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- PDB-4ij8: Crystal structure of the complex of SETD8 with SAM -

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Basic information

Entry
Database: PDB / ID: 4ij8
TitleCrystal structure of the complex of SETD8 with SAM
Components
  • N-lysine methyltransferase SETD8
  • helical peptide
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC / N-lysine methyltransferase
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 / regulation of DNA damage response, signal transduction by p53 class mediator ...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 / negative regulation of double-strand break repair via homologous recombination / histone methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / Condensation of Prophase Chromosomes / regulation of signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / transcription corepressor activity / cell division / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / 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 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / N-lysine methyltransferase KMT5A
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsYu, W. / Tempel, W. / Li, Y. / El Bakkouri, M. / Shapira, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the complex of SETD8 with SAM
Authors: Yu, W. / Tempel, W. / Li, Y. / El Bakkouri, M. / Shapira, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
History
DepositionDec 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Source and taxonomy
Revision 1.2Sep 20, 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_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_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: N-lysine methyltransferase SETD8
B: N-lysine methyltransferase SETD8
I: helical peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,10027
Polymers38,3033
Non-polymers79724
Water2,342130
1
A: N-lysine methyltransferase SETD8
B: N-lysine methyltransferase SETD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,23126
Polymers37,4342
Non-polymers79724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-10 kcal/mol
Surface area15380 Å2
MethodPISA
2
I: helical peptide


  • defined by software
  • 869 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)8691
Polymers8691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.439, 101.439, 140.799
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-658-

HOH

21B-631-

HOH

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Components

#1: Protein N-lysine methyltransferase SETD8 / H4-K20-HMTase SETD8 / Histone-lysine N-methyltransferase SETD8 / Lysine N-methyltransferase 5A / ...H4-K20-HMTase SETD8 / Histone-lysine N-methyltransferase SETD8 / Lysine N-methyltransferase 5A / PR/SET domain-containing protein 07 / PR-Set7 / PR/SET07 / SET domain-containing protein 8


Mass: 18717.139 Da / Num. of mol.: 2 / Mutation: C343S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD8, KMT5A, PRSET7, SET07, SET8 / Plasmid: pHIS2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2
References: UniProt: Q9NQR1, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Protein/peptide helical peptide


Mass: 869.063 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 22 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE MODEL INCLUDES A DISJOINT APPARENT ALPHA-HELIX THAT COULD NOT BE ASSIGNED TO A SPECIFIC SECTION ...THE MODEL INCLUDES A DISJOINT APPARENT ALPHA-HELIX THAT COULD NOT BE ASSIGNED TO A SPECIFIC SECTION OF THE AMINO ACID SEQUENCE OF THE TARGET PROTEIN.

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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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 1.2 M sodium citrate, 0.1 M HEPES, 10-fold excess SAM, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 25, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→87.849 Å / Num. all: 29619 / Num. obs: 29619 / % possible obs: 100 % / Redundancy: 21.6 % / Rsym value: 0.112 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.11220.9420.89308642310.942100
2.11-2.24220.5911.38796239900.591100
2.24-2.3921.90.4041.98301837830.404100
2.39-2.58220.2862.77772835350.286100
2.58-2.8321.90.184.27167032720.18100
2.83-3.1621.70.1136.36484129840.113100
3.16-3.6521.40.0817.95660626490.081100
3.65-4.47210.0649.24770422720.064100
4.47-6.3220.40.0619.43702118110.061100
6.32-46.92818.30.0589.22001610920.05899.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZKK

1zkk


Resolution: 2→43.96 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.1892 / WRfactor Rwork: 0.1704 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8803 / SU B: 6.332 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1405 / SU Rfree: 0.1248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED ARP/WARP, COOT, AND THE MOLPROBITY SERVER WERE ALSO USED DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 1516 5.1 %THIN SHELLS (SFTOOLS)
Rwork0.1757 ---
obs0.1769 29561 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.23 Å2 / Biso mean: 37.7619 Å2 / Biso min: 15.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.14 Å2-0 Å2
2---0.14 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 76 130 2646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192575
X-RAY DIFFRACTIONr_bond_other_d0.0020.022342
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.993497
X-RAY DIFFRACTIONr_angle_other_deg0.7235383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1424.107112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8415418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0861515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022945
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02583
X-RAY DIFFRACTIONr_mcbond_it1.6452.2241303
X-RAY DIFFRACTIONr_mcbond_other1.6452.2231302
X-RAY DIFFRACTIONr_mcangle_it2.383.3231624
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 2 -
Rwork0.222 2116 -
all-2118 -
obs--99.95 %
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)
12.39180.031-0.16071.40720.4081.7877-0.07960.04870.0541-0.05580.0252-0.35960.0240.26520.05440.0592-0.01570.04470.05530.01080.1252-11.208934.09384.9505
22.8454-0.2796-0.10132.2859-0.15081.7569-0.01040.1036-0.4324-0.1415-0.14160.26940.3434-0.19250.1520.1112-0.05920.03490.0561-0.06030.1106-37.989320.17463.5645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A233 - 393
2X-RAY DIFFRACTION2B244 - 393

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