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- PDB-3oq5: Crystal structure of the 3-MBT domain from human L3MBTL1 in compl... -

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Basic information

Entry
Database: PDB / ID: 3oq5
TitleCrystal structure of the 3-MBT domain from human L3MBTL1 in complex with p53K382me1
Components
  • Cellular tumor antigen p53
  • Lethal(3)malignant brain tumor-like protein
KeywordsTRANSCRIPTION / L(3)MBT-LIKE PROTEIN / protein lysine methyltransferase / malignant brain tumor / Chromatin regulator / DNA-binding / Metal-binding / Nucleus / Repressor / Transcription regulation / Zinc-finger / Chromosomal protein / Methylation / Three-Leaved Beta-Propeller / p53
Function / homology
Function and homology information


SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / 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 ...SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / 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 / 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 / microtubule organizing center / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / regulation of mitotic nuclear division / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / T cell lineage commitment / 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 / hemopoiesis / 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 formation / 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 / nucleosome binding
Similarity search - Function
: / : / Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat ...: / : / Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / SH3 type barrels. - #140 / 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 / p53-like transcription factor, DNA-binding / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Cellular tumor antigen p53 / Cellular tumor antigen p53 / Lethal(3)malignant brain tumor-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5005 Å
AuthorsRoy, S. / West, L.E. / Weiner, K.L. / Hayashi, R. / Shi, X. / Appella, E. / Gozani, O. / Kutateladze, T.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The MBT Repeats of L3MBTL1 Link SET8-mediated p53 Methylation at Lysine 382 to Target Gene Repression.
Authors: West, L.E. / Roy, S. / Lachmi-Weiner, K. / Hayashi, R. / Shi, X. / Appella, E. / Kutateladze, T.G. / Gozani, O.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lethal(3)malignant brain tumor-like protein
B: Lethal(3)malignant brain tumor-like protein
C: Lethal(3)malignant brain tumor-like protein
D: Cellular tumor antigen p53
E: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)119,9975
Polymers119,9975
Non-polymers00
Water8,935496
1
A: Lethal(3)malignant brain tumor-like protein
D: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)40,4302
Polymers40,4302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-3 kcal/mol
Surface area15540 Å2
MethodPISA
2
B: Lethal(3)malignant brain tumor-like protein


Theoretical massNumber of molelcules
Total (without water)39,1371
Polymers39,1371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lethal(3)malignant brain tumor-like protein
E: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)40,4302
Polymers40,4302
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-3 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.080, 109.080, 90.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 206:309 or resseq 314:518 )
211chain B and (resseq 206:309 or resseq 314:518 )
311chain C and (resseq 206:309 or resseq 314:518 )

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Components

#1: Protein Lethal(3)malignant brain tumor-like protein / L(3)mbt-like / H-l(3)mbt protein / H-l(3)mbt / L(3)mbt protein homolog / L3MBTL1


Mass: 39136.637 Da / Num. of mol.: 3 / Fragment: MBT Repeats residues 191-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL, KIAA0681, L3MBT, L3MBTL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9Y468
#2: Protein/peptide Cellular tumor antigen p53


Mass: 1293.623 Da / Num. of mol.: 2 / Fragment: C-terminal residues 377-386 / Source method: obtained synthetically / Details: Synthetic construct / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5U0E4, UniProt: P04637*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1 M sodium acetate pH 4.8, 4% PEG 4000 and 0.1 M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→46.651 Å / Num. obs: 41472 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.28 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4189 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RJE

2rje


Resolution: 2.5005→46.651 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 27.75 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 2086 5.03 %Random
Rwork0.205 ---
obs0.2066 41449 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.959 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.181 Å2-0 Å2-0 Å2
2--6.181 Å20 Å2
3----12.3619 Å2
Refinement stepCycle: LAST / Resolution: 2.5005→46.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7547 0 0 496 8043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067841
X-RAY DIFFRACTIONf_angle_d0.78110714
X-RAY DIFFRACTIONf_dihedral_angle_d14.182796
X-RAY DIFFRACTIONf_chiral_restr0.0551070
X-RAY DIFFRACTIONf_plane_restr0.0041397
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2509X-RAY DIFFRACTIONPOSITIONAL
12B2509X-RAY DIFFRACTIONPOSITIONAL0.087
13C2509X-RAY DIFFRACTIONPOSITIONAL0.086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5005-2.55870.33361510.31542625X-RAY DIFFRACTION95
2.5587-2.62260.37241410.31852656X-RAY DIFFRACTION95
2.6226-2.69350.38691390.32412568X-RAY DIFFRACTION95
2.6935-2.77270.31091460.31382661X-RAY DIFFRACTION95
2.7727-2.86220.28361250.30452614X-RAY DIFFRACTION95
2.8622-2.96440.29771330.28252636X-RAY DIFFRACTION95
2.9644-3.0830.24511310.26392614X-RAY DIFFRACTION95
3.083-3.22320.22451540.2342624X-RAY DIFFRACTION94
3.2232-3.3930.25181350.19732610X-RAY DIFFRACTION95
3.393-3.60530.21081340.18812638X-RAY DIFFRACTION95
3.6053-3.88320.18131430.16522615X-RAY DIFFRACTION95
3.8832-4.27320.19341390.15472628X-RAY DIFFRACTION95
4.2732-4.88980.19121320.14772613X-RAY DIFFRACTION95
4.8898-6.15390.22151530.17642609X-RAY DIFFRACTION94
6.1539-32.59290.2521300.20322629X-RAY DIFFRACTION95

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