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- PDB-3kmt: Crystal structure of vSET/SAH/H3 ternary complex -

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Basic information

Entry
Database: PDB / ID: 3kmt
TitleCrystal structure of vSET/SAH/H3 ternary complex
Components
  • A612L protein
  • Histone H3
KeywordsVIRAL PROTEIN / SET domain / ternary complex
Function / homology
Function and homology information


histone H3K37 methyltransferase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression ...histone H3K37 methyltransferase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / methylation / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus
Similarity search - Function
Histone-lysine N-methyltransferase, H3 lysine-37 specific / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Histone H3 signature 1. ...Histone-lysine N-methyltransferase, H3 lysine-37 specific / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H3K27 methylase / Histone H3.1
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsWei, H. / Zhou, M.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Dimerization of a viral SET protein endows its function.
Authors: Wei, H. / Zhou, M.M.
History
DepositionNov 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A612L protein
B: A612L protein
C: A612L protein
G: Histone H3
H: Histone H3
I: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4219
Polymers43,2686
Non-polymers1,1533
Water5,242291
1
A: A612L protein
G: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8073
Polymers14,4232
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-5 kcal/mol
Surface area6910 Å2
MethodPISA
2
B: A612L protein
H: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8073
Polymers14,4232
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-4 kcal/mol
Surface area6820 Å2
MethodPISA
3
C: A612L protein
I: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8073
Polymers14,4232
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-5 kcal/mol
Surface area6960 Å2
MethodPISA
4
A: A612L protein
B: A612L protein
G: Histone H3
H: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6146
Polymers28,8454
Non-polymers7692
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-27 kcal/mol
Surface area11790 Å2
MethodPISA
5
C: A612L protein
I: Histone H3
hetero molecules

C: A612L protein
I: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6146
Polymers28,8454
Non-polymers7692
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4620 Å2
ΔGint-26 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.085, 38.722, 73.208
Angle α, β, γ (deg.)90.00, 107.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-286-

HOH

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Components

#1: Protein A612L protein


Mass: 13606.623 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: O41094
#2: Protein/peptide Histone H3


Mass: 815.938 Da / Num. of mol.: 3 / Fragment: residues 26-33 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 2, 2009
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→20 Å / Num. all: 40160 / Num. obs: 40039 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KMA

3kma


Resolution: 1.78→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.224 1944 random
Rwork0.196 --
all0.21 40160 -
obs0.21 40039 -
Refinement stepCycle: LAST / Resolution: 1.78→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 78 291 3324
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
LS refinement shellResolution: 1.78→1.8 Å / Rfactor Rfree error: 0.005
RfactorNum. reflection% reflection
Rfree0.326 37 -
Rwork0.262 --
obs-905 99.9 %

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