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- PDB-4fl6: Crystal structure of the complex of the 3-MBT repeat domain of L3... -

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Basic information

Entry
Database: PDB / ID: 4fl6
TitleCrystal structure of the complex of the 3-MBT repeat domain of L3MBTL3 and UNC1215
ComponentsLethal(3)malignant brain tumor-like protein 3
KeywordsTRANSCRIPTION / Structural Genomics Consortium / SGC / chromatin modification / transcription repression / MBT repeat
Function / homology
Function and homology information


methylation-dependent protein binding / granulocyte differentiation / regulation of DNA methylation-dependent heterochromatin formation / positive regulation of ubiquitin-dependent protein catabolic process / erythrocyte maturation / macrophage differentiation / chromatin organization / histone binding / negative regulation of DNA-templated transcription / chromatin binding ...methylation-dependent protein binding / granulocyte differentiation / regulation of DNA methylation-dependent heterochromatin formation / positive regulation of ubiquitin-dependent protein catabolic process / erythrocyte maturation / macrophage differentiation / chromatin organization / histone binding / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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 / SH3 type barrels. - #140 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. ...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 / SH3 type barrels. - #140 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-UWN / Lethal(3)malignant brain tumor-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsZhong, N. / Tempel, W. / Ravichandran, M. / Dong, A. / Ingerman, L.A. / Graslund, S. / Frye, S.V. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...Zhong, N. / Tempel, W. / Ravichandran, M. / Dong, A. / Ingerman, L.A. / Graslund, S. / Frye, S.V. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat. Chem. Biol. / Year: 2013
Title: Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain.
Authors: James, L.I. / Barsyte-Lovejoy, D. / Zhong, N. / Krichevsky, L. / Korboukh, V.K. / Herold, J.M. / MacNevin, C.J. / Norris, J.L. / Sagum, C.A. / Tempel, W. / Marcon, E. / Guo, H. / Gao, C. / ...Authors: James, L.I. / Barsyte-Lovejoy, D. / Zhong, N. / Krichevsky, L. / Korboukh, V.K. / Herold, J.M. / MacNevin, C.J. / Norris, J.L. / Sagum, C.A. / Tempel, W. / Marcon, E. / Guo, H. / Gao, C. / Huang, X.P. / Duan, S. / Emili, A. / Greenblatt, J.F. / Kireev, D.B. / Jin, J. / Janzen, W.P. / Brown, P.J. / Bedford, M.T. / Arrowsmith, C.H. / Frye, S.V.
History
DepositionJun 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 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_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: Lethal(3)malignant brain tumor-like protein 3
B: Lethal(3)malignant brain tumor-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,08133
Polymers77,0212
Non-polymers1,05931
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-11 kcal/mol
Surface area29450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.026, 54.372, 65.549
Angle α, β, γ (deg.)90.00, 97.11, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT BIOLOGICAL UNIT HAS NOT BEEN DETERMINED

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Components

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


Mass: 38510.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1798, L3MBTL3, MBT1 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q96JM7
#2: Chemical ChemComp-UWN / [2-(phenylamino)benzene-1,4-diyl]bis{[4-(pyrrolidin-1-yl)piperidin-1-yl]methanone}


Mass: 529.716 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H43N5O2
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 29 / Source method: obtained synthetically

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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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 25% PEG-3350, 0.2M ammonium acetate, 0.1M Bis-Tris, pH 5.5, vapor diffusion, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
sbc1001
11
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.55→45.57 Å / Num. obs: 26075 / % possible obs: 99.22 % / Redundancy: 3.68 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.2968
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
2.55-2.693.480.98129283717198.3
2.69-2.853.790.61137393621199.41
2.85-3.053.80.34126973345199.38
3.05-3.293.780.17119073153199.56
3.29-3.613.760.09108812896199.56
3.61-4.033.70.0597422630199.53
4.03-4.663.620.0483862317199.2
4.66-5.73.550.0370341980199.4
5.7-8.063.590.0355451545199.66
8.06-45.573.430.022991871197.45

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20data scaling
PHASERphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: related to pdb entry 3UT1

3ut1


Resolution: 2.55→44.11 Å / Cor.coef. Fo:Fc: 0.9424 / Cor.coef. Fo:Fc free: 0.8965 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.415 / Cross valid method: THROUGHOUT / σ(F): 0
Details: Ligand geometry restraints were prepared with PRODRG. COOT, REFMAC and the MOLPROBITY server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 1330 5.1 %THIN SHELLS (SFTOOLS)
Rwork0.1947 ---
obs0.1981 26070 98.9 %-
Displacement parametersBiso max: 170.1 Å2 / Biso mean: 76.7327 Å2 / Biso min: 31.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.7047 Å20 Å26.4007 Å2
2--1.9731 Å20 Å2
3----1.2684 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: LAST / Resolution: 2.55→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 107 0 4804
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1456SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes745HARMONIC5
X-RAY DIFFRACTIONt_it4964HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion622SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5336SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4964HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6817HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion16.97
LS refinement shellResolution: 2.55→2.65 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rwork0.2308 2874 -
all0.2308 --
obs--98.9 %
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)
12.5461-0.12160.58732.40110.8812.3223-0.04840.23020.1724-0.2095-0.09870.3507-0.2589-0.2430.147-0.20020.04740.0105-0.23020.0356-0.212131.5396-22.859232.9375
22.7077-0.2724-0.53492.23650.47112.73510.1418-0.10080.05620.0441-0.16790.45250.0489-0.39890.0262-0.2381-0.05540.0317-0.23190.0003-0.255120.0836-18.873359.3347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A231 - 1001
2X-RAY DIFFRACTION2{ B|* }B - A231 - 1002

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