93.6 %-
all-52790 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.34 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.85 Å20 Å20 Å2
2---8.43 Å20 Å2
3---0.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11528 0 66 299 11893
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 591 8.2 %
Rwork0.271 6633 -
obs--83.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_MOD.PARAMPROTEIN_MOD.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CAPPING.PARAMCAPPING.TOP

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