[English] 日本語
Yorodumi
- EMDB-0323: Structural insights into the ability of nucleoplasmin to assemble... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0323
TitleStructural insights into the ability of nucleoplasmin to assemble and chaperone histone octamers for DNA deposition
Map dataComplex between two nucleoplasmin molecules (each one a homopentamer) and an histone octamer
Sample
  • Complex: Nucleoplasmin-histone octamer complex
    • Complex: Nucleoplasmin
      • Protein or peptide: Nucleoplasmin
    • Complex: Histones
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
Biological speciesXenopus laevis (African clawed frog) / Gallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.7 Å
AuthorsValpuesta JM / Arranz R / Martin-Benito J
Funding support Spain, 1 items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-75984 Spain
CitationJournal: Sci Rep / Year: 2019
Title: Structural insights into the ability of nucleoplasmin to assemble and chaperone histone octamers for DNA deposition.
Authors: Aitor Franco / Rocío Arranz / Noelia Fernández-Rivero / Adrián Velázquez-Campoy / Jaime Martín-Benito / Joan Segura / Adelina Prado / José M Valpuesta / Arturo Muga /
Abstract: Nucleoplasmin (NP) is a pentameric histone chaperone that regulates the condensation state of chromatin in different cellular processes. We focus here on the interaction of NP with the histone ...Nucleoplasmin (NP) is a pentameric histone chaperone that regulates the condensation state of chromatin in different cellular processes. We focus here on the interaction of NP with the histone octamer, showing that NP could bind sequentially the histone components to assemble an octamer-like particle, and crosslinked octamers with high affinity. The three-dimensional reconstruction of the NP/octamer complex generated by single-particle cryoelectron microscopy, revealed that several intrinsically disordered tail domains of two NP pentamers, facing each other through their distal face, encage the histone octamer in a nucleosome-like conformation and prevent its dissociation. Formation of this complex depended on post-translational modification and exposure of the acidic tract at the tail domain of NP. Finally, NP was capable of transferring the histone octamers to DNA in vitro, assembling nucleosomes. This activity may have biological relevance for processes in which the histone octamer must be rapidly removed from or deposited onto the DNA.
History
DepositionOct 29, 2018-
Header (metadata) releaseJul 17, 2019-
Map releaseJul 17, 2019-
UpdateJul 17, 2019-
Current statusJul 17, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.094
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.094
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0323.png

Downloads & links

-
Map

FileDownload / File: emd_0323.map.gz / Format: CCP4 / Size: 549.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComplex between two nucleoplasmin molecules (each one a homopentamer) and an histone octamer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.35 Å/pix.
x 52 pix.
= 226.2 Å		4.35 Å/pix.
x 52 pix.
= 226.2 Å		4.35 Å/pix.
x 52 pix.
= 226.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.094 / Movie #1: 0.094
Minimum - Maximum-0.07121008 - 0.26907974
Average (Standard dev.)0.011250387 (±0.03724214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions525252
Spacing525252
CellA=B=C: 226.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.354.354.35
M x/y/z525252
origin x/y/z0.0000.0000.000
length x/y/z226.200226.200226.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS525252
D min/max/mean-0.0710.2690.011

-
Supplemental data

-
Sample components

-
Entire : Nucleoplasmin-histone octamer complex

EntireName: Nucleoplasmin-histone octamer complex
Components
  • Complex: Nucleoplasmin-histone octamer complex
    • Complex: Nucleoplasmin
      • Protein or peptide: Nucleoplasmin
    • Complex: Histones
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4

-
Supramolecule #1: Nucleoplasmin-histone octamer complex

SupramoleculeName: Nucleoplasmin-histone octamer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 320 KDa

-
Supramolecule #2: Nucleoplasmin

SupramoleculeName: Nucleoplasmin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Supramolecule #3: Histones

SupramoleculeName: Histones / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#5
Source (natural)Organism: Gallus gallus (chicken)

-
Macromolecule #1: Nucleoplasmin

MacromoleculeName: Nucleoplasmin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASTVSNTSK LEKPVSLIW G CELNEQDK TF EFKVEDD EEK CEHQLA LRTV CLGDK AKDEF NIVE IVTQEE GAE KSVPIAT LK PSILPMAT M VGIELTPPV TFRLKAGSGP LYISGQHVA M EEDYSWAE EE DEGEAEG EEE EEEEED QESP PKAVK ...String:
MASTVSNTSK LEKPVSLIW G CELNEQDK TF EFKVEDD EEK CEHQLA LRTV CLGDK AKDEF NIVE IVTQEE GAE KSVPIAT LK PSILPMAT M VGIELTPPV TFRLKAGSGP LYISGQHVA M EEDYSWAE EE DEGEAEG EEE EEEEED QESP PKAVK RPAAT KKAG QAKKKK LDK EDESSEE DS PTKKGKGA G RGRKPAAKK

-
Macromolecule #2: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
SequenceString:
MSGRGKQGGK ARAKAKSRS S RAGLQFPV GR VHRLLRK GNY AERVGA GAPV YLAAV LEYLT AEIL ELAGNA ARD NKKTRII PR HLQLAIRN D EELNKLLGK

-
Macromolecule #3: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
SequenceString:
MPEPAKSAPA PKKGSKKAV T KTQKKGDK KR KKSRKES YSI YVYKVL KQVH PDTGI SSKAM GIMN SFVNDI FER IAGEASR LA HYNKRSTI T SREIQTAVR LLLPGELAKH AVSEGTKAV T KYTSSK

-
Macromolecule #4: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
SequenceString:
MARTKQTARK FTGGKAPRK Q LATKAARK SA PSTGGVK KPH RYRPGT VALR EIRRY QKSTE LLIR KLPFQR LVR EIAQDFK TD LRFQSAAI G ALQEASEAY LVGLFEDTNL CAIHAKRVT I MPKDIQLA RR IRGERA

-
Macromolecule #5: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
SequenceString:
MSGRGKGGKG LGKGGAKRH R KVLRDNIQ GI TKPAIRR LAR RGGVKR ISGL IYEET RGVLK VFLE NVIRDA VTY TEHAKRK TV TAMDVVYA L KRQGRTLYG FGG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 240 mM NaCl, 2 mM MgCl2, 25 mM Hepes pH 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 5 / Number real images: 897 / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 80500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 166976
CTF correctionSoftware - Name: CTFFIND
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 14.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 11438
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: Xmipp
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

-
Atomic model buiding 1

Initial model(PDB ID:

1k5j

,

1aoi

)
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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