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- PDB-5icn: HDAC1:MTA1 in complex with inositol-6-phosphate and a novel pepti... -

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Basic information

Entry
Database: PDB / ID: 5icn
TitleHDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4
Components
  • GLY-ALA-6A0-ARG-HIS
  • Histone deacetylase 1
  • Metastasis-associated protein MTA1
KeywordsTRANSCRIPTION / Transcription repression Inositol phosphate Corepressor Histone deacetylase HDAC1 HDAC3 Histones / Metastasis associated protein / IP6
Function / homology
Function and homology information


Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / protein lysine delactylase activity / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism ...Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / protein lysine delactylase activity / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / p75NTR negatively regulates cell cycle via SC1 / histone H4K12 deacetylase activity, hydrolytic mechanism / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / histone H3K9 deacetylase activity, hydrolytic mechanism / negative regulation of androgen receptor signaling pathway / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / endoderm development / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / protein deacetylation / histone deacetylase / regulation of stem cell differentiation / Regulation of MITF-M-dependent genes involved in apoptosis / STAT3 nuclear events downstream of ALK signaling / positive regulation of protein autoubiquitination / Transcription of E2F targets under negative control by DREAM complex / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / embryonic digit morphogenesis / histone deacetylase activity / response to ionizing radiation / DNA methylation-dependent constitutive heterochromatin formation / positive regulation of intracellular estrogen receptor signaling pathway / Notch-HLH transcription pathway / negative regulation of gene expression, epigenetic / entrainment of circadian clock by photoperiod / Sin3-type complex / E-box binding / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / negative regulation of intrinsic apoptotic signaling pathway / locomotor rhythm / eyelid development in camera-type eye / odontogenesis of dentin-containing tooth / oligodendrocyte differentiation / SUMOylation of transcription factors / RNA Polymerase I Transcription Initiation / positive regulation of oligodendrocyte differentiation / histone deacetylase complex / G0 and Early G1 / Regulation of MECP2 expression and activity / hair follicle placode formation / host-mediated suppression of viral transcription / NF-kappaB binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / core promoter sequence-specific DNA binding / MECP2 regulates neuronal receptors and channels / Nuclear events stimulated by ALK signaling in cancer / cellular response to platelet-derived growth factor stimulus / Regulation of TP53 Activity through Acetylation / negative regulation of canonical NF-kappaB signal transduction / transcription repressor complex / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of chromatin organization proteins / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / hippocampus development / transcription corepressor binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of smooth muscle cell proliferation / HDACs deacetylate histones / Deactivation of the beta-catenin transactivating complex / negative regulation of transforming growth factor beta receptor signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / circadian regulation of gene expression / promoter-specific chromatin binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of canonical Wnt signaling pathway / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / neuron differentiation / transcription corepressor activity / p53 binding / nuclear envelope / heterochromatin formation / double-strand break repair
Similarity search - Function
Metastasis-associated protein MTA1, R1 domain / Mesoderm induction early response protein/metastasis-associated protein / MTA R1 domain / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 ...Metastasis-associated protein MTA1, R1 domain / Mesoderm induction early response protein/metastasis-associated protein / MTA R1 domain / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Histone deacetylase / Histone deacetylase domain / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / SANT domain profile. / Arginase; Chain A / SANT domain / Myb-like DNA-binding domain / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Homeodomain-like / SANT/Myb domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / : / Metastasis-associated protein MTA1 / Histone deacetylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMillard, C.J. / Robertson, N.S. / Watson, P.J. / Jameson, A.G. / Schwabe, J.W.R.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Wellcome TrustWT085408 United Kingdom
Wellcome TrustWT100237 United Kingdom
Wellcome TrustWT082837 United Kingdom
Wellcome TrustWT101010 United Kingdom
Wolfson Foundation United Kingdom
CitationJournal: Nat Commun / Year: 2016
Title: Insights into the activation mechanism of class I HDAC complexes by inositol phosphates.
Authors: Watson, P.J. / Millard, C.J. / Riley, A.M. / Robertson, N.S. / Wright, L.C. / Godage, H.Y. / Cowley, S.M. / Jamieson, A.G. / Potter, B.V. / Schwabe, J.W.
History
DepositionFeb 23, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_organ / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Oct 7, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site
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.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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 / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metastasis-associated protein MTA1
B: Histone deacetylase 1
C: GLY-ALA-6A0-ARG-HIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1587
Polymers66,3543
Non-polymers8044
Water00
1
A: Metastasis-associated protein MTA1
B: Histone deacetylase 1
C: GLY-ALA-6A0-ARG-HIS
hetero molecules

