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- PDB-1xqh: Crystal structure of a ternary complex of the methyltransferase S... -

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Basic information

Entry
Database: PDB / ID: 1xqh
TitleCrystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53 peptide and SAH
Components
  • 9-mer peptide from tumor protein p53
  • Histone-lysine N-methyltransferase, H3 lysine-4 specific
KeywordsTRANSFERASE / Set9-p53 complex / Set-domain / Lysine methylation
Function / homology
Function and homology information


peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate ...peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / histone H3 methyltransferase activity / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / histone methyltransferase activity / negative regulation of DNA replication / ER overload response / B cell lineage commitment / positive regulation of cardiac muscle cell apoptotic process / thymocyte apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / mitophagy / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C / : / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / chromosome organization / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / T cell proliferation involved in immune response / glial cell proliferation / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to actinomycin D / somitogenesis / heterochromatin organization / type II interferon-mediated signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation
Similarity search - Function
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Beta-clip-like / SET domain / Cellular tumor antigen p53, transactivation domain 2 ...Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Beta-clip-like / SET domain / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / p53-like transcription factor, DNA-binding / Single Sheet / Beta Complex / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Cellular tumor antigen p53 / Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChuikov, S. / Kurash, J.K. / Wilson, J.R. / Xiao, B. / Justin, N. / Ivanov, G.S. / McKinney, K. / Tempst, P. / Prives, C. / Gamblin, S.J. ...Chuikov, S. / Kurash, J.K. / Wilson, J.R. / Xiao, B. / Justin, N. / Ivanov, G.S. / McKinney, K. / Tempst, P. / Prives, C. / Gamblin, S.J. / Barlev, N.A. / Reinberg, D.
CitationJournal: Nature / Year: 2004
Title: Regulation of p53 activity through lysine methylation
Authors: Chuikov, S. / Kurash, J.K. / Wilson, J.R. / Xiao, B. / Justin, N. / Ivanov, G.S. / McKinney, K. / Tempst, P. / Prives, C. / Gamblin, S.J. / Barlev, N.A. / Reinberg, D.
History
DepositionOct 12, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: Histone-lysine N-methyltransferase, H3 lysine-4 specific
B: 9-mer peptide from tumor protein p53
E: Histone-lysine N-methyltransferase, H3 lysine-4 specific
F: 9-mer peptide from tumor protein p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7276
Polymers60,9584
Non-polymers7692
Water12,917717
1
A: Histone-lysine N-methyltransferase, H3 lysine-4 specific
B: 9-mer peptide from tumor protein p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8633
Polymers30,4792
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-5 kcal/mol
Surface area13010 Å2
MethodPISA
2
E: Histone-lysine N-methyltransferase, H3 lysine-4 specific
F: 9-mer peptide from tumor protein p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8633
Polymers30,4792
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-5 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.374, 103.123, 67.165
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONSISTS OF TWO BIOLOGICAL MOLECULES, THE DIMER IS FORMED BY THE COMPLEX OF CHAIN A WITH A PEPTIDE CHAIN B AND CHAIN E WITH A PEPTIDE CHAIN F. CHAINS A AND E ARE MONOMERIC IN THE PHYSIOLOGICAL STATE.

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-4 specific / LYSINE N-METHYLTRANSFERASE / Histone H3-K4 methyltransferase / H3-K4-HMTase / SET domain- ...LYSINE N-METHYLTRANSFERASE / Histone H3-K4 methyltransferase / H3-K4-HMTase / SET domain- containing Set7 / Set9 / SET7/9


Mass: 29323.588 Da / Num. of mol.: 2 / Fragment: N-domain, SET-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase
#2: Protein/peptide 9-mer peptide from tumor protein p53


Mass: 1155.345 Da / Num. of mol.: 2 / Fragment: mono-methylated p53 peptide / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P04637
#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.: 717 / 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: 2.46 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.8
Details: PEG3350, Tris-HCL, pH 7.8, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 55234 / Num. obs: 52283 / % possible obs: 94.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 15 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 24.8
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3706 / % possible all: 67.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1o9s

1o9s


Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.783 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.282 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22325 2667 5.1 %RANDOM
Rwork0.18371 ---
obs0.18571 49595 94.72 %-
all-52262 --
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: 7.381 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å20.65 Å2
2--0.28 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4002 0 52 717 4771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214158
X-RAY DIFFRACTIONr_bond_other_d00.023552
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.975640
X-RAY DIFFRACTIONr_angle_other_deg1.73238336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5363504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84615709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1660.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024600
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02818
X-RAY DIFFRACTIONr_nbd_refined0.2680.3925
X-RAY DIFFRACTIONr_nbd_other0.2410.33638
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.2920.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.5682
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0780.56
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.357
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.548
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0240.53
X-RAY DIFFRACTIONr_mcbond_it0.5511.52550
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05824108
X-RAY DIFFRACTIONr_scbond_it1.42931608
X-RAY DIFFRACTIONr_scangle_it2.3144.51532
X-RAY DIFFRACTIONr_rigid_bond_restr0.88724158
X-RAY DIFFRACTIONr_sphericity_free0.9522717
X-RAY DIFFRACTIONr_sphericity_bonded0.57724054
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 128 -
Rwork0.259 2513 -
obs-2513 66.5 %
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)
11.93380.722-0.24814.05250.03621.9738-0.0655-0.03830.3120.19340.01150.4713-0.1678-0.11230.0540.49230.0123-0.02890.2651-0.01410.26230.01418.54318.213
22.4508-0.2193-0.16242.28380.08591.266-0.0341-0.0527-0.35470.215-0.003-0.01030.25390.02550.03720.5087-0.0045-0.02080.25980.00110.18959.5-7.11315.782
31.72360.60190.11914.5383-0.10781.7579-0.0429-0.0536-0.28970.2033-0.0153-0.44840.15240.11910.05820.48440.0094-0.03990.27080.01370.259820.15429.52418.227
42.4083-0.23790.11722.5017-0.11941.3441-0.041-0.05220.37210.22580.00430.0056-0.2711-0.02290.03670.5105-0.0035-0.05340.2587-0.00010.193110.66255.31915.717
50.31490.1148-0.00541.5654-0.02780.32960.00310.0221-0.00450.1393-0.0356-0.009-0.00610.00020.03250.3222-0.0018-0.04630.1954-0.00180.006710.40124.1715.034
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA117 - 19215 - 90
2X-RAY DIFFRACTION2AA193 - 36691 - 264
3X-RAY DIFFRACTION2BB369 - 3741 - 6
4X-RAY DIFFRACTION2AE15011
5X-RAY DIFFRACTION3EC117 - 19215 - 90
6X-RAY DIFFRACTION4EC193 - 36691 - 264
7X-RAY DIFFRACTION4FD369 - 3741 - 6
8X-RAY DIFFRACTION4AE15011
9X-RAY DIFFRACTION5AG1502 - 18521 - 351

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