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- PDB-3f70: Crystal structure of L3MBTL2-H4K20me1 complex -

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Basic information

Entry
Database: PDB / ID: 3f70
TitleCrystal structure of L3MBTL2-H4K20me1 complex
ComponentsLethal(3)malignant brain tumor-like 2 protein
KeywordsTRANSCRIPTION REGULATOR / MBT / chromatin regulator / metal-binding / nucleus / transcription / transcription regulation / zinc-finger / Structural Genomics / Structural Genomics Consortium / SGC / Phosphoprotein
Function / homology
Function and homology information


Transcriptional Regulation by E2F6 / methylated histone binding / SUMOylation of chromatin organization proteins / chromatin organization / histone binding / negative regulation of DNA-templated transcription / chromatin binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat ...: / : / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
N-METHYL-LYSINE / Lethal(3)malignant brain tumor-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsGuo, Y. / Qi, C. / Allali-Hassani, A. / Pan, P. / Zhu, H. / Dong, A. / Mackenzie, F. / Crombet, L. / Loppnau, P. / Kozieradzki, I. ...Guo, Y. / Qi, C. / Allali-Hassani, A. / Pan, P. / Zhu, H. / Dong, A. / Mackenzie, F. / Crombet, L. / Loppnau, P. / Kozieradzki, I. / Vedadi, M. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Botchkarev, A. / Read, R. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.
Authors: Guo, Y. / Nady, N. / Qi, C. / Allali-Hassani, A. / Zhu, H. / Pan, P. / Adams-Cioaba, M.A. / Amaya, M.F. / Dong, A. / Vedadi, M. / Schapira, M. / Read, R.J. / Arrowsmith, C.H. / Min, J.
History
DepositionNov 7, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionJan 6, 2009ID: 3DBB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Lethal(3)malignant brain tumor-like 2 protein
B: Lethal(3)malignant brain tumor-like 2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6144
Polymers104,2942
Non-polymers3202
Water5,224290
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-8 kcal/mol
Surface area38780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.590, 55.489, 324.101
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lethal(3)malignant brain tumor-like 2 protein / L(3)mbt-like 2 protein / H-l(3)mbt-like protein


Mass: 52147.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q969R5
#2: Chemical ChemComp-MLZ / N-METHYL-LYSINE


Type: L-peptide linking / Mass: 160.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsL3MBTL2 PROTEIN WAS CO-CRYSTALLIZED WITH H4K20ME1 BUT ONLY THE METHYLATED LYSINE MLZ IS VISIBLE IN ...L3MBTL2 PROTEIN WAS CO-CRYSTALLIZED WITH H4K20ME1 BUT ONLY THE METHYLATED LYSINE MLZ IS VISIBLE IN THE ELECTRON DENSITY.

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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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10% PEG 4000, 0.1M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 54977 / % possible obs: 86.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.068 / Χ2: 1.281 / Net I/σ(I): 24.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.06-2.133.30.72338680.863162.4
2.13-2.224.60.55948210.924177.1
2.22-2.325.30.46952260.981184.3
2.32-2.445.70.3554731.034187.8
2.44-2.65.80.25354891.137187.9
2.6-2.85.80.15655261.271187.5
2.8-3.085.70.09757021.508190.3
3.08-3.525.50.06159151.62193.3
3.52-4.445.20.05162531.491197.2
4.44-506.10.04167041.469199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2.1→45.79 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.49 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2662 5 %RANDOM
Rwork0.199 ---
obs0.203 52838 88.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.79 Å2 / Biso mean: 33.105 Å2 / Biso min: 10.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6274 0 20 290 6584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0226481
X-RAY DIFFRACTIONr_angle_refined_deg2.1851.9358827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0375793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52823.162272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.8515981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1051531
X-RAY DIFFRACTIONr_chiral_restr0.1660.2958
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024933
X-RAY DIFFRACTIONr_nbd_refined0.230.22739
X-RAY DIFFRACTIONr_nbtor_refined0.3150.24275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2333
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.219
X-RAY DIFFRACTIONr_mcbond_it1.4841.54125
X-RAY DIFFRACTIONr_mcangle_it2.31526430
X-RAY DIFFRACTIONr_scbond_it3.41532847
X-RAY DIFFRACTIONr_scangle_it4.6754.52397
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 145 -
Rwork0.248 2782 -
all-2927 -
obs--66.9 %
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)
10.3728-0.3382-0.40061.97661.46011.6418-0.0762-0.0069-0.08120.0534-0.0030.12170.0707-0.0340.07920.15190.0130.03160.02840.01080.109222.5667-10.8276-73.7899
21.5232-0.9278-1.83370.8121.01453.31590.1936-0.03550.1118-0.0697-0.0114-0.0222-0.4928-0.0277-0.18230.23680.02320.08130.0137-0.01010.094412.009514.5879-49.5783
32.40230.45191.66480.23970.30181.15460.0063-0.02190.0173-0.0428-0.0499-0.0191-0.01620.03720.04370.03160.01590.00250.1995-0.00280.077915.77-10.9649-8.4209
40.5822-0.60720.36370.7762-0.40552.24410.10210.002-0.064-0.08580.02840.09050.1007-0.1467-0.13050.0595-0.0036-0.03040.15610.01460.0728-10.4883-9.3831-33.9578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A172 - 317
2X-RAY DIFFRACTION2A318 - 609
3X-RAY DIFFRACTION3B172 - 321
4X-RAY DIFFRACTION4B322 - 609

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