[English] 日本語
Yorodumi
- PDB-7x8f: Crystal structure of ENL T4 mutant YEATS domain in complex with h... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7x8f
TitleCrystal structure of ENL T4 mutant YEATS domain in complex with histone H3 acetylation at K27
Components
  • H3K27ac(24-27) peptide
  • Protein ENL
KeywordsTRANSCRIPTION / YEATS domain / Complex / histone
Function / homology
Function and homology information


RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / : / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / fibrillar center / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm / cytosol
Similarity search - Function
YEATS domain / AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsLi, Y. / Peng, B. / Li, H.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91753203 China
National Natural Science Foundation of China (NSFC)31725014 China
National Natural Science Foundation of China (NSFC)31871283 China
National Natural Science Foundation of China (NSFC)31922016 China
CitationJournal: Mol.Cell / Year: 2022
Title: Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer.
Authors: Song, L. / Yao, X. / Li, H. / Peng, B. / Boka, A.P. / Liu, Y. / Chen, G. / Liu, Z. / Mathias, K.M. / Xia, L. / Li, Q. / Mir, M. / Li, Y. / Li, H. / Wan, L.
History
DepositionMar 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein ENL
B: H3K27ac(24-27) peptide
C: Protein ENL
D: H3K27ac(24-27) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8425
Polymers38,8074
Non-polymers351
Water75742
1
A: Protein ENL
B: H3K27ac(24-27) peptide


Theoretical massNumber of molelcules
Total (without water)19,4032
Polymers19,4032
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein ENL
D: H3K27ac(24-27) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4393
Polymers19,4032
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.556, 48.592, 47.259
Angle α, β, γ (deg.)90.000, 101.160, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Protein ENL / YEATS domain-containing protein 1


Mass: 18915.779 Da / Num. of mol.: 2 / Mutation: insertions
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT1, ENL, LTG19, YEATS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03111
#2: Protein/peptide H3K27ac(24-27) peptide


Mass: 487.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20 % (w/v) PEG 4000, 0.1 M sodium citrate pH 5.6, 20 % (v/v) 2-propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.44→40 Å / Num. obs: 13211 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.063 / Rrim(I) all: 0.163 / Χ2: 0.69 / Net I/σ(I): 3.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.4950.9316620.5710.4611.0430.458100
2.49-2.545.40.8646500.6720.4080.9590.473100
2.54-2.595.90.8416520.6830.3810.9260.472100
2.59-2.646.40.7956760.8030.3410.8660.448100
2.64-2.76.50.7746400.830.3290.8420.487100
2.7-2.766.70.6576550.8910.2740.7130.493100
2.76-2.836.70.5476570.8690.2290.5940.496100
2.83-2.96.80.4956420.9210.2050.5360.518100
2.9-2.996.60.416590.9570.170.4450.565100
2.99-3.096.60.3496630.9440.1460.3790.63100
3.09-3.26.20.2946560.9530.1270.3210.627100
3.2-3.326.30.2326440.9740.1010.2530.661100
3.32-3.486.80.1836620.9810.0760.1980.75100
3.48-3.6670.146640.990.0570.1510.824100
3.66-3.896.80.1246490.9890.0510.1350.84100
3.89-4.196.80.1026600.9920.0420.1110.949100
4.19-4.616.40.0816700.9940.0350.0880.973100
4.61-5.276.40.0736790.9950.0310.0790.919100
5.27-6.646.80.0786700.9940.0320.0840.749100
6.64-406.10.0817010.9920.0350.0881.29699.9

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J9S

5j9s


Resolution: 2.44→38.4 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 643 4.87 %
Rwork0.2019 12560 -
obs0.2044 13203 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.58 Å2 / Biso mean: 52.6988 Å2 / Biso min: 26.06 Å2
Refinement stepCycle: final / Resolution: 2.44→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 1 42 2585
Biso mean--51.09 47.78 -
Num. residues----305
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.44-2.620.34891220.27232484260698
2.62-2.890.33771260.251324802606100
2.89-3.310.2311340.224424842618100
3.31-4.170.25291390.188925142653100
4.17-38.40.21961220.177325982720100

+
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