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- PDB-6nfx: MBTD1 MBT repeats -

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Basic information

Entry
Database: PDB / ID: 6nfx
TitleMBTD1 MBT repeats
ComponentsMBT domain-containing protein 1,Enhancer of polycomb homolog 1
KeywordsPROTEIN BINDING / MBT domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


NuA4 histone acetyltransferase complex binding / : / : / vascular associated smooth muscle cell differentiation / piccolo histone acetyltransferase complex / embryonic skeletal system development / regulation of double-strand break repair / negative regulation of G0 to G1 transition / regulation of growth / NuA4 histone acetyltransferase complex ...NuA4 histone acetyltransferase complex binding / : / : / vascular associated smooth muscle cell differentiation / piccolo histone acetyltransferase complex / embryonic skeletal system development / regulation of double-strand break repair / negative regulation of G0 to G1 transition / regulation of growth / NuA4 histone acetyltransferase complex / negative regulation of gene expression, epigenetic / Transcriptional Regulation by E2F6 / positive regulation of double-strand break repair via homologous recombination / methylated histone binding / double-strand break repair via homologous recombination / nucleosome / site of double-strand break / chromatin organization / HATs acetylate histones / regulation of apoptotic process / nuclear membrane / nuclear body / regulation of cell cycle / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Enhancer of polycomb, C-terminal / Enhancer of Polycomb C-terminus / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Enhancer of polycomb protein / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 ...Enhancer of polycomb, C-terminal / Enhancer of Polycomb C-terminus / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Enhancer of polycomb protein / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like
Similarity search - Domain/homology
MBT domain-containing protein 1 / Enhancer of polycomb homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhang, H. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Cell Rep / Year: 2020
Title: Structural Basis for EPC1-Mediated Recruitment of MBTD1 into the NuA4/TIP60 Acetyltransferase Complex.
Authors: Zhang, H. / Devoucoux, M. / Song, X. / Li, L. / Ayaz, G. / Cheng, H. / Tempel, W. / Dong, C. / Loppnau, P. / Cote, J. / Min, J.
History
DepositionDec 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MBT domain-containing protein 1,Enhancer of polycomb homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,37941
Polymers52,2631
Non-polymers11540
Water1,56787
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-10 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.607, 124.724, 70.057
Angle α, β, γ (deg.)90.000, 92.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-715-

UNX

21A-729-

UNX

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Components

#1: Protein MBT domain-containing protein 1,Enhancer of polycomb homolog 1


Mass: 52263.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBTD1, EPC1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q05BQ5, UniProt: Q9H2F5
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 38 / Source method: obtained synthetically
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 10% PEG-6000, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.95→46.6 Å / Num. obs: 42419 / % possible obs: 99.1 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.05 / Rrim(I) all: 0.094 / Net I/σ(I): 10.7 / Num. measured all: 145714 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-23.41.2421013629690.3310.7861.475198.8
8.94-46.63.30.02614724450.9990.0170.03140.697.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3feo

3feo


Resolution: 1.95→44.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.005 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.2213 2154 5.1 %
Rwork0.1854 --
obs0.1872 40261 99.05 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.95 Å2 / Biso mean: 33.087 Å2 / Biso min: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20.66 Å2
2--0.65 Å20 Å2
3----0.29 Å2
Refinement stepCycle: final / Resolution: 1.95→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 45 87 3449
Biso mean--39.93 37.19 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133439
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173065
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.6344694
X-RAY DIFFRACTIONr_angle_other_deg1.3861.5667078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6915427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.97621.688160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10215503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1081517
X-RAY DIFFRACTIONr_chiral_restr0.0770.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023862
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02765
X-RAY DIFFRACTIONr_mcbond_it3.1033.5181716
X-RAY DIFFRACTIONr_mcbond_other3.1023.521717
X-RAY DIFFRACTIONr_mcangle_it4.145.2572141
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 148 -
Rwork0.303 2963 -
all-3111 -
obs--98.73 %

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