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- PDB-5i3l: DPF3b in complex with H3K14ac peptide -

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Basic information

Entry
Database: PDB / ID: 5i3l
TitleDPF3b in complex with H3K14ac peptide
Components
  • H3K14ac peptide
  • Zinc finger protein DPF3
KeywordsPEPTIDE BINDING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


nBAF complex / brahma complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / muscle organ development / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle ...nBAF complex / brahma complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / muscle organ development / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of cell differentiation / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nervous system development / nucleosome assembly / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / cadherin binding / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
DPF1-3, N-terminal domain / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / PHD-finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. ...DPF1-3, N-terminal domain / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / PHD-finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / Zinc finger protein DPF3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsTempel, W. / Liu, Y. / Walker, J.R. / Zhao, A. / Qin, S. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystal structure of DPF3b in complex with an acetylated histone peptide.
Authors: Li, W. / Zhao, A. / Tempel, W. / Loppnau, P. / Liu, Y.
History
DepositionFeb 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Aug 9, 2017Group: Database references / Derived calculations / Source and taxonomy
Category: citation / pdbx_entity_src_syn ...citation / pdbx_entity_src_syn / pdbx_related_exp_data_set / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._citation.journal_id_CSD / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_related_exp_data_set.data_reference / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Aug 15, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.5Sep 27, 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 / struct_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Nov 13, 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: Zinc finger protein DPF3
B: Zinc finger protein DPF3
C: H3K14ac peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,60145
Polymers27,9933
Non-polymers60842
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-18 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.822, 121.641, 56.446
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein Zinc finger protein DPF3 / BRG1-associated factor 45C / BAF45C / Zinc finger protein cer-d4


Mass: 12881.659 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF3, BAF45C, CERD4 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q92784
#2: Protein/peptide H3K14ac peptide


Mass: 2229.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others) / References: UniProt: P68431*PLUS

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Non-polymers , 5 types, 133 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 32 / Source method: obtained synthetically
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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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: 1

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.4 M sodium citrate, 0.1 M HEPES, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.28215 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28215 Å / Relative weight: 1
ReflectionResolution: 1.85→50.01 Å / Num. obs: 29753 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.041 / Rrim(I) all: 0.11 / Net I/σ(I): 17.7 / Num. measured all: 210147 / Scaling rejects: 38
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.125 / Mean I/σ(I) obs: 2 / Num. measured all: 12925 / Num. unique all: 1817 / CC1/2: 0.717 / Rpim(I) all: 0.453 / Rrim(I) all: 1.214 / Rejects: 0 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementStarting model: unpublished model, ultimately derived from PDB entry 3V43.

3v43


Resolution: 1.85→50.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.877 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 1624 5.5 %thin shells (sftools)
Rwork0.1817 ---
obs0.1833 28115 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.56 Å2 / Biso mean: 34.598 Å2 / Biso min: 7.87 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å2-0 Å20 Å2
2--0.42 Å2-0 Å2
3---1.79 Å2
Refinement stepCycle: final / Resolution: 1.85→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 45 91 1973
Biso mean--32.57 35.64 -
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021960
X-RAY DIFFRACTIONr_bond_other_d0.0020.021736
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9722656
X-RAY DIFFRACTIONr_angle_other_deg1.1533.0144015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.315254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.47524.93779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93415313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.861158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212210
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02419
X-RAY DIFFRACTIONr_mcbond_it1.5782.261982
X-RAY DIFFRACTIONr_mcbond_other1.5762.261982
X-RAY DIFFRACTIONr_mcangle_it2.3283.3781226
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 204 -
Rwork0.269 1973 -
all-2177 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6613-2.13761.10853.7201-1.10731.7797-0.0422-0.2074-0.29750.27770.22440.1180.0584-0.0593-0.18210.04650.00990.00070.01980.01170.07756.072135.10140.2264
23.15210.10482.34990.4011-0.58173.517-0.10740.0880.03590.131-0.02260.0502-0.12970.04330.130.0971-0.03180.06220.0125-0.02040.056523.341149.82-2.2779
39.2399-4.85922.58222.9066-0.68782.0103-0.2429-0.9032-0.19830.14590.44640.0279-0.0847-0.3178-0.20340.21590.03470.03140.21270.07660.16223.0058139.72627.4216
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A256 - 1004
2X-RAY DIFFRACTION2B255 - 1004
3X-RAY DIFFRACTION3C1 - 17

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