[English] 日本語
Yorodumi
- PDB-4cy5: Crystal structure of the NSL1-WDS-NSL2 complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cy5
TitleCrystal structure of the NSL1-WDS-NSL2 complex.
Components
  • CG4699, ISOFORM D
  • DIM GAMMA-TUBULIN 1
  • PROTEIN WILL DIE SLOWLY
KeywordsTRANSCRIPTION / EPIGENETIC REGULATOR / HISTONE ACETYLATION / CHROMATIN
Function / homology
Function and homology information


polytene chromosome interband / Formation of WDR5-containing histone-modifying complexes / haltere development / germarium-derived female germ-line cyst formation / Neddylation / larval somatic muscle development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HATs acetylate histones / germ-line stem cell population maintenance / eye development ...polytene chromosome interband / Formation of WDR5-containing histone-modifying complexes / haltere development / germarium-derived female germ-line cyst formation / Neddylation / larval somatic muscle development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HATs acetylate histones / germ-line stem cell population maintenance / eye development / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / oogenesis / neuromuscular junction development / histone acetyltransferase binding / regulation of endocytosis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / heart development / chromatin organization / histone binding / chromatin remodeling / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Potential DNA-binding domain / KAT8 regulatory NSL complex subunit 2 / KANL2-like, probable zinc-finger domain / KAT8 regulatory NSL complex subunit 1 / PEHE domain / PEHE / WDR5 beta-propeller domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...Potential DNA-binding domain / KAT8 regulatory NSL complex subunit 2 / KANL2-like, probable zinc-finger domain / KAT8 regulatory NSL complex subunit 1 / PEHE domain / PEHE / WDR5 beta-propeller domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Non-specific lethal 1, isoform D / Protein will die slowly / KAT8 regulatory NSL complex subunit 2
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDias, J. / Brettschneider, J. / Cusack, S. / Kadlec, J.
CitationJournal: Genes Dev. / Year: 2014
Title: Structural Analysis of the Kansl1/Wdr5/Kansl2 Complex Reveals that Wdr5 is Required for Efficient Assembly and Chromatin Targeting of the Nsl Complex.
Authors: Dias, J. / Van Nguyen, N. / Georgiev, P. / Gaub, A. / Brettschneider, J. / Cusack, S. / Kadlec, J. / Akhtar, A.
History
DepositionApr 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN WILL DIE SLOWLY
C: DIM GAMMA-TUBULIN 1
D: CG4699, ISOFORM D


Theoretical massNumber of molelcules
Total (without water)38,0033
Polymers38,0033
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-12.6 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.480, 86.210, 47.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein PROTEIN WILL DIE SLOWLY / WDS


Mass: 34673.297 Da / Num. of mol.: 1 / Fragment: RESIDUES 50-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PFASTBACHTB / Cell line (production host): High Five / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9V3J8
#2: Protein/peptide DIM GAMMA-TUBULIN 1 / NSL2 / LD12439P


Mass: 1561.607 Da / Num. of mol.: 1 / Fragment: RESIDUES 155-166 / Source method: obtained synthetically / Source: (synth.) DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q9VAF4, inorganic diphosphatase
#3: Protein/peptide CG4699, ISOFORM D / NSL1


Mass: 1768.003 Da / Num. of mol.: 1 / Fragment: RESIDUES 714-729 / Source method: obtained synthetically / Source: (synth.) DROSOPHILA MELANOGASTER (fruit fly)
References: UniProt: A4V2Z1, Ligases; Forming carbon-oxygen bonds; Ligases forming aminoacyl-tRNA and related compounds
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.12 Å3/Da / Density % sol: 0.44 % / Description: NONE
Crystal growpH: 6.6
Details: 20% (W/V) PEG 3350, 0.2 M DI-AMMONIUM TARTRATE, PH 6.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97876
DetectorType: MARRESEARCH / Detector: CCD / Date: May 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 15438 / % possible obs: 99.4 % / Observed criterion σ(I): 2.3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.3 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G99

2g99


Resolution: 2.3→37.11 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.314 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24471 775 5 %RANDOM
Rwork0.20689 ---
obs0.20881 14628 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.275 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2---1.46 Å20 Å2
3---2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 0 28 2511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192538
X-RAY DIFFRACTIONr_bond_other_d0.0010.022411
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.9453439
X-RAY DIFFRACTIONr_angle_other_deg0.69235579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8485316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.92624.69498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65415441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.134157
X-RAY DIFFRACTIONr_chiral_restr0.0670.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022809
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02558
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_it1.6824.1131276
X-RAY DIFFRACTIONr_mcbond_other1.6824.1111275
X-RAY DIFFRACTIONr_mcangle_it2.6546.1531588
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8424.3391262
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 59 -
Rwork0.344 1045 -
obs--98.48 %

+
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