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- PDB-3rc0: Human SETD6 in complex with RelA Lys310 peptide -

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Basic information

Entry
Database: PDB / ID: 3rc0
TitleHuman SETD6 in complex with RelA Lys310 peptide
Components
  • N-lysine methyltransferase SETD6
  • Transcription factor p65 peptide
KeywordsTRANSFERASE / Epigenetics / protein lysine monomethylation / Mammalian nuclear factor kB (NF-kB)
Function / homology
Function and homology information


peptidyl-lysine monomethylation / acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / Regulated proteolysis of p75NTR / cellular response to peptidoglycan / ankyrin repeat binding ...peptidyl-lysine monomethylation / acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / Regulated proteolysis of p75NTR / cellular response to peptidoglycan / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / protein-lysine N-methyltransferase activity / CLEC7A/inflammasome pathway / SUMOylation of immune response proteins / S-adenosyl-L-methionine binding / negative regulation of protein sumoylation / nucleotide-binding oligomerization domain containing 2 signaling pathway / postsynapse to nucleus signaling pathway / defense response to tumor cell / Interleukin-1 processing / cellular response to interleukin-6 / negative regulation of non-canonical NF-kappaB signal transduction / actinin binding / NF-kappaB complex / cellular response to angiotensin / response to UV-B / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / Regulation of NFE2L2 gene expression / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of miRNA metabolic process / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / stem cell population maintenance / positive regulation of T cell receptor signaling pathway / response to cobalamin / negative regulation of NF-kappaB transcription factor activity / phosphate ion binding / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / cellular response to lipoteichoic acid / response to muramyl dipeptide / The NLRP3 inflammasome / general transcription initiation factor binding / Transcriptional Regulation by VENTX / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / positive regulation of vascular endothelial growth factor production / RNA polymerase II core promoter sequence-specific DNA binding / response to amino acid / cellular response to interleukin-1 / canonical NF-kappaB signal transduction / cellular defense response / Purinergic signaling in leishmaniasis infection / response to cAMP / negative regulation of insulin receptor signaling pathway / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / Transferases; Transferring one-carbon groups; Methyltransferases / NF-kB is activated and signals survival / positive regulation of interleukin-12 production / CD209 (DC-SIGN) signaling / response to interleukin-1 / negative regulation of angiogenesis / negative regulation of miRNA transcription / response to progesterone / liver development / response to organic substance / positive regulation of interleukin-1 beta production / response to cytokine / positive regulation of interleukin-8 production / response to ischemia / stem cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / negative regulation of extrinsic apoptotic signaling pathway / Activation of NF-kappaB in B cells / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / animal organ morphogenesis / protein catabolic process / TAK1-dependent IKK and NF-kappa-B activation / response to insulin / negative regulation of protein catabolic process / transcription coactivator binding / chromatin DNA binding / cellular response to hydrogen peroxide / PKMTs methylate histone lysines / CLEC7A (Dectin-1) signaling / DNA-binding transcription repressor activity, RNA polymerase II-specific / FCERI mediated NF-kB activation / Transcriptional regulation of white adipocyte differentiation / positive regulation of interleukin-6 production / positive regulation of miRNA transcription / Interleukin-1 signaling / cytokine-mediated signaling pathway / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to nicotine / histone deacetylase binding
Similarity search - Function
N-lysine methyltransferase SETD6 / SETD6, SET domain / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 2 / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / Rubisco LSMT substrate-binding / Transcription factor RelA (p65) ...N-lysine methyltransferase SETD6 / SETD6, SET domain / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 2 / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / Rubisco LSMT substrate-binding / Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Transcription factor p65 / N-lysine methyltransferase SETD6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.19 Å
AuthorsChang, Y. / Levy, D. / Horton, J.R. / Peng, J. / Zhang, X. / Gozani, O. / Cheng, X.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling.
Authors: Chang, Y. / Levy, D. / Horton, J.R. / Peng, J. / Zhang, X. / Gozani, O. / Cheng, X.
History
DepositionMar 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Sep 7, 2011Group: Database references
Revision 1.4Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 SETD6
P: Transcription factor p65 peptide
B: N-lysine methyltransferase SETD6
Q: Transcription factor p65 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,28422
Polymers105,4944
Non-polymers1,79018
Water8,737485
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A: N-lysine methyltransferase SETD6
P: Transcription factor p65 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,76613
Polymers52,7472
Non-polymers1,01911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint13 kcal/mol
Surface area20380 Å2
MethodPISA
2
B: N-lysine methyltransferase SETD6
Q: Transcription factor p65 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5189
Polymers52,7472
Non-polymers7717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint7 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.621, 64.501, 73.759
Angle α, β, γ (deg.)78.73, 70.60, 64.21
Int Tables number1
Space group name H-MP1

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Components

#1: Protein N-lysine methyltransferase SETD6 / SET domain-containing protein 6


Mass: 50837.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD6 / Plasmid: pXC862 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TBK2, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein/peptide Transcription factor p65 peptide / Nuclear factor NF-kappa-B p65 subunit / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3


Mass: 1909.300 Da / Num. of mol.: 2 / Fragment: UNP Q04206 residues 302-316 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO ISOFORM 2 OF HUMAN SETD6 (NP_079136)

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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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.6
Details: 15% (w/v) polyethylene glycol (PEG) 3350, 0.1 M di-ammonium hydrogen citrate, pH 4.6, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97918 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.19→34.72 Å / Num. obs: 48552 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 22.27 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 11.4
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4776 / % possible all: 97.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SGXPROmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 3QXY

3qxy


Resolution: 2.19→34.72 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 1923 4.18 %RANDOM
Rwork0.1661 ---
obs0.1688 46006 92.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.727 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.9117 Å20.9514 Å2-2.3711 Å2
2--4.7731 Å2-6.8429 Å2
3---4.1386 Å2
Refinement stepCycle: LAST / Resolution: 2.19→34.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6563 0 118 485 7166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066832
X-RAY DIFFRACTIONf_angle_d0.959277
X-RAY DIFFRACTIONf_dihedral_angle_d14.8172488
X-RAY DIFFRACTIONf_chiral_restr0.0611062
X-RAY DIFFRACTIONf_plane_restr0.0041176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.26530.27891570.19053698X-RAY DIFFRACTION78
2.2653-2.3560.24051870.17534132X-RAY DIFFRACTION87
2.356-2.46320.25811920.17354307X-RAY DIFFRACTION89
2.4632-2.5930.24471930.1744321X-RAY DIFFRACTION91
2.593-2.75540.24041860.18154391X-RAY DIFFRACTION93
2.7554-2.9680.25981760.18344519X-RAY DIFFRACTION94
2.968-3.26650.24481950.174607X-RAY DIFFRACTION97
3.2665-3.73870.19982110.15134683X-RAY DIFFRACTION98
3.7387-4.70850.1942130.13374702X-RAY DIFFRACTION99
4.7085-34.72810.25042130.17854723X-RAY DIFFRACTION99

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