[English] 日本語
Yorodumi
- EMDB-44120: Cryo-EM structure of yeast (Nap1)2-Kap114-H2A-H2B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44120
TitleCryo-EM structure of yeast (Nap1)2-Kap114-H2A-H2B
Map dataComposite map of consensus and locally refined map for Nap1.
Sample
  • Complex: Crosslinked mixture of Kap114 with Nap1 and H2A-H2B
    • Protein or peptide: KAP114 isoform 1
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: NAP1 isoform 1
KeywordsHistone / Chaperone / Import / Nucleosome Assembly / TRANSPORT PROTEIN
Function / homology: / : / : / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJiou J / Fung HYJ / Chook YM
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM141461 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM069909 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008203 United States
Welch FoundationI-1532 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP220582 United States
CitationJournal: J Cell Biol / Year: 2025
Title: Nap1 and Kap114 co-chaperone H2A-H2B and facilitate targeted histone release in the nucleus.
Authors: Ho Yee Joyce Fung / Jenny Jiou / Ashley B Niesman / Natalia E Bernardes / Yuh Min Chook /
Abstract: Core histones, synthesized and processed in the cytoplasm, must be chaperoned as they are transported into the nucleus for nucleosome assembly. The importin Kap114 transports H2A-H2B into the yeast ...Core histones, synthesized and processed in the cytoplasm, must be chaperoned as they are transported into the nucleus for nucleosome assembly. The importin Kap114 transports H2A-H2B into the yeast nucleus, where RanGTP facilitates histone release. Kap114 and H2A-H2B also bind the histone chaperone Nap1, but how Nap1 and Kap114 cooperate in transport and nucleosome assembly remains unclear. Here, biochemical and structural analyses show that Kap114, H2A-H2B, and a Nap1 dimer (Nap12) associate in the absence and presence of RanGTP to form equimolar complexes. A previous study had shown that RanGTP reduces Kap114's ability to chaperone H2A-H2B, but a new cryo-EM structure of the Nap12•H2A-H2B•Kap114•RanGTP complex explains how both Kap114 and Nap12 interact with H2A-H2B, restoring its chaperoning within the assembly while effectively depositing it into nucleosomes. Together, our results suggest that Kap114 and Nap12 provide a sheltered path that facilitates the transfer of H2A-H2B from Kap114 to Nap12, ultimately directing its specific deposition into nucleosomes.
History
DepositionMar 18, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44120.png

Downloads & links

-
Map

FileDownload / File: emd_44120.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of consensus and locally refined map for Nap1.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.1466796 - 0.58191586
Average (Standard dev.)0.0006120962 (±0.008269151)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Crosslinked mixture of Kap114 with Nap1 and H2A-H2B

EntireName: Crosslinked mixture of Kap114 with Nap1 and H2A-H2B
Components
  • Complex: Crosslinked mixture of Kap114 with Nap1 and H2A-H2B
    • Protein or peptide: KAP114 isoform 1
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: NAP1 isoform 1

-
Supramolecule #1: Crosslinked mixture of Kap114 with Nap1 and H2A-H2B

SupramoleculeName: Crosslinked mixture of Kap114 with Nap1 and H2A-H2B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Nap1 and H2A-H2B were pre-complexed with excess histones, and Kap114 was added before mild crosslinking and SEC separation.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 72 KDa

