[English] 日本語
Yorodumi
- PDB-2f5k: Crystal structure of the chromo domain of human MRG15 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2f5k
TitleCrystal structure of the chromo domain of human MRG15
ComponentsMortality factor 4-like protein 1
KeywordsGENE REGULATION / beta barrel
Function / homology
Function and homology information


regulation of double-strand break repair / NuA4 histone acetyltransferase complex / Sin3-type complex / positive regulation of double-strand break repair via homologous recombination / double-strand break repair via homologous recombination / nucleosome / chromatin organization / HATs acetylate histones / fibroblast proliferation / regulation of apoptotic process ...regulation of double-strand break repair / NuA4 histone acetyltransferase complex / Sin3-type complex / positive regulation of double-strand break repair via homologous recombination / double-strand break repair via homologous recombination / nucleosome / chromatin organization / HATs acetylate histones / fibroblast proliferation / regulation of apoptotic process / regulation of cell cycle / nuclear speck / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm
Similarity search - Function
MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo-like domain superfamily / SH3 type barrels. ...MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo-like domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Mortality factor 4-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZhang, P. / Du, J. / Ding, J.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3.
Authors: Zhang, P. / Du, J. / Sun, B. / Dong, X. / Xu, G. / Zhou, J. / Huang, Q. / Liu, Q. / Hao, Q. / Ding, J.
History
DepositionNov 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mortality factor 4-like protein 1
B: Mortality factor 4-like protein 1
C: Mortality factor 4-like protein 1
D: Mortality factor 4-like protein 1
E: Mortality factor 4-like protein 1
F: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)73,5076
Polymers73,5076
Non-polymers00
Water8,233457
1
A: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)12,2511
Polymers12,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)12,2511
Polymers12,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)12,2511
Polymers12,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)12,2511
Polymers12,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)12,2511
Polymers12,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)12,2511
Polymers12,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.480, 80.313, 81.285
Angle α, β, γ (deg.)90.00, 123.91, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Mortality factor 4-like protein 1 / MORF-related gene 15 isoform 1


Mass: 12251.144 Da / Num. of mol.: 6 / Fragment: chromo domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MORF4L1, MRG15, FWP006, HSPC008, HSPC061, PP368 / Plasmid: pET-3E-His / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UBU8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F210.9793
SYNCHROTRONCHESS F120.9124
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 14, 2005
ADSC QUANTUM 42CCDJul 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.91241
ReflectionResolution: 2.2→50 Å / Num. all: 29640 / Num. obs: 29581 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.6

-
Processing

Software
NameVersionClassificationNB
REFMAC5refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.247 / SU B: 20.364 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 1485 5 %RANDOM
Rwork0.22447 ---
all0.227 29667 --
obs0.22697 28095 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.674 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-1.38 Å2
2---1.04 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 0 457 4571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214231
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9355695
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7393477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.1115818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023257
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2870.32054
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2720.5589
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3190.349
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5281.52418
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.70123897
X-RAY DIFFRACTIONr_scbond_it2.17431813
X-RAY DIFFRACTIONr_scangle_it3.4574.51798
X-RAY DIFFRACTIONr_rigid_bond_restr1.49624231
X-RAY DIFFRACTIONr_sphericity_free2.7762457
X-RAY DIFFRACTIONr_sphericity_bonded1.65224119
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.348 98
Rwork0.262 2036
obs-2134

+
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