[English] 日本語
Yorodumi
- PDB-4ns5: Crystal structure of human BS69 Bromo-Zinc finger-PWWP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ns5
TitleCrystal structure of human BS69 Bromo-Zinc finger-PWWP
ComponentsZinc finger MYND domain-containing protein 11
KeywordsTRANSCRIPTION REGULATOR / Zinc Finger / chromatin binding / histone / nucleus
Function / homology
Function and homology information


regulation of transcription elongation by RNA polymerase II / negative regulation of JNK cascade / regulation of signal transduction / negative regulation of canonical NF-kappaB signal transduction / methylated histone binding / negative regulation of extrinsic apoptotic signaling pathway / transcription corepressor activity / chromatin organization / chromosome / double-stranded DNA binding ...regulation of transcription elongation by RNA polymerase II / negative regulation of JNK cascade / regulation of signal transduction / negative regulation of canonical NF-kappaB signal transduction / methylated histone binding / negative regulation of extrinsic apoptotic signaling pathway / transcription corepressor activity / chromatin organization / chromosome / double-stranded DNA binding / defense response to virus / cell cycle / negative regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / SH3 type barrels. - #140 / domain with conserved PWWP motif ...: / : / : / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Zinc finger MYND domain-containing protein 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWang, J.C. / Qin, S. / Li, F.D. / Li, S. / Zhang, W. / Wu, J.H. / Shi, Y.Y.
CitationJournal: Cell Res. / Year: 2014
Title: Crystal structure of human BS69 Bromo-ZnF-PWWP reveals its role in H3K36me3 nucleosome binding.
Authors: Wang, J. / Qin, S. / Li, F. / Li, S. / Zhang, W. / Peng, J. / Zhang, Z. / Gong, Q. / Wu, J. / Shi, Y.
History
DepositionNov 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zinc finger MYND domain-containing protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3622
Polymers27,2961
Non-polymers651
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.760, 64.380, 73.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Zinc finger MYND domain-containing protein 11 / Adenovirus 5 E1A-binding protein / Protein BS69


Mass: 27296.227 Da / Num. of mol.: 1
Fragment: Bromo-Zinc finger-PWWP domains (UNP residues 154-371)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZMYND11, BS69 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15326
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3748.1
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2851vapor diffusion, sitting drop90.1M Tris-HCl pH 9.0, 4% w/v Polyethylene glycol (PEG) 8000, VAPOR DIFFUSION, SITTING DROP, temperature 285K
2852vapor diffusion, sitting drop8.40.1 M Bicine, pH8.4, 2% v/v 1, 4-Dioxane, 2% w/v PEG 20000, VAPOR DIFFUSION, SITTING DROP, temperature 285K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.9793
SYNCHROTRONSSRF BL17U20.9793
Detector
TypeIDDetectorDate
RAYONIX MX-2251CCDSep 22, 2010
RAYONIX MX-2252CCDNov 14, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→48.4 Å / Num. all: 20832 / Num. obs: 20832 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rsym value: 0.102 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-27.40.5481.32196729520.54898.4
2-2.127.40.332.22095628240.3398.7
2.12-2.277.40.2163.31973326590.21698.8
2.27-2.457.40.1664.11840024880.16699
2.45-2.697.40.1284.91700823020.12899
2.69-37.40.1015.91544321000.10199.5
3-3.477.30.0915.81369518790.09199.6
3.47-4.257.20.0856.31161016170.08599.8
4.25-6.017.10.0746.9892112630.07499.8
6.01-31.8836.50.0697.148347480.06998.9

-
Phasing

PhasingMethod: SAD
Phasing MADD res high: 2 Å / D res low: 1000 Å / FOM : 0.24 / Reflection: 17913
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se17.7470.9990.4640.261.655
2Se30.3330.6440.8110.1360.862
3Se59.8380.3830.4170.1911.386
4Se47.2770.1560.8690.1061.01
5Se39.5870.0550.5230.2370.919
6Se10.7160.3710.0490.208
7Se20.3030.9510.3780.2380.273
Phasing MAD shell
Resolution (Å)FOM Reflection
7.3-10000.34871
4.58-7.30.371495
3.57-4.580.331899
3.02-3.570.312230
2.66-3.020.272500
2.41-2.660.212740
2.22-2.410.162981
2.06-2.220.133197
Phasing dmFOM : 0.34 / FOM acentric: 0.36 / FOM centric: 0.28 / Reflection: 9306 / Reflection acentric: 7831 / Reflection centric: 1475
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-31.8830.510.550.44446280166
4.5-7.10.480.520.361281993288
3.6-4.50.510.540.3315621298264
3.1-3.60.390.410.2715631339224
2.7-3.10.250.260.1827472403344
2.5-2.70.160.160.1317071518189

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
SOLVE2.13phasing
RESOLVE2.15phasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.9→31.88 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.22 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 1067 5.2 %RANDOM
Rwork0.2065 ---
obs0.2087 20667 98.17 %-
all-20832 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.58 Å2 / Biso mean: 37.0629 Å2 / Biso min: 19.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 1 94 1653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191601
X-RAY DIFFRACTIONr_bond_other_d0.0010.021492
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9172157
X-RAY DIFFRACTIONr_angle_other_deg0.70733421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5365183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33823.59689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18315285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.9351512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02418
X-RAY DIFFRACTIONr_mcbond_it1.9533.475738
X-RAY DIFFRACTIONr_mcbond_other1.9543.473737
X-RAY DIFFRACTIONr_mcangle_it3.1045.191919
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 65 -
Rwork0.277 1346 -
all-1411 -
obs--92.65 %

+
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://pdbjlvh1.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