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- PDB-3mp6: Complex Structure of Sgf29 and dimethylated H3K4 -

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Basic information

Entry
Database: PDB / ID: 3mp6
TitleComplex Structure of Sgf29 and dimethylated H3K4
Components
  • H3K4me2 peptide
  • Maltose-binding periplasmic protein,LINKER,SAGA-associated factor 29
KeywordsHISTONE BINDING PROTEIN / Histone / Tudor Domain / H3K4me2 / SAGA
Function / homology
Function and homology information


ADA complex / SAGA complex localization to transcription regulatory region / SLIK (SAGA-like) complex / SAGA complex / detection of maltose stimulus / maltose transport complex / : / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding ...ADA complex / SAGA complex localization to transcription regulatory region / SLIK (SAGA-like) complex / SAGA complex / detection of maltose stimulus / maltose transport complex / : / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Chromatin modifying enzymes / telomere organization / ATP-binding cassette (ABC) transporter complex / 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 / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / cell chemotaxis / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 / intracellular protein localization / nucleosome / nucleosome assembly / outer membrane-bounded periplasmic space / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / 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 / periplasmic space / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
SGF29 tudor-like domain / SAGA-associated factor 29 / : / : / SGF29 tudor-like domain / SGF29 C-terminal domain profile. / SH3 type barrels. - #140 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...SGF29 tudor-like domain / SAGA-associated factor 29 / : / : / SGF29 tudor-like domain / SGF29 C-terminal domain profile. / SH3 type barrels. - #140 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / SH3 type barrels. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / SAGA complex subunit SGF29 / Histone H3.1
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
unidentified (others)
Saccharomyces cerevisiae S288c (yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsLi, J. / Wu, M. / Ruan, J. / Zang, J.
CitationJournal: Embo J. / Year: 2011
Title: Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation
Authors: Bian, C. / Xu, C. / Ruan, J. / Lee, K.K. / Burke, T.L. / Tempel, W. / Barsyte, D. / Li, J. / Wu, M. / Zhou, B.O. / Fleharty, B.E. / Paulson, A. / Allali-Hassani, A. / Zhou, J.Q. / Mer, G. / ...Authors: Bian, C. / Xu, C. / Ruan, J. / Lee, K.K. / Burke, T.L. / Tempel, W. / Barsyte, D. / Li, J. / Wu, M. / Zhou, B.O. / Fleharty, B.E. / Paulson, A. / Allali-Hassani, A. / Zhou, J.Q. / Mer, G. / Grant, P.A. / Workman, J.L. / Zang, J. / Min, J.
History
DepositionApr 25, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3Jun 21, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / struct_ref / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 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 / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,LINKER,SAGA-associated factor 29
P: H3K4me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3683
Polymers58,0262
Non-polymers3421
Water11,367631
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-4 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.169, 85.333, 119.313
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Maltose-binding periplasmic protein,LINKER,SAGA-associated factor 29 / MBP / Sgf29


Mass: 57521.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of Maltose-binding periplasmic protein, SAGA-associated factor 29
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) unidentified (others), (gene. exp.) Saccharomyces cerevisiae S288c (yeast)
Strain: K12, S288c / Gene: malE, SGF29 / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9, UniProt: P25554
#2: Protein/peptide H3K4me2 peptide


Mass: 503.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others) / References: UniProt: P68431*PLUS
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.2 Å3/Da / Density % sol: 44.11 % / Mosaicity: 0.312 °
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% PEG3350, 0.1M sodium acetate, pH 4.5, vapor diffusion, hanging drop, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. all: 86450 / Num. obs: 86450 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.06 / Χ2: 0.976 / Net I/σ(I): 25.7
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4216 / Rsym value: 0.4 / Χ2: 0.728 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HSJ

1hsj


Resolution: 1.48→31.17 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1662 2 %RANDOM
Rwork0.183 ---
obs0.183 81179 95.91 %-
all-84640 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 43.17 Å2 / Biso mean: 15.248 Å2 / Biso min: 2.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.48→31.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3984 0 23 631 4638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224273
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9795834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2265556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63925.211190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87415723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1211518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213272
LS refinement shellResolution: 1.478→1.516 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 82 -
Rwork0.236 5389 -
all-5471 -
obs-3750 88.94 %

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