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- EMDB-26625: Structure of Importin-4 bound to the H3-H4-ASF1 histone-histone c... -

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Basic information

Entry
Database: EMDB / ID: EMD-26625
TitleStructure of Importin-4 bound to the H3-H4-ASF1 histone-histone chaperone complex
Map data
Sample
  • Complex: Nuclear import complex of Imp4-H3-H4-Asf1
    • Protein or peptide: Importin-4
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone chaperone
    • Protein or peptide: Histone H4
KeywordsImportin / Nuclear Import / Chaperone / Histones / H3 / H4 / ASF1 / NUCLEAR PROTEIN
Function / homology
Function and homology information


DNA replication-dependent chromatin assembly / nucleosome disassembly / nuclear import signal receptor activity / nuclear localization sequence binding / protein localization to nucleus / small GTPase binding / protein import into nucleus / structural constituent of chromatin / nucleosome / nucleosome assembly ...DNA replication-dependent chromatin assembly / nucleosome disassembly / nuclear import signal receptor activity / nuclear localization sequence binding / protein localization to nucleus / small GTPase binding / protein import into nucleus / structural constituent of chromatin / nucleosome / nucleosome assembly / histone binding / protein heterodimerization activity / chromatin / protein-containing complex / DNA binding / membrane / nucleus / cytoplasm
Similarity search - Function
Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Importin beta family / TOG domain / TOG / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain ...Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Importin beta family / TOG domain / TOG / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Histone chaperone / Histone H4 / Importin-4 / Histone H3
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsBernardes NE / Chook YM / Fung HYJ / Chen Z / Li Y
Funding support United States, 4 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP170644 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141461 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069909 United States
Welch FoundationI-1532 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structure of IMPORTIN-4 bound to the H3-H4-ASF1 histone-histone chaperone complex.
Authors: Natália Elisa Bernardes / Ho Yee Joyce Fung / Yang Li / Zhe Chen / Yuh Min Chook /
Abstract: IMPORTIN-4, the primary nuclear import receptor of core histones H3 and H4, binds the H3-H4 dimer and histone chaperone ASF1 prior to nuclear import. However, how H3-H3-ASF1 is recognized for ...IMPORTIN-4, the primary nuclear import receptor of core histones H3 and H4, binds the H3-H4 dimer and histone chaperone ASF1 prior to nuclear import. However, how H3-H3-ASF1 is recognized for transport cannot be explained by available crystal structures of IMPORTIN-4-histone tail peptide complexes. Our 3.5-Å IMPORTIN-4-H3-H4-ASF1 cryoelectron microscopy structure reveals the full nuclear import complex and shows a binding mode different from suggested by previous structures. The N-terminal half of IMPORTIN-4 clamps the globular H3-H4 domain and H3 αN helix, while its C-terminal half binds the H3 N-terminal tail weakly; tail contribution to binding energy is negligible. ASF1 binds H3-H4 without contacting IMPORTIN-4. Together, ASF1 and IMPORTIN-4 shield nucleosomal H3-H4 surfaces to chaperone and import it into the nucleus where RanGTP binds IMPORTIN-4, causing large conformational changes to release H3-H4-ASF1. This work explains how full-length H3-H4 binds IMPORTIN-4 in the cytoplasm and how it is released in the nucleus.
History
DepositionApr 11, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26625.png

Downloads & links

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Map

FileDownload / File: emd_26625.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 250.2 Å		0.83 Å/pix.
x 300 pix.
= 250.2 Å		0.83 Å/pix.
x 300 pix.
= 250.2 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.67588687 - 1.1471598
Average (Standard dev.)0.00023186555 (±0.028965825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 250.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_26625_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26625_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Nuclear import complex of Imp4-H3-H4-Asf1

EntireName: Nuclear import complex of Imp4-H3-H4-Asf1
Components
  • Complex: Nuclear import complex of Imp4-H3-H4-Asf1
    • Protein or peptide: Importin-4
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone chaperone
    • Protein or peptide: Histone H4

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Supramolecule #1: Nuclear import complex of Imp4-H3-H4-Asf1

SupramoleculeName: Nuclear import complex of Imp4-H3-H4-Asf1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 167 KDa

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Macromolecule #1: Importin-4

