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- EMDB-42289: Cryo-EM map of human clamp-clamp loader ATAD5-RFC-cracked PCNA co... -
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Open data
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Basic information
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Title | Cryo-EM map of human clamp-clamp loader ATAD5-RFC-cracked PCNA complex in intermediate state 2 | ||||||||||||
![]() | Final sharpened Cryo-EM map | ||||||||||||
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![]() | AAA ATPase / Clamp unloader / MOTOR PROTEIN | ||||||||||||
Function / homology | ![]() DNA clamp unloader activity / positive regulation of cell cycle G2/M phase transition / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / response to organophosphorus / Ctf18 RFC-like complex / DNA clamp loader activity / nuclear DNA replication / DNA replication factor C complex ...DNA clamp unloader activity / positive regulation of cell cycle G2/M phase transition / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / response to organophosphorus / Ctf18 RFC-like complex / DNA clamp loader activity / nuclear DNA replication / DNA replication factor C complex / Elg1 RFC-like complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / positive regulation of isotype switching to IgG isotypes / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / Activation of ATR in response to replication stress / regulation of mitotic cell cycle phase transition / DNA duplex unwinding / response to L-glutamate / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA strand elongation involved in DNA replication / histone acetyltransferase binding / DNA synthesis involved in DNA repair / DNA polymerase processivity factor activity / positive regulation of DNA replication / G1/S-Specific Transcription / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / replication fork processing / response to dexamethasone / leading strand elongation / nuclear replication fork / cyclin-dependent protein kinase holoenzyme complex / Presynaptic phase of homologous DNA pairing and strand exchange / SUMOylation of DNA replication proteins / estrous cycle / epithelial cell differentiation / PCNA-Dependent Long Patch Base Excision Repair / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / positive regulation of DNA repair / ATP-dependent activity, acting on DNA / mismatch repair / male germ cell nucleus / translesion synthesis / response to cadmium ion / DNA polymerase binding / positive regulation of B cell proliferation / liver regeneration / Translesion synthesis by REV1 / Translesion synthesis by POLK / base-excision repair, gap-filling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / G2/M DNA damage checkpoint / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to xenobiotic stimulus / cellular response to UV / Processing of DNA double-strand break ends / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / chromosome, telomeric region / DNA replication / Regulation of TP53 Activity through Phosphorylation / cell population proliferation / damaged DNA binding / nuclear body / DNA repair / chromatin binding / centrosome / chromatin / protein-containing complex binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
![]() | Wang F / He Q / Li H | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The human ATAD5 has evolved unique structural elements to function exclusively as a PCNA unloader. Authors: Feng Wang / Qing He / Nina Y Yao / Michael E O'Donnell / Huilin Li / ![]() Abstract: Humans have three different proliferating cell nuclear antigen (PCNA) clamp-loading complexes: RFC and CTF18-RFC load PCNA onto DNA, but ATAD5-RFC can only unload PCNA from DNA. The underlying ...Humans have three different proliferating cell nuclear antigen (PCNA) clamp-loading complexes: RFC and CTF18-RFC load PCNA onto DNA, but ATAD5-RFC can only unload PCNA from DNA. The underlying structural basis of ATAD5-RFC unloading is unknown. We show here that ATAD5 has two unique locking loops that appear to tie the complex into a rigid structure, and together with a domain that plugs the DNA-binding chamber, prevent conformation changes required for DNA binding, likely explaining why ATAD5-RFC is exclusively a PCNA unloader. These features are conserved in the yeast PCNA unloader Elg1-RFC. We observe intermediates in which PCNA bound to ATAD5-RFC exists as a closed planar ring, a cracked spiral or a gapped spiral. Surprisingly, ATAD5-RFC can open a PCNA gap between PCNA protomers 2 and 3, different from the PCNA protomers 1 and 3 gap observed in all previously characterized clamp loaders. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 118 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.6 KB 26.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 63.8 KB | ||
Filedesc metadata | ![]() | 7.7 KB | ||
Others | ![]() ![]() ![]() ![]() | 61.8 MB 111.2 MB 116.2 MB 116.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ui9MC ![]() 8ui7C ![]() 8ui8C ![]() 8uiiC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Final sharpened Cryo-EM map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: unsharpened Cryo-EM map
File | emd_42289_additional_1.map | ||||||||||||
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Annotation | unsharpened Cryo-EM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Sharpened Cryo-EM map by DeepEMhancer
File | emd_42289_additional_2.map | ||||||||||||
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Annotation | Sharpened Cryo-EM map by DeepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map A
File | emd_42289_half_map_1.map | ||||||||||||
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Annotation | Half Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map B
File | emd_42289_half_map_2.map | ||||||||||||
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Annotation | Half Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : ATAD5-RFC-cracked PCNA
+Supramolecule #1: ATAD5-RFC-cracked PCNA
+Macromolecule #1: ATPase family AAA domain-containing protein 5
+Macromolecule #2: Replication factor C subunit 2
+Macromolecule #3: Replication factor C subunit 5
+Macromolecule #4: Replication factor C subunit 4
+Macromolecule #5: Replication factor C subunit 3
+Macromolecule #6: Proliferating cell nuclear antigen
+Macromolecule #7: MAGNESIUM ION
+Macromolecule #8: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
+Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |