[English] 日本語
Yorodumi
- EMDB-78482: RomA Bound to H3K14Nle Nucleosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-78482
TitleRomA Bound to H3K14Nle Nucleosome
Map dataMap of RomA bound to H3K14Nle nucleosome. This map was obtained using homo-refinement.
Sample
  • Complex: RomA bound to H3K14Nle Nucleosome
    • Complex: Xenopus nucleosome
    • Complex: RomA
    • Protein or peptide: MBP-RomA
    • Protein or peptide: Histone H3K14Nle
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: 147 bp 601 Widom DNA Sequence
KeywordsRomA / H3K14Nle / Nucleosome / histone methylation / Legionella pneumophila / complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Biological speciesXenopus (frog) / Legionella pneumophila (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsMiller S / Worden EJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI173758 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Histone modification cross talk between a host and pathogen.
Authors: Shantinique S Miller / Joel A Hrit / Scott B Rothbart / Evan J Worden /
Abstract: Bacterial pathogens modulate host cell physiology by secreting effector proteins that rewire host signaling pathways. A subset of these effectors directly modify host chromatin to reprogram gene ...Bacterial pathogens modulate host cell physiology by secreting effector proteins that rewire host signaling pathways. A subset of these effectors directly modify host chromatin to reprogram gene expression and promote infection. While these enzymes are thought to function autonomously, the extent to which the host epigenetic landscape regulates their activity remains largely unknown. RomA and its homolog LegAs4 are Set domain-containing lysine methyltransferases from that methylate histone H3 at lysine 14 (H3K14) to suppress host immune responses and enhance intracellular bacterial replication. Here, we demonstrate that RomA activity is constrained by preexisting host histone posttranslational modifications (PTMs) through multiple layers of histone PTM cross talk. RomA selectively binds and methylates unmodified histone H3 tails and is inhibited by histone PTMs associated with active transcription, including H3K4 trimethylation, H3K4 acetylation, and H4K12 mono-methylation. We identify both cis- and trans-histone regulatory mechanisms, whereby unmodified H3K4 and H3K14 must reside on the same H3 tail to support RomA activity, while H4K12me1 inhibits RomA across the nucleosome. Notably, cryo-electron microscopy analysis and biochemical data reveal that RomA does not engage the nucleosome acidic patch but instead associates flexibly through histone tails. Together, these findings establish the host epigenetic regulation of bacterial effectors as a fundamental and previously unrecognized layer of host-pathogen interactions.
History
DepositionAug 5, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_78482.png

Downloads & links

-
Map

FileDownload / File: emd_78482.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of RomA bound to H3K14Nle nucleosome. This map was obtained using homo-refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 150 pix.
= 248.4 Å		1.66 Å/pix.
x 150 pix.
= 248.4 Å		1.66 Å/pix.
x 150 pix.
= 248.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.121
Minimum - Maximum-0.17470276 - 0.60453945
Average (Standard dev.)0.0036759984 (±0.028102554)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 248.40001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_78482_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half Map A of the RomA-bound H3K14Nle nucleosome....

Fileemd_78482_additional_1.map
AnnotationHalf Map A of the RomA-bound H3K14Nle nucleosome. This map was obtained using local-refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half Map B of the RomA-bound H3K14Nle nucleosome....

Fileemd_78482_additional_2.map
AnnotationHalf Map B of the RomA-bound H3K14Nle nucleosome. This map was obtained using local-refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: local refined map of the RomA-bound H3K14Nle nucleosome....

Fileemd_78482_additional_3.map
Annotationlocal refined map of the RomA-bound H3K14Nle nucleosome. This map was obtained using local-refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A of RomA bound to H3K14Nle...

Fileemd_78482_half_map_1.map
AnnotationHalf Map A of RomA bound to H3K14Nle nucleosome. This map was obtained using homo-refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B of RomA bound to H3K14Nle...

