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- EMDB-44121: Local refined map for Nap1 region from (Nap1)2-Kap114-H2A-H2B str... -

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Basic information

Entry
Database: EMDB / ID: EMD-44121
TitleLocal refined map for Nap1 region from (Nap1)2-Kap114-H2A-H2B structure
Map dataLocally refined map for Nap1.
Sample
  • Complex: Crosslinked mixture of Kap114 with Nap1 and H2A-H2B
    • Protein or peptide: Yeast Nap1
KeywordsHistone / Chaperone / Import / Nucleosome Assembly / TRANSPORT PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.84 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

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Structure visualization

Supplemental images

emd_44121.png

Downloads & links

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Map

FileDownload / File: emd_44121.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally 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: 0.06
Minimum - Maximum-0.3010523 - 0.4643329
Average (Standard dev.)-0.00023000201 (±0.0038402732)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: Half map A.

Fileemd_44121_half_map_1.map
AnnotationHalf map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B.

Fileemd_44121_half_map_2.map
AnnotationHalf map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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: Yeast Nap1

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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

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Macromolecule #1: Yeast Nap1

MacromoleculeName: Yeast Nap1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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.

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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

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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: 4.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: Particle subtraction was performed using mask covering Kap114 and its bound H2A-H2B, and local refinement was performed over the Nap1 region.
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
FSC plot (resolution estimation)

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