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- EMDB-39571: PML-RBCC dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-39571
TitlePML-RBCC dimer
Map data
Sample
  • Complex: Promyelocytic leukemia protein
    • Protein or peptide: Protein PML
KeywordsPML nuclear body / RBCC dimer / NUCLEAR PROTEIN
Function / homology
Function and homology information


regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / suppression of viral release by host / PML body organization / SUMO binding / positive regulation of apoptotic process involved in mammary gland involution / fibroblast migration / SMAD protein signal transduction ...regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / suppression of viral release by host / PML body organization / SUMO binding / positive regulation of apoptotic process involved in mammary gland involution / fibroblast migration / SMAD protein signal transduction / myeloid cell differentiation / protein-containing complex localization / maintenance of protein location in nucleus / endoplasmic reticulum calcium ion homeostasis / regulation of double-strand break repair / branching involved in mammary gland duct morphogenesis / oncogene-induced cell senescence / Regulation of RUNX1 Expression and Activity / negative regulation of mitotic cell cycle / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / positive regulation of extrinsic apoptotic signaling pathway / cobalt ion binding / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of interleukin-1 beta production / SUMOylation of ubiquitinylation proteins / entrainment of circadian clock by photoperiod / SMAD binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / protein sumoylation / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of signal transduction by p53 class mediator / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cell fate commitment / protein targeting / regulation of cell adhesion / SUMOylation of DNA damage response and repair proteins / response to UV / retinoic acid receptor signaling pathway / Regulation of TP53 Activity through Acetylation / extrinsic apoptotic signaling pathway / positive regulation of defense response to virus by host / response to cytokine / cellular response to interleukin-4 / transforming growth factor beta receptor signaling pathway / Regulation of PTEN localization / negative regulation of angiogenesis / cellular response to leukemia inhibitory factor / response to gamma radiation / DNA damage response, signal transduction by p53 class mediator / circadian regulation of gene expression / negative regulation of cell growth / regulation of circadian rhythm / PML body / nuclear matrix / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage / Interferon gamma signaling / protein import into nucleus / HCMV Early Events / cellular senescence / protein-containing complex assembly / early endosome membrane / nuclear membrane / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / response to hypoxia / chromosome, telomeric region / regulation of cell cycle / protein stabilization / chromatin remodeling / protein heterodimerization activity / negative regulation of cell population proliferation / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / regulation of DNA-templated transcription / endoplasmic reticulum membrane / nucleolus / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein of unknown function DUF3583 / PML-like, coiled-coil / PML, C-terminal domain / : / ANCHR-like B-box zinc-binding domain / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) ...Protein of unknown function DUF3583 / PML-like, coiled-coil / PML, C-terminal domain / : / ANCHR-like B-box zinc-binding domain / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsTan Y / Li J / Zhang S / Zhang Y / Cong Y / Meng G
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)20152504 China
CitationJournal: Cell Discov / Year: 2024
Title: Cryo-EM structure of PML RBCC dimer reveals CC-mediated octopus-like nuclear body assembly mechanism.
Authors: Yangxia Tan / Jiawei Li / Shiyan Zhang / Yonglei Zhang / Zhiyi Zhuo / Xiaodan Ma / Yue Yin / Yanling Jiang / Yao Cong / Guoyu Meng /
Abstract: Promyelocytic leukemia protein (PML) nuclear bodies (NBs) are essential in regulating tumor suppression, antiviral response, inflammation, metabolism, aging, and other important life processes. The ...Promyelocytic leukemia protein (PML) nuclear bodies (NBs) are essential in regulating tumor suppression, antiviral response, inflammation, metabolism, aging, and other important life processes. The re-assembly of PML NBs might lead to an ~100% cure of acute promyelocytic leukemia. However, until now, the molecular mechanism underpinning PML NB biogenesis remains elusive due to the lack of structural information. In this study, we present the cryo-electron microscopy (cryo-EM) structure of the PML dimer at an overall resolution of 5.3 Å, encompassing the RING, B-box1/2 and part of the coiled-coil (RBCC) domains. The integrated approach, combining crosslinking and mass spectrometry (XL-MS) and functional analyses, enabled us to observe a unique folding event within the RBCC domains. The RING and B-box1/2 domains fold around the α3 helix, and the α6 helix serves as a pivotal interface for PML dimerization. More importantly, further characterizations of the cryo-EM structure in conjugation with AlphaFold2 prediction, XL-MS, and NB formation assays, help unveil an unprecedented octopus-like mechanism in NB assembly, wherein each CC helix of a PML dimer (PML dimer A) interacts with a CC helix from a neighboring PML dimer (PML dimer B) in an anti-parallel configuration, ultimately leading to the formation of a 2 µm membrane-less subcellular organelle.
History
DepositionMar 25, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39571.png

Downloads & links

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Map

FileDownload / File: emd_39571.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 160 pix.
= 142.4 Å		0.89 Å/pix.
x 160 pix.
= 142.4 Å		0.89 Å/pix.
x 160 pix.
= 142.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0665
Minimum - Maximum-0.0014906195 - 1.8237264
Average (Standard dev.)0.0030954534 (±0.040438727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 142.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39571_half_map_1.map
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Half map: #1

Fileemd_39571_half_map_2.map
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Sample components

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Entire : Promyelocytic leukemia protein

EntireName: Promyelocytic leukemia protein
Components
  • Complex: Promyelocytic leukemia protein
    • Protein or peptide: Protein PML

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Supramolecule #1: Promyelocytic leukemia protein

SupramoleculeName: Promyelocytic leukemia protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein PML

MacromoleculeName: Protein PML / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Aminoacyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.824133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PASEEEFQFL RCQQCQAEAK CPKLLPCLHT LCSGCLEASG MQCPICQAPW PLGADTPALD NVFFESLQRR LSVYRQIVDA QAVCTRCKE SADFWCFECE QLLCAKCFEA HQWFLKHEAR PLAELRNQSV REFLDGTRKT NNIFCSNPNH RTPTLTSIYC R GCSKPLCC ...String:
PASEEEFQFL RCQQCQAEAK CPKLLPCLHT LCSGCLEASG MQCPICQAPW PLGADTPALD NVFFESLQRR LSVYRQIVDA QAVCTRCKE SADFWCFECE QLLCAKCFEA HQWFLKHEAR PLAELRNQSV REFLDGTRKT NNIFCSNPNH RTPTLTSIYC R GCSKPLCC SCALLDSSHS ELKCDISAEI QQRQEELDAM TQALQEQDSA FGA

UniProtKB: Protein PML

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
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: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 307216
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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