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- PDB-9ivd: Cryo-EM structure of CyclinD1 bound AMBRA1-DDB1 -

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Basic information

Entry
Database: PDB / ID: 9ivd
TitleCryo-EM structure of CyclinD1 bound AMBRA1-DDB1
Components
  • Activating molecule in BECN1-regulated autophagy protein 1
  • DNA damage-binding protein 1
  • G1/S-specific cyclin-D1
KeywordsSIGNALING PROTEIN / E3 ligase
Function / homology
Function and homology information


positive regulation of free ubiquitin chain polymerization / cyclin D1-CDK4 complex / re-entry into mitotic cell cycle / cyclin D1-CDK6 complex / Drug-mediated inhibition of CDK4/CDK6 activity / RUNX3 regulates WNT signaling / response to mitochondrial depolarisation / response to leptin / positive regulation of mitophagy / positive regulation of mammary gland epithelial cell proliferation ...positive regulation of free ubiquitin chain polymerization / cyclin D1-CDK4 complex / re-entry into mitotic cell cycle / cyclin D1-CDK6 complex / Drug-mediated inhibition of CDK4/CDK6 activity / RUNX3 regulates WNT signaling / response to mitochondrial depolarisation / response to leptin / positive regulation of mitophagy / positive regulation of mammary gland epithelial cell proliferation / Transcriptional regulation by RUNX2 / positive regulation by virus of viral protein levels in host cell / positive regulation of cyclin-dependent protein serine/threonine kinase activity / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / cyclin-dependent protein serine/threonine kinase activator activity / UV-damage excision repair / proline-rich region binding / Regulation of RUNX1 Expression and Activity / neural tube development / biological process involved in interaction with symbiont / positive regulation of regulatory T cell differentiation / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of mitotic cell cycle phase transition / mammary gland epithelial cell proliferation / WD40-repeat domain binding / negative regulation of cardiac muscle cell apoptotic process / response to UV-A / Cul4A-RING E3 ubiquitin ligase complex / negative regulation of epithelial cell differentiation / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Macroautophagy / PTK6 Regulates Cell Cycle / fat cell differentiation / negative regulation of reproductive process / negative regulation of developmental process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / microtubule organizing center / regulation of G1/S transition of mitotic cell cycle / cullin family protein binding / viral release from host cell / Transcriptional Regulation by VENTX / RUNX3 regulates p14-ARF / protein phosphatase activator activity / axoneme / autophagosome assembly / mammary gland alveolus development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / bicellular tight junction / positive regulation of G1/S transition of mitotic cell cycle / ectopic germ cell programmed cell death / ubiquitin-like ligase-substrate adaptor activity / positive regulation of viral genome replication / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / proteasomal protein catabolic process / endoplasmic reticulum unfolded protein response / mitophagy / cyclin-dependent protein kinase holoenzyme complex / phagocytic vesicle / positive regulation of autophagy / mitotic G1 DNA damage checkpoint signaling / positive regulation of G2/M transition of mitotic cell cycle / lactation / transcription repressor complex / positive regulation of gluconeogenesis / autophagosome / cellular response to starvation / liver regeneration / nucleotide-excision repair / Ubiquitin-dependent degradation of Cyclin D / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Pre-NOTCH Transcription and Translation / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / SCF(Skp2)-mediated degradation of p27/p21 / Wnt signaling pathway / RMTs methylate histone arginines / G1/S transition of mitotic cell cycle / histone deacetylase binding / Formation of Incision Complex in GG-NER / neuron differentiation / Dual incision in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription corepressor activity / Cyclin D associated events in G1 / cellular response to UV / rhythmic process / positive regulation of protein phosphorylation / site of double-strand break / Neddylation / GTPase binding / ubiquitin-dependent protein catabolic process / protein phosphatase binding
Similarity search - Function
: / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal ...: / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
G1/S-specific cyclin-D1 / DNA damage-binding protein 1 / Activating molecule in BECN1-regulated autophagy protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsWang, Y. / Liu, M. / Su, M.-Y. / Stjepanovic, G.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2024A1515011683 China
CitationJournal: To Be Published
Title: Mechanism of D-type cyclins recognition by the AMBRA1 E3 ligase receptor
Authors: Wang, Y. / Liu, M. / Su, M.-Y. / Stjepanovic, G.
History
DepositionJul 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: G1/S-specific cyclin-D1
B: Activating molecule in BECN1-regulated autophagy protein 1
A: DNA damage-binding protein 1


Theoretical massNumber of molelcules
Total (without water)205,4413
Polymers205,4413
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 G1/S-specific cyclin-D1 / B-cell lymphoma 1 protein / BCL-1 / BCL-1 oncogene / PRAD1 oncogene


Mass: 33847.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCND1, BCL1, PRAD1 / Production host: Homo sapiens (human) / References: UniProt: P24385
#2: Protein Activating molecule in BECN1-regulated autophagy protein 1 / DDB1- and CUL4-associated factor 3


Mass: 44496.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMBRA1, DCAF3, KIAA1736 / Production host: Homo sapiens (human) / References: UniProt: Q9C0C7
#3: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127097.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Homo sapiens (human) / References: UniProt: Q16531
Has ligand of interestY
Has protein modificationY

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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: Complex of AMBRA1-DDB1 bound to CyclinD1-CDK4 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.244 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1.198 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1015935 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048806
ELECTRON MICROSCOPYf_angle_d0.63811999
ELECTRON MICROSCOPYf_dihedral_angle_d5.5021237
ELECTRON MICROSCOPYf_chiral_restr0.0461424
ELECTRON MICROSCOPYf_plane_restr0.0051520

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