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- PDB-2rhi: Crystal structure of the 3-MBT domain from human L3MBTL1 in compl... -

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Basic information

Entry
Database: PDB / ID: 2rhi
TitleCrystal structure of the 3-MBT domain from human L3MBTL1 in complex with H1.5K27me2 at 1.66 angstrom
Components
  • Histone H1.5
  • Lethal(3)malignant brain tumor-like protein
KeywordsTranscription/Nuclear Protein / BETA BARREL / Protein-peptide Complex / dimethyl-lysine / Alternative splicing / Chromatin regulator / DNA-binding / Metal-binding / Nucleus / Repressor / Transcription / Transcription regulation / Zinc / Zinc-finger / Transcription-Nuclear Protein COMPLEX
Function / homology
Function and homology information


: / : / heterochromatin => GO:0000792 / : / euchromatin => GO:0000791 / SAM domain binding / chromatin lock complex / establishment of protein localization to chromatin / chromatin => GO:0000785 / regulation of megakaryocyte differentiation ...: / : / heterochromatin => GO:0000792 / : / euchromatin => GO:0000791 / SAM domain binding / chromatin lock complex / establishment of protein localization to chromatin / chromatin => GO:0000785 / regulation of megakaryocyte differentiation / negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / chromosome condensation / muscle organ development / regulation of mitotic nuclear division / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / hemopoiesis / heterochromatin formation / nucleosome binding / condensed chromosome / nucleosomal DNA binding / methylated histone binding / Regulation of TP53 Activity through Methylation / chromatin DNA binding / histone deacetylase binding / nucleosome / nucleosome assembly / chromatin organization / histone binding / positive regulation of cell growth / double-stranded DNA binding / protein stabilization / regulation of cell cycle / negative regulation of DNA-templated transcription / chromatin binding / host cell nucleus / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus
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 / Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / SH3 type barrels. - #140 / SH3 type barrels. / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Histone H1.5 / Lethal(3)malignant brain tumor-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsLi, H. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural Basis for Lower Lysine Methylation State-Specific Readout by MBT Repeats of L3MBTL1 and an Engineered PHD Finger.
Authors: Li, H. / Fischle, W. / Wang, W. / Duncan, E.M. / Liang, L. / Murakami-Ishibe, S. / Allis, C.D. / Patel, D.J.
History
DepositionOct 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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: Lethal(3)malignant brain tumor-like protein
B: Histone H1.5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1014
Polymers39,8012
Non-polymers3002
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.864, 93.318, 58.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Lethal(3)malignant brain tumor-like protein / L3 / mbt-like / L3 / mbt protein homolog / H-l3 / mbt protein / H-L3 / MBT / L3MBTL1


Mass: 39195.727 Da / Num. of mol.: 1 / Fragment: Repeats MBT-1, MBT-2, MBT-3; Residues 197-526
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL, KIAA0681, L3MBT / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2 / References: UniProt: Q9Y468
#2: Protein/peptide Histone H1.5


Mass: 604.782 Da / Num. of mol.: 1 / Fragment: N-terminal tail resideus 23-27 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: P16401
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: L3MBTL1(197-526) (15 mg/ml in 25 mM Tris-HCl, pH 8.0, 1 mM DTT) was pre-incubated with two-fold molar excess of H1.5(23-27)K27me2 peptide. Drops were prepared by mixing 1 l complex solution ...Details: L3MBTL1(197-526) (15 mg/ml in 25 mM Tris-HCl, pH 8.0, 1 mM DTT) was pre-incubated with two-fold molar excess of H1.5(23-27)K27me2 peptide. Drops were prepared by mixing 1 l complex solution with 1 l reservoir solution (7% PEG3350, 0.2 M NaAc pH 5.0). Rod-like crystals usually appear overnight and are ready for data collection after two days. Crystals were flash-frozen in liquid nitrogen with the reservoir solution augmented with an additional 30% PEG 400 as cryoprotectant prior to data collectioin., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0858 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0858 Å / Relative weight: 1
ReflectionResolution: 1.66→20 Å / Num. all: 56401 / Num. obs: 56401 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 31.5
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.1 / Num. unique all: 5561 / Rsym value: 0.46 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OZ2

1oz2


Resolution: 1.66→20 Å / Isotropic thermal model: Isotopic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.201 4490 -Random
Rwork0.187 ---
all-56362 --
obs-54919 97.4 %-
Displacement parametersBiso mean: 20.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.66→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 13 571 3233
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 1.66→1.72 Å
RfactorNum. reflection% reflection
Rfree0.25 410 -
Rwork0.28 --
obs-5111 92 %

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