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- PDB-9v17: Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant -

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Basic information

Entry
Database: PDB / ID: 9v17
TitleCrystal structure of E. coli glycogen phosphorylase N185A/R267E mutant
ComponentsGlycogen phosphorylase
KeywordsTRANSFERASE / glycogen phosphorylase
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Phosphorylase pyridoxal-phosphate attachment site. / Glycosyl transferase, family 35 / Carbohydrate phosphorylase
Similarity search - Domain/homology
Glycogen phosphorylase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsTakai, M. / Shobu, K. / Fukuda, Y. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Sci Adv / Year: 2026
Title: Structural basis of transcription-coupled H3K36 trimethylation by Set2 in coordination with FACT.
Authors: Tomoya Kujirai / Haruhiko Ehara / Tomoko Ito / Masami Henmi / Eriko Oya / Takehiko Kobayashi / Shun-Ichi Sekine / Hitoshi Kurumizaka /
Abstract: Trimethylation of the histone H3K36 residue (H3K36me3) plays an indispensable role in ensuring transcription fidelity by suppressing undesired cryptic transcription in chromatin. H3K36me3 ...Trimethylation of the histone H3K36 residue (H3K36me3) plays an indispensable role in ensuring transcription fidelity by suppressing undesired cryptic transcription in chromatin. H3K36me3 modification is accomplished by Set2/SETD2 during transcription elongation by the RNA polymerase II elongation complex (EC). Here, we found that Set2-mediated H3K36me3 deposition occurs on the nucleosome reassembling behind the EC. The histone chaperone FACT suppresses H3K36me3 deposition on the downstream nucleosome, thereby ensuring that Set2 targets specifically on the reassembling upstream nucleosome. Cryo-electron microscopy structures of the nucleosome-transcribing EC complexed with Set2 revealed that Set2 is anchored by the Spt6 subunit of the EC to capture both of the H3 N-terminal tails in a stepwise manner during the nucleosome reassembly process. Abrogation of the Set2-EC interaction leads to defective transcription-coupled H3K36me3 deposition. These insights elucidate the structure-based mechanism of transcription-coupled H3K36me3 deposition in chromatin.
History
DepositionMay 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen phosphorylase
B: Glycogen phosphorylase
C: Glycogen phosphorylase
D: Glycogen phosphorylase


Theoretical massNumber of molelcules
Total (without water)374,5064
Polymers374,5064
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.297, 187.297, 449.824
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
Glycogen phosphorylase


Mass: 93626.562 Da / Num. of mol.: 4 / Mutation: N185A/R267E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: glgP, glgY, b3428, JW3391 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AC86, glycogen phosphorylase
Has ligand of interestN
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: 5.27 Å3/Da / Density % sol: 76.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2% v/v 1,4-dioxane, 0.1M Tris pH 8.0, 15% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.7→49.6 Å / Num. obs: 84810 / % possible obs: 98.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 126.86 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.082 / Rrim(I) all: 0.262 / Net I/σ(I): 9
Reflection shellResolution: 3.7→3.77 Å / Redundancy: 9 % / Rmerge(I) obs: 2.95 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4444 / CC1/2: 0.782 / Rpim(I) all: 0.995 / Rrim(I) all: 3.13 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→49.6 Å / SU ML: 0.4497 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2294 4286 5.06 %
Rwork0.1958 80358 -
obs0.1975 84644 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 137.87 Å2
Refinement stepCycle: LAST / Resolution: 3.7→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25758 0 0 0 25758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326334
X-RAY DIFFRACTIONf_angle_d0.642435721
X-RAY DIFFRACTIONf_chiral_restr0.04323896
X-RAY DIFFRACTIONf_plane_restr0.00494633
X-RAY DIFFRACTIONf_dihedral_angle_d6.98653539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.740.37961280.35322665X-RAY DIFFRACTION98.97
3.74-3.790.3651240.33842665X-RAY DIFFRACTION98.73
3.79-3.830.37881400.31172649X-RAY DIFFRACTION98.66
3.83-3.880.33281300.30812643X-RAY DIFFRACTION98.58
3.88-3.930.31881310.28882652X-RAY DIFFRACTION98.72
3.93-3.990.25391590.27242658X-RAY DIFFRACTION98.63
3.99-4.040.31881560.2732621X-RAY DIFFRACTION98.86
4.04-4.10.31131370.27322649X-RAY DIFFRACTION98.69
4.1-4.170.30191600.26132653X-RAY DIFFRACTION98.77
4.17-4.240.31151620.25722632X-RAY DIFFRACTION98.87
4.24-4.310.24011510.24482636X-RAY DIFFRACTION98.94
4.31-4.390.29691470.22012677X-RAY DIFFRACTION98.74
4.39-4.470.25371400.21462661X-RAY DIFFRACTION98.73
4.47-4.560.23671590.21552650X-RAY DIFFRACTION98.84
4.56-4.660.24281560.20862649X-RAY DIFFRACTION98.73
4.66-4.770.22071290.19732669X-RAY DIFFRACTION98.73
4.77-4.890.21461310.19382690X-RAY DIFFRACTION98.57
4.89-5.020.23931440.19572655X-RAY DIFFRACTION98.35
5.02-5.170.22831520.18882670X-RAY DIFFRACTION98.22
5.17-5.330.25381300.19982676X-RAY DIFFRACTION98.15
5.34-5.530.23491230.20342697X-RAY DIFFRACTION97.98
5.53-5.750.24461410.20942663X-RAY DIFFRACTION98.35
5.75-6.010.25841440.20582697X-RAY DIFFRACTION98.44
6.01-6.320.22151430.18862691X-RAY DIFFRACTION98.3
6.32-6.720.22171300.18252709X-RAY DIFFRACTION98.2
6.72-7.240.21741440.19252719X-RAY DIFFRACTION98.08
7.24-7.960.18531430.15322710X-RAY DIFFRACTION97.97
7.96-9.110.17941590.13932731X-RAY DIFFRACTION97.77
9.11-11.450.13271430.11072753X-RAY DIFFRACTION96.66
11.45-49.60.19551500.15882868X-RAY DIFFRACTION95.36

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