Fileemd_78482_half_map_2.map
AnnotationHalf Map B of RomA bound to H3K14Nle nucleosome. This map was obtained using homo-refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RomA bound to H3K14Nle Nucleosome

EntireName: RomA bound to H3K14Nle Nucleosome
Components
  • Complex: RomA bound to H3K14Nle Nucleosome
    • Complex: Xenopus nucleosome
    • Complex: RomA
    • Protein or peptide: MBP-RomA
    • Protein or peptide: Histone H3K14Nle
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: 147 bp 601 Widom DNA Sequence

-
Supramolecule #1: RomA bound to H3K14Nle Nucleosome

SupramoleculeName: RomA bound to H3K14Nle Nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus (frog)

-
Supramolecule #2: Xenopus nucleosome

SupramoleculeName: Xenopus nucleosome / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Xenopus (frog)

-
Supramolecule #3: RomA

SupramoleculeName: RomA / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Legionella pneumophila (bacteria)

-
Macromolecule #1: MBP-RomA

MacromoleculeName: MBP-RomA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW PLIAADGGYA ...String:
MAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW PLIAADGGYA FKYENGKYDI KDVGVDNAGA KAGLTFLVDL IKNKHMNADT DYSIAEAAFN KGETAMTING PWAWSNIDTS KVNYGVTVLP TFKGQPSKPF VGVLSAGINA ASPNKELAKE FLENYLLTDE GLEAVNKDKP LGAVALKSYE EELAKDPRIA ATMENAQKGE IMPNIPQMSA FWYAVRTAVI NAASGRQTVD EALKDAQTGS QNRAKNTLIE YNGSLMIILY DFLQESSVMP RSKNDSNLKK KSALQSKFKE QQWNHGSKEH KSKFKFTQRK AKKKGPGMTH LPGNIYTLFT PVNGLKNNAQ LTDTSKIMVN LHIDNMSSSD YIPSAIDRTD LVIVQPVHLL RKTGGRGLFA REDIPKGTCI GIYTGEVYSE QEFEQYLMEH VGSDKSYAMY VGGRVVDAAR KGNLTRYINF SDSQDNAEFV ETTLNRKKVV KVITTKNIKA GQQLLINYNT YEEQASRYYY FLNPGDGWLS AQEFYQTYQS QYRLEQMPYN LEGFDLKAGD RILMTQIGRI IFANYSLAKE QELNASDIDL PFLKVGSDEK ILDFDEADTF TPLMAACYLG QVENVKWLIE HGANIDQQQS HSGHCPLSLT LKGYSLAKDT KKYIDIIQLL IKNQVNLLVH DRSDKTFLHN AALVLNNLDF QSVVKFLIGQ NPIDINEYFT YIDENDFDIV MHCYNNKLFD KALVLLAFYP DYFKRNYMSD NEGHNQFNIN AFRKAIKDFN SNERNLLLMQ LRESSLHLPE DLLEQLGIMD SNITLESKFF

-
Macromolecule #2: Histone H3K14Nle

MacromoleculeName: Histone H3K14Nle / type: protein_or_peptide / ID: 2 / Details: Lysine 14 was mutated to Norleucine(NLE) / Enantiomer: LEVO
Source (natural)Organism: Xenopus (frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGG(NLE)APRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

-
Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3
Details: Purified histone was obtained from Histone Source at Colorado State University
Enantiomer: LEVO
Source (natural)Organism: Xenopus (frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYAL KRQGRTLYGF GG

-
Macromolecule #4: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus (frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRND EELNKLLGRV TIAQGGVLPN IQSVLLPKKT ESSKSAKSK

-
Macromolecule #5: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Xenopus (frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPDPAKSAPA AKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

-
Macromolecule #6: 147 bp 601 Widom DNA Sequence

MacromoleculeName: 147 bp 601 Widom DNA Sequence / type: dna / ID: 6 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
ATCGAGAATC CCGGTGCCGA GGCCGCTCAA TTGGTCGTAG ACAGCTCTAG CACCGCTTAA ACGCACGTAC GCGCTGTCCC CCGCGTTTTA ACCGCCAAGG GGATTACTCC CTAGTCTCCA GGCACGTGTC AGATATATAC ATCCGAT

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 10881930 / Details: Blob Picking + Template Picking
CTF correctionDetails: Patch CTF Estimation was used. / Type: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: Homo-Refinement yield 4.19 Angstroms Local-Refinement after masking yield 3.80 Angstroms
Number images used: 88079
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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