[English] 日本語
Yorodumi
- PDB-3p8h: Crystal structure of L3MBTL1 (MBT repeat) in complex with a nicot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p8h
TitleCrystal structure of L3MBTL1 (MBT repeat) in complex with a nicotinamide antagonist
ComponentsLethal(3)malignant brain tumor-like protein
KeywordsTRANSCRIPTION / Lethal(3) malignant brain tumor-like protein / L(3)mbt-like protein / Structural Genomics Consortium / SGC / MBT repeat / transcriptional repression / methylated lysines on histone proteins
Function / homology
Function and homology information


SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation / heterochromatin formation ...SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation / heterochromatin formation / 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 / : ...: / : / 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-P8H / Lethal(3)malignant brain tumor-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsLam, R. / Herold, J.M. / Ouyang, H. / Tempel, W. / Gao, C. / Ravichandran, M. / Senisterra, G. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. ...Lam, R. / Herold, J.M. / Ouyang, H. / Tempel, W. / Gao, C. / Ravichandran, M. / Senisterra, G. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. / Kireev, D. / Frye, S.V. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2011
Title: Small-molecule ligands of methyl-lysine binding proteins.
Authors: Herold, J.M. / Wigle, T.J. / Norris, J.L. / Lam, R. / Korboukh, V.K. / Gao, C. / Ingerman, L.A. / Kireev, D.B. / Senisterra, G. / Vedadi, M. / Tripathy, A. / Brown, P.J. / Arrowsmith, C.H. / ...Authors: Herold, J.M. / Wigle, T.J. / Norris, J.L. / Lam, R. / Korboukh, V.K. / Gao, C. / Ingerman, L.A. / Kireev, D.B. / Senisterra, G. / Vedadi, M. / Tripathy, A. / Brown, P.J. / Arrowsmith, C.H. / Jin, J. / Janzen, W.P. / Frye, S.V.
History
DepositionOct 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: Lethal(3)malignant brain tumor-like protein
C: Lethal(3)malignant brain tumor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,48110
Polymers111,3323
Non-polymers1,1497
Water68538
1
A: Lethal(3)malignant brain tumor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7295
Polymers37,1111
Non-polymers6184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lethal(3)malignant brain tumor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5453
Polymers37,1111
Non-polymers4342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lethal(3)malignant brain tumor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2072
Polymers37,1111
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.264, 106.264, 90.144
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
12B
22A
13C
23A
14A
24C
15C
25A
16C
26A

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASNASNBB357 - 358158 - 159
21METMETASNASNCC357 - 358158 - 159
12GLYGLYTYRTYRBB308 - 309109 - 110
22GLYGLYTYRTYRAA308 - 309109 - 110
13GLYGLYGLYGLYCC308109
23GLYGLYGLYGLYAA308109
14ASPASPASPASPAA420221
24ASPASPASPASPCC420221
15LYSLYSLYSLYSCC405206
25LYSLYSLYSLYSAA405206
16ASPASPASPASPCC372173
26ASPASPASPASPAA372173

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

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


Mass: 37110.566 Da / Num. of mol.: 3 / Fragment: UNP residues 200-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0681, L3MBT, L3MBTL, L3MBTL1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIPL / References: UniProt: Q9Y468
#2: Chemical ChemComp-P8H / 3-bromo-5-[(4-pyrrolidin-1-ylpiperidin-1-yl)carbonyl]pyridine


Mass: 338.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20BrN3O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.1M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97911 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 22, 2010 / Details: Double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 37137 / % possible obs: 100 % / Redundancy: 3 % / Rmerge(I) obs: 0.118 / Χ2: 1.012 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.55-2.6430.53336771.019100
2.64-2.7530.40737490.971100
2.75-2.8730.3437351.022100
2.87-3.0230.25537171.045100
3.02-3.2130.16836841.031100
3.21-3.4630.11337110.993100
3.46-3.8130.08837050.983100
3.81-4.3630.08437270.999100
4.36-5.493.10.06137001.018100
5.49-503.10.0537321.037100

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.68 Å46.01 Å
Translation2.68 Å46.01 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.6.0081refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RJC

2rjc


Resolution: 2.55→45.77 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.813 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 1854 5 %RANDOM
Rwork0.1913 ---
obs0.194 37108 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 118.69 Å2 / Biso mean: 43.2464 Å2 / Biso min: 17.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.39 Å20 Å2
2--0.78 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.55→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7568 0 67 38 7673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217929
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.9310839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.915930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.00623.866388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.022151148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3631532
X-RAY DIFFRACTIONr_chiral_restr0.0830.21079
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226304
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B8TIGHT POSITIONAL0.020.05
1B8LOOSE POSITIONAL0.045
1B8TIGHT THERMAL5.920.5
1B8LOOSE THERMAL8.9710
2B8TIGHT POSITIONAL0.040.05
2B8LOOSE POSITIONAL0.055
2B8TIGHT THERMAL3.920.5
2B8LOOSE THERMAL5.0710
3C4TIGHT POSITIONAL0.020.05
3C4TIGHT THERMAL7.950.5
4A4TIGHT POSITIONAL0.010.05
4A1LOOSE POSITIONAL0.025
4A4TIGHT THERMAL4.960.5
4A1LOOSE THERMAL12.0610
5C4TIGHT POSITIONAL0.010.05
5C5LOOSE POSITIONAL0.055
5C4TIGHT THERMAL9.70.5
5C5LOOSE THERMAL11.4910
6C4TIGHT POSITIONAL0.010.05
6C4LOOSE POSITIONAL0.065
6C4TIGHT THERMAL3.170.5
6C4LOOSE THERMAL4.3610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.6160.3611240.282604272999.963
2.616-2.6880.311300.2522559269299.889
2.688-2.7660.321330.2682454258899.961
2.766-2.8510.2911260.2492395252299.96
2.851-2.9440.3281210.25723162437100
2.944-3.0470.3041070.2282309241799.959
3.047-3.1620.2851300.20621602290100
3.162-3.2910.266990.20320552154100
3.291-3.4370.262970.19520502147100
3.437-3.6050.2311110.17819032014100
3.605-3.7990.231040.17318031907100
3.799-4.0290.2361060.16217061812100
4.029-4.3070.201870.15216121699100
4.307-4.6510.149820.12815191601100
4.651-5.0940.189640.13413891453100
5.094-5.6930.188670.16612421309100
5.693-6.5690.192550.17311271182100
6.569-8.0360.202540.165926980100
8.036-11.3210.194390.162719758100
11.321-92.0270.211180.24340642799.297

+
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://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