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- PDB-3me9: Crystal structure of SGF29 in complex with H3K4me3 peptide -

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Basic information

Entry
Database: PDB / ID: 3me9
TitleCrystal structure of SGF29 in complex with H3K4me3 peptide
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 / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / 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 / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / 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 / SYNCHROTRON / SAD / sad / Resolution: 1.37 Å
AuthorsBian, C. / Tempel, W. / Xu, C. / Guo, Y. / Dong, A. / Crombet, L. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. ...Bian, C. / Tempel, W. / Xu, C. / Guo, Y. / Dong, A. / Crombet, L. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)43,46318
Polymers43,1794
Non-polymers28414
Water5,441302
1
B: SAGA-associated factor 29 homolog
D: Histone H3
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)43,46318
Polymers43,1794
Non-polymers28414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3620 Å2
ΔGint-46 kcal/mol
Surface area18260 Å2
MethodPISA
2
A: SAGA-associated factor 29 homolog
C: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6859
Polymers21,5892
Non-polymers967
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-19 kcal/mol
Surface area9930 Å2
MethodPISA
3
B: SAGA-associated factor 29 homolog
D: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7779
Polymers21,5892
Non-polymers1887
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-19 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.038, 65.434, 105.619
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 / H3K4me3 8mer


Mass: 1293.516 Da / Num. of mol.: 2 / Fragment: UNP Residues 2-9 / Source method: obtained synthetically / Details: H3K4me3 8mer / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: Q92133

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Non-polymers , 4 types, 316 molecules

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


Num. of mol.: 11 / Source method: obtained synthetically
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 302 / 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: 38.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.1M ammonium sulfate, 0.1M Bis-Tris, pH 5.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97927
ROTATING ANODERIGAKU FR-E SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 15, 2009
RIGAKU RAXIS2IMAGE PLATEOct 5, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979271
21.54181
ReflectionResolution: 1.37→20 Å / Num. obs: 73960 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.37-1.396.90.9721,2100
1.39-1.4270.8271,2100
1.42-1.457.10.7071,2100
1.45-1.487.10.5951,2100
1.48-1.517.10.5211,2100
1.51-1.547.10.4381,2100
1.54-1.587.20.3621,2100
1.58-1.627.20.3271,2100
1.62-1.677.20.2751,2100
1.67-1.737.20.2251,2100
1.73-1.797.20.1861,2100
1.79-1.867.20.1471,2100
1.86-1.947.20.1271,2100
1.94-2.057.20.1061,2100
2.05-2.177.20.0961,2100
2.17-2.347.20.0881,2100
2.34-2.587.10.0751,2100
2.58-2.956.90.0591,2100
2.95-3.717.20.0461,2100
3.71-206.90.0411,299.9

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Phasing

PhasingMethod: sad

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.37→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / Matrix type: sparse / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.186 / SU B: 0.979 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21353 2001 2.719 %RANDOM
Rwork0.19105 71590 --
obs0.19167 73591 99.995 %-
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: 11.704 Å2
Baniso -1Baniso -2Baniso -3
1-0.317 Å20 Å20 Å2
2---0.372 Å20 Å2
3---0.056 Å2
Refinement stepCycle: LAST / Resolution: 1.37→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 27 302 3151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223052
X-RAY DIFFRACTIONr_bond_other_d0.0010.022106
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9864193
X-RAY DIFFRACTIONr_angle_other_deg0.91335143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7315392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.56523.504137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67915472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3351526
X-RAY DIFFRACTIONr_chiral_restr0.0950.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
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_it0.9421.51899
X-RAY DIFFRACTIONr_mcbond_other0.2711.5734
X-RAY DIFFRACTIONr_mcangle_it1.64523089
X-RAY DIFFRACTIONr_scbond_it2.56431153
X-RAY DIFFRACTIONr_scangle_it3.6954.51093
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
1.37-1.4050.2971440.29451950.29453391000.28
1.405-1.4440.2781510.25151000.25252511000.233
1.444-1.4850.2341400.21749280.21850681000.196
1.485-1.5310.2241230.20848140.20949371000.184
1.531-1.5810.2451280.19646690.19847971000.171
1.581-1.6360.2411070.18645240.18746311000.161
1.636-1.6970.227880.18243910.18344791000.159
1.697-1.7660.221970.1841160.18243131000.156
1.766-1.8440.257840.18340790.18441631000.16
1.844-1.9330.19770.1839100.1839871000.161
1.933-2.0360.1951340.1836420.1837761000.164
2.036-2.1590.237720.17335370.17436091000.162
2.159-2.3060.1761100.17832820.17833921000.169
2.306-2.4880.2371160.18630560.18831721000.179
2.488-2.7210.207450.19928810.19929261000.195
2.721-3.0350.216710.18925950.1926661000.192
3.035-3.4910.197930.19522830.19523761000.201
3.491-4.2440.168510.16820010.16820521000.183
4.244-5.8710.192420.17415960.17516381000.199
5.871-200.264280.2619910.261102399.6090.301

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