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- PDB-3met: Crystal structure of SGF29 in complex with H3K4me2 -

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Basic information

Entry
Database: PDB / ID: 3met
TitleCrystal structure of SGF29 in complex with H3K4me2
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 / establishment of protein localization to chromatin / ATAC complex / SAGA complex / regulation of tubulin deacetylation / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair ...SAGA-type complex / establishment of protein localization to chromatin / ATAC complex / SAGA complex / regulation of tubulin deacetylation / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair / transcription initiation-coupled chromatin remodeling / methylated histone binding / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...SGF29 tudor-like domain / SAGA-associated factor 29 / : / : / SGF29 tudor-like domain / SGF29 C-terminal domain profile. / SH3 type barrels. - #140 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / SH3 type barrels. / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBian, C.B. / Xu, C. / Lam, R. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / 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

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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: SAGA-associated factor 29 homolog
C: Histone H3
D: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,43310
Polymers43,1484
Non-polymers2846
Water3,549197
1
A: SAGA-associated factor 29 homolog
C: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6705
Polymers21,5742
Non-polymers963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-19 kcal/mol
Surface area9820 Å2
MethodPISA
2
B: SAGA-associated factor 29 homolog
D: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7625
Polymers21,5742
Non-polymers1883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-19 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.162, 65.411, 105.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 20295.742 Da / Num. of mol.: 2 / Fragment: UNP Residues 115-293
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(DE3)-V2R-pRARE2 / References: UniProt: Q96ES7
#2: Protein/peptide Histone H3 / / H3K4me2 11mer


Mass: 1278.482 Da / Num. of mol.: 2 / Fragment: UNP Residues 2-12 / Source method: obtained synthetically / Details: H3K4me2 11mer / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: Q92133

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Non-polymers , 4 types, 203 molecules

#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20-28% PEG3350, 0.1M Bis-Tris pH 5.5, vapor diffusion, Sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→55.65 Å / Num. all: 24231 / Num. obs: 24197
Reflection shellResolution: 2→2.03 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.139 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24273 1233 5.1 %RANDOM
Rwork0.1958 ---
obs0.19813 22916 99.89 %-
all-22964 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.243 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 19 197 2999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222960
X-RAY DIFFRACTIONr_bond_other_d0.0010.022024
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9824058
X-RAY DIFFRACTIONr_angle_other_deg0.90134941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4965377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.08623.566129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67115450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2741523
X-RAY DIFFRACTIONr_chiral_restr0.090.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02576
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_it0.8111.51857
X-RAY DIFFRACTIONr_mcbond_other0.1981.5717
X-RAY DIFFRACTIONr_mcangle_it1.45723007
X-RAY DIFFRACTIONr_scbond_it2.33331103
X-RAY DIFFRACTIONr_scangle_it3.4254.51043
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 91 -
Rwork0.25 1604 -
obs--98.49 %

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