A: Metastasis-associated protein MTA1
B: Histone deacetylase 1
C: GLY-ALA-6A0-ARG-HIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,31514
Polymers132,7086
Non-polymers1,6078
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area16140 Å2
ΔGint-139 kcal/mol
Surface area42340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.815, 107.815, 134.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Metastasis-associated protein MTA1


Mass: 22165.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTA1 / Plasmid: pcDNA3 / Cell line (production host): HEK293F / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q13330
#2: Protein Histone deacetylase 1 / HDAC1


Mass: 43203.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC1, RPD3L1 / Plasmid: pcDNA3 / Cell line (production host): HEK293F / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q13547, histone deacetylase

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide GLY-ALA-6A0-ARG-HIS


Mass: 984.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 3 types, 4 molecules

#4: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H18O24P6 / Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC1 / Plasmid: pcDNA3 / Cell line (production host): HEK293F / Organ (production host): Kidney / Production host: Homo sapiens (human)
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Zn / Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC1 / Plasmid: pcDNA3 / Cell line (production host): HEK293F / Organ (production host): Kidney / Production host: Homo sapiens (human)
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: K / Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC1 / Plasmid: pcDNA3 / Cell line (production host): HEK293F / Organ (production host): Kidney / Production host: Homo sapiens (human)

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M NA HEPES PH7.5, 2M AMMONIUM SULPHATE, 5% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 3.3→93.4 Å / Num. obs: 13008 / % possible obs: 93.1 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.38 / Net I/σ(I): 2.5
Reflection shellResolution: 3.3→3.56 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.3 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLM7.1.1data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BKX

4bkx


Resolution: 3.3→93.4 Å / Cor.coef. Fo:Fc: 0.835 / Cor.coef. Fo:Fc free: 0.759 / SU B: 41.5 / SU ML: 0.643 / Cross valid method: THROUGHOUT / ESU R Free: 0.617 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29949 695 5.4 %RANDOM
Rwork0.25452 ---
obs0.25694 12263 92.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.47 Å20 Å2
2--0.93 Å20 Å2
3----3.02 Å2
Refinement stepCycle: 1 / Resolution: 3.3→93.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4365 0 0 0 4365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194466
X-RAY DIFFRACTIONr_bond_other_d0.0020.024066
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9576050
X-RAY DIFFRACTIONr_angle_other_deg0.763.0019346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7065538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24823.982221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76615730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9761525
X-RAY DIFFRACTIONr_chiral_restr0.0610.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021073
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.423.4162164
X-RAY DIFFRACTIONr_mcbond_other1.4213.4152163
X-RAY DIFFRACTIONr_mcangle_it2.4565.1142697
X-RAY DIFFRACTIONr_mcangle_other2.4565.1162698
X-RAY DIFFRACTIONr_scbond_it1.3113.512302
X-RAY DIFFRACTIONr_scbond_other1.313.5112303
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3225.2023354
X-RAY DIFFRACTIONr_long_range_B_refined4.25226.6725140
X-RAY DIFFRACTIONr_long_range_B_other4.25226.6815141
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å
RfactorNum. reflection% reflection
Rfree0.405 48 -
Rwork0.35 910 -
obs--92.74 %

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