[English] 日本語
Yorodumi
- PDB-5yc4: Crystal structure of AL3 PHD finger bound to H3K4me3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yc4
TitleCrystal structure of AL3 PHD finger bound to H3K4me3
Components
  • Histone H3K4me3
  • PHD finger protein ALFIN-LIKE 3
KeywordsTRANSCRIPTION / PHD finger
Function / homology
Function and homology information


chromocenter / plastid / transcription coregulator activity / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / transcription cis-regulatory region binding / protein heterodimerization activity / regulation of DNA-templated transcription ...chromocenter / plastid / transcription coregulator activity / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / transcription cis-regulatory region binding / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Alfin / Alfin1-like, PHD finger / Alfin, N-terminal / Alfin / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. ...Alfin / Alfin1-like, PHD finger / Alfin, N-terminal / Alfin / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Histone H3 signature 2. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / PHD finger protein ALFIN-LIKE 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.697 Å
AuthorsZhao, S. / Zhang, B. / Li, H.
CitationJournal: Cell Rep / Year: 2018
Title: Systematic Profiling of Histone Readers in Arabidopsis thaliana.
Authors: Zhao, S. / Zhang, B. / Yang, M. / Zhu, J. / Li, H.
History
DepositionSep 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHD finger protein ALFIN-LIKE 3
P: Histone H3K4me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7654
Polymers7,6342
Non-polymers1312
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-8 kcal/mol
Surface area5360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.775, 30.775, 157.333
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

-
Components

#1: Protein PHD finger protein ALFIN-LIKE 3 / / Protein AL3


Mass: 6528.371 Da / Num. of mol.: 1 / Fragment: PHD finger, UNP residues 191-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AL3, At3g42790, T21C14_10 / Plasmid: pGEX6p / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9M2B4
#2: Protein/peptide Histone H3K4me3


Mass: 1105.334 Da / Num. of mol.: 1 / Fragment: H3 peptide 1-15 / Mutation: K4 trimethylation / Source method: obtained synthetically / Details: chemically synthesized H3K4me3 peptide / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8M Ammonium citrate tribasic, pH 7.0.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2016 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 2491 / % possible obs: 100 % / Redundancy: 19.2 % / Biso Wilson estimate: 43.35 Å2 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.05 / Rrim(I) all: 0.223 / Χ2: 1.601 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.7520.51.0351210.9610.2331.0620.797100
2.75-2.8211.011240.9440.2221.0350.873100
2.8-2.8520.90.9551140.9960.2120.9790.848100
2.85-2.9120.50.831130.9430.1840.8510.973100
2.91-2.9720.70.6671130.9790.1460.6830.96100
2.97-3.0420.80.5641180.9720.1250.5781.051100
3.04-3.1219.40.5011320.9690.1140.5151.165100
3.12-3.220.20.3961030.9890.0890.4071.202100
3.2-3.320.90.371190.9750.0810.3791.392100
3.3-3.420.40.2881260.9950.0640.2951.556100
3.4-3.5219.80.2411150.990.0540.2471.656100
3.52-3.6619.20.2071270.9940.0470.2131.945100
3.66-3.8320.30.2131280.9950.0480.2192.135100
3.83-4.0318.80.1631150.9940.0390.1672.179100
4.03-4.2918.90.1581290.9970.0360.1622.271100
4.29-4.6218.20.141230.9930.0340.1452.665100
4.62-5.0818.60.1281320.9960.030.1312.125100
5.08-5.8116.80.1081270.9970.0270.1121.672100
5.81-7.3217.50.0941440.9980.0230.0971.741100
7.32-5014.10.0911680.9980.0240.0952.99399.4

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FSA
Resolution: 2.697→30.775 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 345 14.09 %Random selection
Rwork0.2272 ---
obs0.2304 2448 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.27 Å2 / Biso mean: 33.9802 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.697→30.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms527 0 2 38 567
Biso mean--31.51 33.69 -
Num. residues----69
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002538
X-RAY DIFFRACTIONf_angle_d0.562723
X-RAY DIFFRACTIONf_chiral_restr0.02673
X-RAY DIFFRACTIONf_plane_restr0.00393
X-RAY DIFFRACTIONf_dihedral_angle_d12.671195
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6973-3.39760.29941630.251510081171
3.3976-30.7770.22881820.216510951277

+
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