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- PDB-8ytc: PML-RBCC dimer -

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Basic information

Entry
Database: PDB / ID: 8ytc
TitlePML-RBCC dimer
ComponentsProtein PML
KeywordsNUCLEAR PROTEIN / PML nuclear body / RBCC dimer
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsTan, Y. / Li, J. / Zhang, S. / Zhang, Y. / Cong, Y. / Meng, G.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
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Revision 1.1Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein PML
B: Protein PML


Theoretical massNumber of molelcules
Total (without water)47,6482
Polymers47,6482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Protein PML / E3 SUMO-protein ligase PML / Promyelocytic leukemia protein / RING finger protein 71 / RING-type E3 ...E3 SUMO-protein ligase PML / Promyelocytic leukemia protein / RING finger protein 71 / RING-type E3 SUMO transferase PML / Tripartite motif-containing protein 19 / TRIM19


Mass: 23824.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PML, MYL, PP8675, RNF71, TRIM19 / Production host: Escherichia coli (E. coli)
References: UniProt: P29590, Transferases; Acyltransferases; Aminoacyltransferases
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Promyelocytic leukemia protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 307216 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0022660
ELECTRON MICROSCOPYf_angle_d0.5353590
ELECTRON MICROSCOPYf_dihedral_angle_d30.785352
ELECTRON MICROSCOPYf_chiral_restr0.04388
ELECTRON MICROSCOPYf_plane_restr0.003470

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