[English] 日本語
Yorodumi
- PDB-5t8r: Crystal structure of human BAZ2A PHD zinc finger in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t8r
TitleCrystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer
Components
  • Bromodomain adjacent to zinc finger domain protein 2A
  • Histone H3.1
KeywordsTRANSCRIPTION / PHD zinc fingers / histone3 / complex
Function / homology
Function and homology information


NoRC complex / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling ...NoRC complex / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / nuclear receptor binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / : / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / histone binding / nuclear speck / cadherin binding / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif ...Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Bromodomain, conserved site / Bromodomain signature. / Histone-fold / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Histone H3.1 / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAmato, A. / Gadd, M.S. / Bortoluzzi, A. / Ciulli, A.
CitationJournal: Biochem. J. / Year: 2017
Title: Structural basis of molecular recognition of helical histone H3 tail by PHD finger domains.
Authors: Bortoluzzi, A. / Amato, A. / Lucas, X. / Blank, M. / Ciulli, A.
History
DepositionSep 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bromodomain adjacent to zinc finger domain protein 2A
B: Bromodomain adjacent to zinc finger domain protein 2A
C: Bromodomain adjacent to zinc finger domain protein 2A
D: Bromodomain adjacent to zinc finger domain protein 2A
E: Histone H3.1
G: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,49717
Polymers28,6916
Non-polymers80511
Water1,72996
1
A: Bromodomain adjacent to zinc finger domain protein 2A
G: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9745
Polymers7,7482
Non-polymers2263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8234
Polymers6,5981
Non-polymers2263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8214
Polymers6,5981
Non-polymers2233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain adjacent to zinc finger domain protein 2A
E: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8794
Polymers7,7482
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Bromodomain adjacent to zinc finger domain protein 2A
C: Bromodomain adjacent to zinc finger domain protein 2A
G: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7949
Polymers14,3463
Non-polymers4496
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-17 kcal/mol
Surface area7290 Å2
MethodPISA
6
B: Bromodomain adjacent to zinc finger domain protein 2A
D: Bromodomain adjacent to zinc finger domain protein 2A
E: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7028
Polymers14,3463
Non-polymers3575
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-17 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.607, 72.607, 99.431
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein / Protein/peptide , 2 types, 6 molecules ABCDEG

#1: Protein
Bromodomain adjacent to zinc finger domain protein 2A / Transcription termination factor I-interacting protein 5 / Tip5 / hWALp3


Mass: 6597.694 Da / Num. of mol.: 4 / Fragment: PHD domain, UNP residues 1673-1728
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UIF9
#2: Protein/peptide Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 1150.332 Da / Num. of mol.: 2 / Fragment: UNP residues 2-11 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431

-
Non-polymers , 4 types, 107 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2 M Na/K phosphate / PH range: 8 - 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.4→45.62 Å / Num. obs: 10901 / % possible obs: 99.6 % / Redundancy: 5.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.113 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.4-2.495.80.7820.7181100
8.98-45.624.50.0570.999195.7

-
Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4qf2

4qf2


Resolution: 2.4→45.62 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.647 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.245
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 556 5.1 %RANDOM
Rwork0.1851 ---
obs0.1877 10309 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 500 Å2 / Biso mean: 52.134 Å2 / Biso min: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å2-0 Å2
2--0.58 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 2.4→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 24 96 1860
Biso mean--67.47 54.85 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191815
X-RAY DIFFRACTIONr_bond_other_d0.0020.021663
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9652438
X-RAY DIFFRACTIONr_angle_other_deg1.1233.0153793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66323.82781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33315294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2991513
X-RAY DIFFRACTIONr_chiral_restr0.0760.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021992
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02401
X-RAY DIFFRACTIONr_mcbond_it1.6093.9902
X-RAY DIFFRACTIONr_mcbond_other1.6083.895901
X-RAY DIFFRACTIONr_mcangle_it2.845.8131117
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 29 -
Rwork0.25 769 -
all-798 -
obs--99.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4857-2.90792.61196.5291-1.81825.52750.15460.3396-0.1716-0.3067-0.2212-0.11340.27710.47850.06660.05070.04250.01840.1140.00170.020512.75932.90319.719
25.3121-0.5201-0.81225.78780.31716.8676-0.0987-0.53230.15460.1420.0829-0.46370.2110.42470.01580.01030.0203-0.01160.0709-0.01490.040139.36524.66145.514
32.30231.5041-1.06366.5595-2.136.0671-0.0126-0.1642-0.00580.20820.0569-0.28710.12190.3274-0.04440.01730.0244-0.01160.0509-0.00690.020611.39238.67634.563
45.74332.3675-3.40964.8077-5.36478.7142-0.26730.33460.0695-0.49560.0795-0.28080.39990.06040.18790.1211-0.03550.05590.0391-0.00250.03933.74823.54230.213
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1676 - 1728
2X-RAY DIFFRACTION2B1676 - 1726
3X-RAY DIFFRACTION3C1676 - 1727
4X-RAY DIFFRACTION4D1676 - 1728

+
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