[English] 日本語
Yorodumi
- PDB-3uwn: The 3-MBT repeat domain of L3MBTL1 in complex with a methyl-lysin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uwn
TitleThe 3-MBT repeat domain of L3MBTL1 in complex with a methyl-lysine mimic
ComponentsLethal(3)malignant brain tumor-like protein 1
KeywordsTRANSCRIPTION / STRUCTURAL GENOMICS CONSORTIUM / SGC / MBT REPEAT / histone modification
Function / homology
Function and homology information


SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / heterochromatin formation / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation ...SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / heterochromatin formation / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation / chromatin organization / histone binding / regulation of cell cycle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / 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 / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-UWN / Lethal(3)malignant brain tumor-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsZhong, N. / Tempel, W. / Wernimont, A.K. / Graslund, S. / Ingerman, L.A. / Korboukh, V. / Kireev, D.B. / Gao, C. / Frye, S.V. / Arrowsmith, C.H. ...Zhong, N. / Tempel, W. / Wernimont, A.K. / Graslund, S. / Ingerman, L.A. / Korboukh, V. / Kireev, D.B. / Gao, C. / Frye, S.V. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The 3-MBT repeat domain of L3MBTL1 in complex with a methyl-lysine mimic
Authors: Zhong, N. / Tempel, W. / Wernimont, A.K. / Graslund, S. / Ingerman, L.A. / Korboukh, V. / Kireev, D.B. / Gao, C. / Frye, S.V. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / ...Authors: Zhong, N. / Tempel, W. / Wernimont, A.K. / Graslund, S. / Ingerman, L.A. / Korboukh, V. / Kireev, D.B. / Gao, C. / Frye, S.V. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Brown, P.J. / Structural Genomics Consortium (SGC)
History
DepositionDec 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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 / diffrn_source / 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 / _diffrn_source.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lethal(3)malignant brain tumor-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,28116
Polymers37,7511
Non-polymers53015
Water1,76598
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.774, 94.530, 58.955
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

-
Components

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


Mass: 37751.211 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 200-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL1, KIAA0681, L3MBT, L3MBTL / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9Y468
#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.: 1 / Source method: obtained synthetically / Formula: C32H43N5O2
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 14 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG-3350, 0.1 M ammonium sulfate, 0.1 M bis-tris. Crystal was soaked for 2 days in a 0.001 M solution of the ligand., pH 5.5, vapor diffusion, sitting drop, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
a2001001
11
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Sep 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→29.58 Å / Num. obs: 26687 / % possible obs: 99.75 % / Redundancy: 6.49 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 15.0444
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
2.15-2.275.490.9209413815199.29
2.27-2.45.90.7212493601199.75
2.4-2.576.360.48219343448199.87
2.57-2.786.730.31214333185199.85
2.78-3.046.960.18206472966199.96
3.04-3.47.030.091884726821100
3.4-3.9370.06168582409199.96
3.93-4.816.990.04142072033199.88
4.81-6.86.860.04110801614199.86
6.8-29.586.30.025881934198.32

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20data scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1oyx

1oyx


Resolution: 2.15→29.58 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.229 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY Ligand geometry restraints were prepared on the PRODRG server. The program COOT and the MOLPROBITY server ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY Ligand geometry restraints were prepared on the PRODRG server. The program COOT and the MOLPROBITY server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1348 5.1 %RANDOM
Rwork0.2309 ---
obs0.2327 26655 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.27 Å2 / Biso mean: 30.8562 Å2 / Biso min: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20 Å2
2--1.3 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 42 98 2672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022707
X-RAY DIFFRACTIONr_bond_other_d0.0020.021817
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9333716
X-RAY DIFFRACTIONr_angle_other_deg0.8553.0064413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.02923.672128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87515373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5041511
X-RAY DIFFRACTIONr_chiral_restr0.080.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02584
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 92 -
Rwork0.307 1673 -
all-1765 -
obs--98.66 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more