-
Macromolecule #1: KAP114 isoform 1

MacromoleculeName: KAP114 isoform 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 114.422055 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GGSGGSMDIN ELIIGAQSAD KHTREVAETQ LLQWCDSDAS QVFKALANVA LQHEASLESR QFALLSLRKL ITMYWSPGFE SYRSTSNVE IDVKDFIREV LLKLCLNDNE NTKIKNGASY CIVQISAVDF PDQWPQLLTV IYDAISHQHS LNAMSLLNEI Y DDVVSEEM ...String:
GGSGGSMDIN ELIIGAQSAD KHTREVAETQ LLQWCDSDAS QVFKALANVA LQHEASLESR QFALLSLRKL ITMYWSPGFE SYRSTSNVE IDVKDFIREV LLKLCLNDNE NTKIKNGASY CIVQISAVDF PDQWPQLLTV IYDAISHQHS LNAMSLLNEI Y DDVVSEEM FFEGGIGLAT MEIVFKVLNT ETSTLIAKIA ALKLLKACLL QMSSHNEYDE ASRKSFVSQC LATSLQILGQ LL TLNFGNV DVISQLKFKS IIYENLVFIK NDFSRKHFSS ELQKQFKIMA IQDLENVTHI NANVETTESE PLLETVHDCS IYI VEFLTS VCTLQFSVEE MNKIITSLTI LCQLSSETRE IWTSDFNTFV SKETGLAASY NVRDQANEFF TSLPNPQLSL IFKV VSNDI EHSTCNYSTL ESLLYLLQCI LLNDDEITGE NIDQSLQILI KTLENILVSQ EIPELILARA ILTIPRVLDK FIDAL PDIK PLTSAFLAKS LNLALKSDKE LIKSATLIAF TYYCYFAELD SVLGPEVCSE TQEKVIRIIN QVSSDAEEDT NGALME VLS QVISYNPKEP HSRKEILQAE FHLVFTISSE DPANVQVVVQ SQECLEKLLD NINMDNYKNY IELCLPSFIN VLDSNNA NN YRYSPLLSLV LEFITVFLKK KPNDGFLPDE INQYLFEPLA KVLAFSTEDE TLQLATEAFS YLIFNTDTRA MEPRLMDI M KVLERLLSLE VSDSAAMNVG PLVVAIFTRF SKEIQPLIGR ILEAVVVRLI KTQNISTEQN LLSVLCFLTC NDPKQTVDF LSSFQIDNTD ALTLVMRKWI EAFEVIRGEK RIKENIVALS NLFFLNDKRL QKVVVNGNLI PYEGDLIITR SMAKKMPDRY VQVPLYTKI IKLFVSELSF QSKQPNPEQL ITSDIKQEVV NANKDDDNDD WEDVDDVLDY DKLKEYIDDD VDEEADDDSD D ITGLMDVK ESVVQLLVRF FKEVASKDVS GFHCIYETLS DSERKVLSEA LL

UniProtKB: UNIPROTKB: A0A8H4BZV8

-
Macromolecule #2: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.88198 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGGKGGKAGS AAKASQSRSA KAGLTFPVGR VHRLLRRGNY AQRIGSGAPV YLTAVLEYLA AEILELAGNA ARDNKKTRII PRHLQLAIR NDDELNKLLG NVTIAQGGVL PNIHQNLLPK KSAKTAKASQ EL

UniProtKB: UNIPROTKB: A0A6A5Q402

-
Macromolecule #3: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.133145 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SSAAEKKPAS KAPAEKKPAA KKTSTSVDGK KRSKVRKETY SSYIYKVLKQ THPDTGISQK SMSILNSFVN DIFERIATEA SKLAAYNKK STISAREIQT AVRLILPGEL AKHAVSEGTR AVTKYSSSTQ A

UniProtKB: UNIPROTKB: A0A6A5Q1U6

-
Macromolecule #4: NAP1 isoform 1

MacromoleculeName: NAP1 isoform 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 36.182355 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MLGSLVGQDS GYVGGLPKNV KEKLLSLKTL QSELFEVEKE FQVEMFELEN KFLQKYKPIW EQRSRIISG QEQPKPEQIA KGQEIVESLN ETELLVDEEE KAQNDSEEEQ VKGIPSFWLT ALENLPIVCD TITDRDAEVL E YLQDIGLE ...String:
MGSSHHHHHH SSGLVPRGSH MLGSLVGQDS GYVGGLPKNV KEKLLSLKTL QSELFEVEKE FQVEMFELEN KFLQKYKPIW EQRSRIISG QEQPKPEQIA KGQEIVESLN ETELLVDEEE KAQNDSEEEQ VKGIPSFWLT ALENLPIVCD TITDRDAEVL E YLQDIGLE YLTDGRPGFK LLFRFDSSAN PFFTNDILCK TYFYQKELGY SGDFIYDHAE GCEISWKDNA HNVTVDLEMR KQ RNKTTKQ VRTIEKITPI ESFFNFFDPP KIQNEDQDEE LEEDLEERLA LDYSIGEQLK DKLIPRAVDW FTGAAL

UniProtKB: UNIPROTKB: A0A8H4BY55

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMTris
150.0 mMsodium chlorideNaCl
2.0 mMTCEP
0.003125 %Triton X-100
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 280 K / Instrument: FEI VITROBOT MARK IV
DetailsCrosslinked sample.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1080 / Average exposure time: 5.4 sec. / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4314112
Details: Blob picking on 100 micrographs and then further template picking.
Startup modelType of model: NONE / Details: Ab-initio reconstruction.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: Composite map was generated by first multiplying the mask used for particle subtraction with the consensus volume (vop multiply), and then composited with the locally refined map covering ...Details: Composite map was generated by first multiplying the mask used for particle subtraction with the consensus volume (vop multiply), and then composited with the locally refined map covering Nap1 region by vop maximum in ChimeraX.
Number images used: 148410
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Details: AlphaFold Multimer was used to generate initial model.
RefinementProtocol: OTHER
Output model

PDB-9b31:
Cryo-EM structure of yeast (Nap1)2-Kap114-H2A-H2B

+
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