[English] 日本語
Yorodumi
- PDB-6fi0: Crystal structure of BAZ2A PHD zinc finger in complex with Fr 19 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fi0
TitleCrystal structure of BAZ2A PHD zinc finger in complex with Fr 19
ComponentsBromodomain adjacent to zinc finger domain protein 2A
KeywordsTRANSCRIPTION / PHD zinc finger / bromodomain / BAZ2A / fragment / Fr 19 / Fr19 / epigenetic / ligandability
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 / : ...NoRC complex / : / : / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / : / negative regulation of transcription by RNA polymerase I / : / heterochromatin formation / nuclear receptor binding / lysine-acetylated histone binding / NoRC negatively regulates rRNA expression / histone binding / nuclear speck / chromatin remodeling / DNA-templated transcription / nucleolus / regulation of DNA-templated transcription / DNA binding / RNA binding / metal ion binding / nucleus / 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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DEW / : / PHOSPHATE ION / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAmato, A. / Lucas, X. / Bortoluzzi, A. / Wright, D. / Ciulli, A.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Targeting Ligandable Pockets on Plant Homeodomain (PHD) Zinc Finger Domains by a Fragment-Based Approach.
Authors: Amato, A. / Lucas, X. / Bortoluzzi, A. / Wright, D. / Ciulli, A.
History
DepositionJan 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,85721
Polymers26,3914
Non-polymers1,46617
Water2,900161
1
A: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8635
Polymers6,5981
Non-polymers2654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0205
Polymers6,5981
Non-polymers4224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1517
Polymers6,5981
Non-polymers5536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 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
MethodPISA
Unit cell
Length a, b, c (Å)72.095, 72.095, 99.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 1 types, 4 molecules ABCD

#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
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

-
Non-polymers , 6 types, 178 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-DEW / 2-azanyl-1-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-yl)ethanone


Mass: 196.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2OS
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 161 / 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: 49.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2-2.4 M sodium/potassium phosphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.9→45.34 Å / Num. obs: 21069 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→1.94 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QF2

4qf2


Resolution: 1.9→45.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.36 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23101 1084 5.2 %RANDOM
Rwork0.18952 ---
obs0.1916 19952 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.775 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å2-0 Å20 Å2
2--0.82 Å20 Å2
3----1.64 Å2
Refinement stepCycle: 1 / Resolution: 1.9→45.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 62 161 1838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191728
X-RAY DIFFRACTIONr_bond_other_d0.0040.021537
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.9922323
X-RAY DIFFRACTIONr_angle_other_deg1.3143.0213534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.91423.76677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7415277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3281512
X-RAY DIFFRACTIONr_chiral_restr0.1090.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021854
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02344
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4022.63828
X-RAY DIFFRACTIONr_mcbond_other1.4022.63827
X-RAY DIFFRACTIONr_mcangle_it2.2293.9231028
X-RAY DIFFRACTIONr_mcangle_other2.2283.9231029
X-RAY DIFFRACTIONr_scbond_it2.2483.037900
X-RAY DIFFRACTIONr_scbond_other2.2483.04901
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.384.4921294
X-RAY DIFFRACTIONr_long_range_B_refined6.23732.231854
X-RAY DIFFRACTIONr_long_range_B_other6.23832.2281854
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 91 -
Rwork0.262 1431 -
obs--98.38 %
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)
13.1725-2.49842.772.6909-1.43673.19070.14270.2706-0.0693-0.0646-0.16420.11440.1580.27560.02150.04090.0213-0.03180.0814-0.01780.060612.758832.903519.7191
21.48141.1714-1.24373.84460.97222.3701-0.0478-0.3132-0.2725-0.1713-0.1799-0.2799-0.03720.29990.22770.0107-0.00290.01810.11880.05790.136339.36524.661445.5144
31.93880.5096-1.54432.9235-0.73521.2696-0.09980.00910.0520.17760.132-0.08810.0538-0.0174-0.03220.10120.0146-0.02740.06510.00730.031611.392238.675834.5627
42.85472.1998-1.11422.8831-2.69893.2951-0.18220.2051-0.0848-0.1950.0569-0.1130.18340.07350.12530.1074-0.03390.05170.05160.01120.055233.747823.541830.2127
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