[English] 日本語
Yorodumi
- PDB-6wxk: PHF23 PHD Domain Apo -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wxk
TitlePHF23 PHD Domain Apo
ComponentsPHD finger protein 23
KeywordsMETAL BINDING PROTEIN / PHF23 / PHD finger / histone / chromatin / NUP98 fusion
Function / homology
Function and homology information


negative regulation of autophagosome maturation / negative regulation of autophagosome assembly / positive regulation of protein ubiquitination / autophagy / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / PHD-finger / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHD finger protein 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsVann, K.R. / Zhang, J. / Zhang, Y. / Kutateladze, T.
CitationJournal: Nat Commun / Year: 2020
Title: Mechanistic insights into chromatin targeting by leukemic NUP98-PHF23 fusion.
Authors: Zhang, Y. / Guo, Y. / Gough, S.M. / Zhang, J. / Vann, K.R. / Li, K. / Cai, L. / Shi, X. / Aplan, P.D. / Wang, G.G. / Kutateladze, T.G.
History
DepositionMay 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHD finger protein 23
B: PHD finger protein 23
C: PHD finger protein 23
D: PHD finger protein 23
E: PHD finger protein 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,62115
Polymers34,9675
Non-polymers65410
Water0
1
A: PHD finger protein 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1243
Polymers6,9931
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHD finger protein 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1243
Polymers6,9931
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PHD finger protein 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1243
Polymers6,9931
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PHD finger protein 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1243
Polymers6,9931
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: PHD finger protein 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1243
Polymers6,9931
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.916, 66.916, 151.048
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein
PHD finger protein 23 / / PDH-containing protein JUNE-1


Mass: 6993.341 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF23 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BUL5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.65 / Details: 0.1 M Tris pH 8.65 and 25% tert-butanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 8025 / % possible obs: 97.8 % / Redundancy: 3.4 % / Rpim(I) all: 0.06 / Rsym value: 0.09 / Net I/σ(I): 13.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 763 / Rpim(I) all: 0.32 / Rsym value: 0.49 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
PHENIXv1.16refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O70

3o70


Resolution: 2.9→40.23 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2938 -10 %
Rwork0.2415 --
obs-7604 93.4 %
Displacement parametersBiso mean: 58.71 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 10 0 1963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682004
X-RAY DIFFRACTIONf_angle_d0.99872695
X-RAY DIFFRACTIONf_chiral_restr0.0552291
X-RAY DIFFRACTIONf_plane_restr0.0065329
X-RAY DIFFRACTIONf_dihedral_angle_d11.80391210

+
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