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- PDB-4bkx: The structure of HDAC1 in complex with the dimeric ELM2-SANT doma... -

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Basic information

Entry
Database: PDB / ID: 4bkx
TitleThe structure of HDAC1 in complex with the dimeric ELM2-SANT domain of MTA1 from the NuRD complex
Components
  • HISTONE DEACETYLASE 1
  • METASTASIS-ASSOCIATED PROTEIN MTA1
KeywordsTRANSCRIPTION / INOSITOL PHOSPHATE SIGNALLING / ELM2-SANT DOMAIN / HDAC / HDAC1 / HISTONE DEACETYLASE / MTA1
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 / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / negative regulation of androgen receptor signaling pathway ...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 / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / negative regulation of androgen receptor signaling pathway / NuRD complex / regulation of cell fate specification / endoderm development / negative regulation of stem cell population maintenance / 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 / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / histone H4K12 deacetylase activity, hydrolytic mechanism / protein deacetylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase / regulation of stem cell differentiation / STAT3 nuclear events downstream of ALK signaling / histone H3K9 deacetylase activity, hydrolytic mechanism / 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 / positive regulation of intracellular estrogen receptor signaling pathway / DNA methylation-dependent constitutive heterochromatin formation / 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 / eyelid development in camera-type eye / positive regulation of stem cell population maintenance / negative regulation of intrinsic apoptotic signaling pathway / locomotor rhythm / oligodendrocyte differentiation / odontogenesis of dentin-containing tooth / SUMOylation of transcription factors / RNA Polymerase I Transcription Initiation / histone deacetylase complex / positive regulation of oligodendrocyte differentiation / Regulation of MECP2 expression and activity / G0 and Early G1 / negative regulation by host of viral transcription / hair follicle placode formation / NF-kappaB binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / heterochromatin / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / core promoter sequence-specific DNA binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / RNA polymerase II core promoter sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / MECP2 regulates neuronal receptors and channels / negative regulation of canonical NF-kappaB signal transduction / Regulation of TP53 Activity through Acetylation / cellular response to platelet-derived growth factor stimulus / transcription repressor complex / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of chromatin organization proteins / negative regulation of cell migration / hippocampus development / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / transcription corepressor binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / positive regulation of smooth muscle cell proliferation / Deactivation of the beta-catenin transactivating complex / promoter-specific chromatin binding / negative regulation of transforming growth factor beta receptor signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / circadian regulation of gene expression / Formation of the beta-catenin:TCF transactivating complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of canonical Wnt signaling pathway / 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
Hormone receptor fold - #50 / 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 / Hormone receptor fold / ELM2 domain / ELM2 domain ...Hormone receptor fold - #50 / 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 / Hormone receptor fold / 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 / Few Secondary Structures / Irregular / Arc Repressor Mutant, subunit A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Metastasis-associated protein MTA1 / Histone deacetylase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMillard, C.J. / Watson, P.J. / Celardo, I. / Gordiyenko, Y. / Cowley, S.M. / Robinson, C.V. / Fairall, L. / Schwabe, J.W.R.
CitationJournal: Mol.Cell / Year: 2013
Title: Class I Hdacs Share a Common Mechanism of Regulation by Inositol Phosphates.
Authors: Millard, C.J. / Watson, P.J. / Celardo, I. / Gordiyenko, Y. / Cowley, S.M. / Robinson, C.V. / Fairall, L. / Schwabe, J.W.R.
History
DepositionApr 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,72710
Polymers75,1402
Non-polymers5878
Water00
1
A: METASTASIS-ASSOCIATED PROTEIN MTA1
B: HISTONE DEACETYLASE 1
hetero molecules

A: METASTASIS-ASSOCIATED PROTEIN MTA1
B: HISTONE DEACETYLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,45420
Polymers150,2804
Non-polymers1,17416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area15800 Å2
ΔGint-277.4 kcal/mol
Surface area40820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.199, 108.199, 133.164
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsDIMER OF A HETERODIMERIC COMPLEX

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein METASTASIS-ASSOCIATED PROTEIN MTA1


Mass: 19961.213 Da / Num. of mol.: 1 / Fragment: ELM2-SANT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: Q13330
#2: Protein HISTONE DEACETYLASE 1 / HD1


Mass: 55178.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: Q13547, histone deacetylase

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 3.71 Å3/Da / Density % sol: 66.8 % / Description: NONE
Crystal growpH: 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: 0.9778
DetectorDate: Oct 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3→76.6 Å / Num. obs: 16916 / % possible obs: 96.7 % / Observed criterion σ(I): 1.8 / Redundancy: 3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6
Reflection shellResolution: 3→3.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.1 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A69

4a69


Resolution: 3→76.75 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.876 / SU B: 17.18 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26149 910 5.1 %RANDOM
Rwork0.21084 ---
obs0.21337 16916 96.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.5 Å20 Å2
2--0.5 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 3→76.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4235 0 27 0 4262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194357
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.9525896
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.835527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69224.055217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65315722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6941524
X-RAY DIFFRACTIONr_chiral_restr0.0680.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213358
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 68 -
Rwork0.329 1261 -
obs--97.51 %

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