MacromoleculeName: Importin-4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.83207 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MESAGLEQLL RELLLPDTER IRRATEQLQI VLRAPAALPA LCDLLASAAD PQIRQFAAVL TRRRLNTRWR RLAAEQRESL KSLILTALQ RETEHCVSLS LAQLSATIFR KEGLEAWPQL LQLLQHSTHS PHSPEREMGL LLLSVVVTSR PEAFQPHHRE L LRLLNETL ...String:
MESAGLEQLL RELLLPDTER IRRATEQLQI VLRAPAALPA LCDLLASAAD PQIRQFAAVL TRRRLNTRWR RLAAEQRESL KSLILTALQ RETEHCVSLS LAQLSATIFR KEGLEAWPQL LQLLQHSTHS PHSPEREMGL LLLSVVVTSR PEAFQPHHRE L LRLLNETL GEVGSPGLLF YSLRTLTTMA PYLSTEDVPL ARMLVPKLIM AMQTLIPIDE AKACEALEAL DELLESEVPV IT PYLSEVL TFCLEVARNV ALGNAIRIRI LCCLTFLVKV KSKALLKNRL LPPLLHTLFP IVAAEPPPGQ LDPEDQDSEE EEL EIELMG ETPKHFAVQV VDMLALHLPP EKLCPQLMPM LEEALRSESP YQRKAGLLVL AVLSDGAGDH IRQRLLPPLL QIVC KGLED PSQVVRNAAL FALGQFSENL QPHISSYSRE VMPLLLAYLK SVPLGHTHHL AKACYALENF VENLGPKVQP YLPEL MECM LQLLRNPSSP RAKELAVSAL GAIATAAQAS LLPYFPAIME HLREFLLTGR EDLQPVQIQS LETLGVLARA VGEPMR PLA EECCQLGLGL CDQVDDPDLR RCTYSLFAAL SGLMGEGLAP HLEQITTLML LSLRSTEGIV PQYDGSSSFL LFDDESD GE EEEELMDEDV EEEDDSEISG YSVENAFFDE KEDTCAAVGE ISVNTSVAFL PYMESVFEEV FKLLECPHLN VRKAAHEA L GQFCCALHKA CQSCPSEPNT AALQAALARV VPSYMQAVNR ERERQVVMAV LEALTGVLRS CGTLTLKPPG RLAELCGVL KAVLQRKTAC QDTDEEEEEE DDDQAEYDAM LLEHAGEAIP ALAAAAGGDS FAPFFAGFLP LLVCKTKQGC TVAEKSFAVG TLAETIQGL GAASAQFVSR LLPVLLSTAQ EADPEVRSNA IFGMGVLAEH GGHPAQEHFP KLLGLLFPLL ARERHDRVRD N ICGALARL LMASPTRKPE PQVLAALLHA LPLKEDLEEW VTIGRLFSFL YQSSPDQVID VAPELLRICS LILADNKIPP DT KAALLLL LTFLAKQHTD SFQAALGSLP VDKAQELQAV LGLS

UniProtKB: Importin-4

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Macromolecule #2: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.407075 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LCGIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

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Macromolecule #3: Histone chaperone

MacromoleculeName: Histone chaperone / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 31.62926 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSIVSLLGIK VLNNPAKFTD PYEFEITFEC LESLKHDLEW KLTYVGSSRS LDHDQELDSI LVGPVPVGVN KFVFSADPPS AELIPASEL VSVTVILLSC SYDGREFVRV GYYVNNEYDE EELRENPPAK VQVDHIVRNI LAEKPRVTRF NIVWDNENEG D LYPPEQPG ...String:
MSIVSLLGIK VLNNPAKFTD PYEFEITFEC LESLKHDLEW KLTYVGSSRS LDHDQELDSI LVGPVPVGVN KFVFSADPPS AELIPASEL VSVTVILLSC SYDGREFVRV GYYVNNEYDE EELRENPPAK VQVDHIVRNI LAEKPRVTRF NIVWDNENEG D LYPPEQPG VDDEEEEDDE EEDDDEDDED DEDDDQEDGE GEAEEAAEEE EEEEEKTEDN ETNLEEEEED IENSDGDEEE GE EEVGSVD KNEDGNDKKR RKIEGGSTDI ESTPKDAARS TN

UniProtKB: Histone chaperone

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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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

BufferpH: 7.5
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.5 µm / Nominal defocus min: -1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146050
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7unk:
Structure of Importin-4 bound to the H3-H4-ASF1 histone-histone chaperone complex

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