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- PDB-3mea: Crystal structure of the SGF29 in complex with H3K4me3 -

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Basic information

Entry
Database: PDB / ID: 3mea
TitleCrystal structure of the SGF29 in complex with H3K4me3
Components
  • Histone H3
  • SAGA-associated factor 29 homolog
KeywordsTRANSCRIPTION / Structural Genomics Consortium / SGC / Nucleus / Transcription regulation / Chromosomal protein / DNA-binding / Nucleosome core
Function / homology
Function and homology information


SAGA-type complex / histone H3K36me3 reader activity / establishment of protein localization to chromatin / ATAC complex / histone H3K4me3 reader activity / SAGA complex / Formation of WDR5-containing histone-modifying complexes / regulation of RNA splicing / : / regulation of embryonic development ...SAGA-type complex / histone H3K36me3 reader activity / establishment of protein localization to chromatin / ATAC complex / histone H3K4me3 reader activity / SAGA complex / Formation of WDR5-containing histone-modifying complexes / regulation of RNA splicing / : / regulation of embryonic development / regulation of cell division / regulation of DNA repair / transcription initiation-coupled chromatin remodeling / response to endoplasmic reticulum stress / mitotic spindle / structural constituent of chromatin / nucleosome / HATs acetylate histones / regulation of cell cycle / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
SGF29 tudor-like domain / SAGA-associated factor 29 / : / : / SGF29 tudor-like domain / SGF29 C-terminal domain profile. / SH3 type barrels. - #140 / SH3 type barrels. / Histone H3 signature 1. / Histone H3 signature 2. ...SGF29 tudor-like domain / SAGA-associated factor 29 / : / : / SGF29 tudor-like domain / SGF29 C-terminal domain profile. / SH3 type barrels. - #140 / 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 / Mainly Beta
Similarity search - Domain/homology
Histone H3 / SAGA-associated factor 29
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.26 Å
AuthorsBian, C. / Xu, C. / Tempel, W. / MacKenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
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
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAGA-associated factor 29 homolog
B: Histone H3


Theoretical massNumber of molelcules
Total (without water)21,7352
Polymers21,7352
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.385, 41.425, 52.527
Angle α, β, γ (deg.)90.000, 121.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SAGA-associated factor 29 homolog / Coiled-coil domain-containing protein 101


Mass: 20441.918 Da / Num. of mol.: 1 / Fragment: UNP Residues 129-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCDC101, SGF29 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q96ES7
#2: Protein/peptide Histone H3 / H3K4me3


Mass: 1293.516 Da / Num. of mol.: 1 / Fragment: UNP Residues 2-4 / Source method: obtained synthetically / Details: H3K4me3 3mer / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: Q92133
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% peg3350, 0.1M HEPES. 0.004M trimethylated H3K3 peptide was present in the protein stock solution, pH 7.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.26→30 Å / Num. obs: 46388 / % possible obs: 99.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.052 / Χ2: 1.437 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.26-1.282.80.97322852.465199.1
1.28-1.313.20.87923052.382199.9
1.31-1.333.40.76323082.2241100
1.33-1.363.50.64223082.011100
1.36-1.393.60.5123321.825199.9
1.39-1.423.60.41923051.6581100
1.42-1.453.60.32222931.5811100
1.45-1.493.60.2623061.405199.9
1.49-1.543.60.223241.341100
1.54-1.593.60.16923221.273199.9
1.59-1.643.60.13723011.225199.9
1.64-1.713.60.10723271.1751100
1.71-1.793.70.08222741.124199.7
1.79-1.883.60.06523481.1481100
1.88-23.70.05422931.303199.9
2-2.153.60.04923371.538199.9
2.15-2.373.60.04323291.454199.8
2.37-2.713.50.02923390.8941100
2.71-3.423.60.0223550.6781100
3.42-303.70.01823970.666199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ME9

3me9


Resolution: 1.26→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.181 / SU B: 1.476 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1445 3.117 %RANDOM
Rwork0.178 ---
obs0.179 46365 99.834 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.384 Å2
Baniso -1Baniso -2Baniso -3
1--0.221 Å20 Å2-0.133 Å2
2--0.129 Å20 Å2
3----0.047 Å2
Refinement stepCycle: LAST / Resolution: 1.26→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 0 156 1450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221359
X-RAY DIFFRACTIONr_bond_other_d0.0010.02912
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9761871
X-RAY DIFFRACTIONr_angle_other_deg0.91932230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3295173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.96523.87162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26415194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.63159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211526
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02268
X-RAY DIFFRACTIONr_mcbond_it1.5561.5851
X-RAY DIFFRACTIONr_mcbond_other0.4371.5326
X-RAY DIFFRACTIONr_mcangle_it2.44721379
X-RAY DIFFRACTIONr_scbond_it3.1893508
X-RAY DIFFRACTIONr_scangle_it4.514.5487
X-RAY DIFFRACTIONr_rigid_bond_restr1.24632271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.26-1.2930.322930.3033303342799.095
1.293-1.3280.2931120.2563180329699.879
1.328-1.3660.2591000.2363122322599.907
1.366-1.4080.2091040.1873006311299.936
1.408-1.4540.196940.1692954304999.967
1.454-1.5050.206830.1482871295699.932
1.505-1.5610.1791020.13427452847100
1.561-1.6250.19780.1392632271599.816
1.625-1.6960.187830.1372561264599.962
1.696-1.7780.195770.1382425250699.84
1.778-1.8740.177730.1432333240999.875
1.874-1.9860.169690.162187225999.867
1.986-2.1220.215640.1672070213699.906
2.122-2.290.187680.1681927199799.9
2.29-2.5050.224560.1811778183799.837
2.505-2.7950.221490.1811631168199.941
2.795-3.2170.18570.19614201477100
3.217-3.9150.212390.19512281267100
3.915-5.4340.158340.168962996100
5.434-200.196100.25858560598.347

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