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- PDB-2bqz: Crystal structure of a ternary complex of the human histone methy... -

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Basic information

Entry
Database: PDB / ID: 2bqz
TitleCrystal structure of a ternary complex of the human histone methyltransferase Pr-SET7 (also known as SET8)
Components
  • HISTONE H4
  • SET8 PROTEIN
KeywordsTRANSFERASE / HISTONE H4 METHYLTRANSFERSAE / LYSINE METHYLTRANSFERASE / SET DOMAIN
Function / homology
Function and homology information


: / histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / peptidyl-lysine monomethylation / polytene chromosome / protein-lysine N-methyltransferase activity / mitotic chromosome condensation ...: / histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / peptidyl-lysine monomethylation / polytene chromosome / protein-lysine N-methyltransferase activity / mitotic chromosome condensation / regulation of DNA damage response, signal transduction by p53 class mediator / histone methyltransferase activity / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / negative regulation of double-strand break repair via homologous recombination / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Transferases; Transferring one-carbon groups; Methyltransferases / 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 / regulation of signal transduction by p53 class mediator / methyltransferase activity / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Regulation of TP53 Activity through Methylation / 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 / transcription corepressor activity / nucleosome / nucleosome assembly / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / methylation / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / cell cycle / protein heterodimerization activity / Amyloid fiber formation / cell division / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / cytosol
Similarity search - Function
Class V SAM-dependent methyltransferases / : / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / 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 ...Class V SAM-dependent methyltransferases / : / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / 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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / Beta Complex / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H4 / SET and MYND domain-containing protein 5 / N-lysine methyltransferase KMT5A / N-lysine methyltransferase KMT5A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 Å
AuthorsXiao, B. / Jing, C. / Kelly, G. / Walker, P.A. / Muskett, F.W. / Frenkiel, T.A. / Martin, S.R. / Sarma, K. / Reinberg, D. / Gamblin, S.J. / Wilson, J.R.
CitationJournal: Genes Dev. / Year: 2005
Title: Specificity and Mechanism of the Histone Methyltransferase Pr-Set7
Authors: Xiao, B. / Jing, C. / Kelly, G. / Walker, P.A. / Muskett, F.W. / Frenkiel, T.A. / Martin, S.R. / Sarma, K. / Reinberg, D. / Gamblin, S.J. / Wilson, J.R.
History
DepositionApr 28, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SET8 PROTEIN
B: HISTONE H4
E: SET8 PROTEIN
F: HISTONE H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2926
Polymers39,5234
Non-polymers7692
Water11,043613
1
A: SET8 PROTEIN
B: HISTONE H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1463
Polymers19,7612
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: SET8 PROTEIN
F: HISTONE H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1463
Polymers19,7612
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.179, 46.322, 51.998
Angle α, β, γ (deg.)64.74, 86.66, 90.61
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98322, -0.12262, 0.13505), (-0.04742, -0.54307, -0.83835), (0.17614, -0.83069, 0.52814)
Vector: 11.6667, 32.69479, 11.51827)
DetailsTHE DIMER IN THIS ENTRY IS FORMED BY THE COMPLEXOF CHAIN A WITH A PEPTIDE CHAIN B AND CHAIN E WITHPEPTIDE CHAIN F. CHAINS A AND E ARE MONOMERIC IN THEPHYSIOLOGICAL STATE.

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Components

#1: Protein SET8 PROTEIN / HISTONE-LYSINE METHYLTRANSFERASE PR-SET7


Mass: 18386.801 Da / Num. of mol.: 2 / Fragment: SET-DOMAIN, RESIDUES 192-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q86W83, UniProt: Q9NQR1*PLUS, histone-lysine N-methyltransferase
#2: Protein/peptide HISTONE H4


Mass: 1374.595 Da / Num. of mol.: 2 / Fragment: RESIDUES 17-25 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P62805, UniProt: Q6GMV2*PLUS
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF CHAINS A AND E CORRESPONDS MOST CLOSELY TO THE NCBI ENTRY NP_065115. THERE IS A ...THE SEQUENCE OF CHAINS A AND E CORRESPONDS MOST CLOSELY TO THE NCBI ENTRY NP_065115. THERE IS A SINGLE SEQUENCE DIFFERENCE BETWEEN NP_065115 AND UNIPROT ENTRY Q86W83, AT POSITION 316, WHICH IS GIVEN AS PRO IN THE NCBI ENTRY BUT ARG IN UNIPROT.

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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: 1.9 Å3/Da / Density % sol: 34.92 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.5→19.9 Å / Num. obs: 63273 / % possible obs: 89.1 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.934 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2663 5 %RANDOM
Rwork0.187 ---
obs0.188 50828 94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20.58 Å2-0.1 Å2
2---1.87 Å20.41 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 50 613 3437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212870
X-RAY DIFFRACTIONr_bond_other_d0.0010.022568
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9853840
X-RAY DIFFRACTIONr_angle_other_deg0.72235988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4323334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12515537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023136
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02592
X-RAY DIFFRACTIONr_nbd_refined0.3220.3639
X-RAY DIFFRACTIONr_nbd_other0.2290.32633
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1390.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.5479
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.358
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3520.3114
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.546
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8931.51694
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5822696
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.11231176
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2994.51144
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 202
Rwork0.255 3734
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.54020.229-0.17451.7726-0.06871.5966-0.0472-0.0387-0.1173-0.01020.02940.01370.0422-0.06630.01770.3989-0.0297-0.0190.5214-0.02440.4322-2.8050.7051.979
21.58240.21920.8311.61090.79142.38880.0145-0.00780.04540.06660.0286-0.1147-0.13090.1389-0.04310.4327-0.08750.01160.5326-0.01410.411114.15526.97720.165
30.5180.37280.21670.80350.32490.81330.0287-0.0274-0.0673-0.0098-0.01560.0136-0.0115-0.0037-0.01320.1487-0.0264-0.00460.2792-0.00610.1573.98312.29410.37
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A192 - 352
2X-RAY DIFFRACTION1B17 - 26
3X-RAY DIFFRACTION2E192 - 352
4X-RAY DIFFRACTION2F17 - 26
5X-RAY DIFFRACTION3W1 - 613

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