+Open data
-Basic information
Entry | Database: PDB / ID: 6xtx | ||||||
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Title | CryoEM structure of human CMG bound to ATPgammaS and DNA | ||||||
Components |
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Keywords | REPLICATION / CMG / Helicase / ATPase / Replisome | ||||||
Function / homology | Function and homology information Switching of origins to a post-replicative state / Unwinding of DNA / GINS complex / DNA strand elongation involved in mitotic DNA replication / mitotic DNA replication preinitiation complex assembly / nuclear origin of replication recognition complex / alpha DNA polymerase:primase complex / mitotic DNA replication / CMG complex / DNA replication checkpoint signaling ...Switching of origins to a post-replicative state / Unwinding of DNA / GINS complex / DNA strand elongation involved in mitotic DNA replication / mitotic DNA replication preinitiation complex assembly / nuclear origin of replication recognition complex / alpha DNA polymerase:primase complex / mitotic DNA replication / CMG complex / DNA replication checkpoint signaling / MCM complex / DNA replication preinitiation complex / regulation of phosphorylation / Activation of the pre-replicative complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / regulation of DNA-templated DNA replication initiation / Activation of ATR in response to replication stress / inner cell mass cell proliferation / DNA strand elongation involved in DNA replication / cochlea development / G1/S-Specific Transcription / DNA unwinding involved in DNA replication / DNA replication origin binding / DNA replication initiation / cellular response to interleukin-4 / DNA helicase activity / ciliary basal body / helicase activity / Assembly of the pre-replicative complex / Orc1 removal from chromatin / cellular response to xenobiotic stimulus / nucleosome assembly / single-stranded DNA binding / histone binding / chromosome, telomeric region / DNA replication / DNA helicase / cell population proliferation / chromatin binding / centrosome / DNA damage response / chromatin / apoptotic process / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å | ||||||
Authors | Rzechorzek, N.J. / Pellegrini, L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nucleic Acids Res / Year: 2020 Title: CryoEM structures of human CMG-ATPγS-DNA and CMG-AND-1 complexes. Authors: Neil J Rzechorzek / Steven W Hardwick / Vincentius A Jatikusumo / Dimitri Y Chirgadze / Luca Pellegrini / Abstract: DNA unwinding in eukaryotic replication is performed by the Cdc45-MCM-GINS (CMG) helicase. Although the CMG architecture has been elucidated, its mechanism of DNA unwinding and replisome interactions ...DNA unwinding in eukaryotic replication is performed by the Cdc45-MCM-GINS (CMG) helicase. Although the CMG architecture has been elucidated, its mechanism of DNA unwinding and replisome interactions remain poorly understood. Here we report the cryoEM structure at 3.3 Å of human CMG bound to fork DNA and the ATP-analogue ATPγS. Eleven nucleotides of single-stranded (ss) DNA are bound within the C-tier of MCM2-7 AAA+ ATPase domains. All MCM subunits contact DNA, from MCM2 at the 5'-end to MCM5 at the 3'-end of the DNA spiral, but only MCM6, 4, 7 and 3 make a full set of interactions. DNA binding correlates with nucleotide occupancy: five MCM subunits are bound to either ATPγS or ADP, whereas the apo MCM2-5 interface remains open. We further report the cryoEM structure of human CMG bound to the replisome hub AND-1 (CMGA). The AND-1 trimer uses one β-propeller domain of its trimerisation region to dock onto the side of the helicase assembly formed by Cdc45 and GINS. In the resulting CMGA architecture, the AND-1 trimer is closely positioned to the fork DNA while its CIP (Ctf4-interacting peptide)-binding helical domains remain available to recruit partner proteins. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6xtx.cif.gz | 935.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xtx.ent.gz | 743.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xtx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xtx_validation.pdf.gz | 543 KB | Display | wwPDB validaton report |
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Full document | 6xtx_full_validation.pdf.gz | 544.9 KB | Display | |
Data in XML | 6xtx_validation.xml.gz | 49.7 KB | Display | |
Data in CIF | 6xtx_validation.cif.gz | 81.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/6xtx ftp://data.pdbj.org/pub/pdb/validation_reports/xt/6xtx | HTTPS FTP |
-Related structure data
Related structure data | 10619MC 6xtyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10471 (Title: CryoEM structure of human CMG bound to ATPgammaS and DNA Data size: 7.7 TB Data #1: Unaligned multiframe micrographs of human CMG bound ATPgammaS and DNA [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA replication licensing factor ... , 6 types, 6 molecules 234567
#1: Protein | Mass: 102034.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM2, BM28, CCNL1, CDCL1, KIAA0030 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P49736, DNA helicase |
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#2: Protein | Mass: 96043.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM3 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P25205, DNA helicase |
#3: Protein | Mass: 99119.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM4, CDC21 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P33991, DNA helicase |
#4: Protein | Mass: 82406.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM5, CDC46 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P33992, DNA helicase |
#5: Protein | Mass: 93010.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM6 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q14566, DNA helicase |
#6: Protein | Mass: 81411.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM7, CDC47, MCM2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P33993, DNA helicase |
-DNA replication complex GINS protein ... , 4 types, 4 molecules ABCD
#7: Protein | Mass: 23022.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GINS1, KIAA0186, PSF1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q14691 |
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#8: Protein | Mass: 25336.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GINS2, PSF2, CGI-122, DC5, HSPC037 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9Y248 |
#9: Protein | Mass: 24562.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GINS3, PSF3 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9BRX5 |
#10: Protein | Mass: 26081.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GINS4, SLD5 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9BRT9 |
-Protein / DNA chain , 2 types, 2 molecules EM
#11: Protein | Mass: 65650.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC45, CDC45L, CDC45L2, UNQ374/PRO710 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: O75419 |
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#12: DNA chain | Mass: 21390.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 13 molecules
#13: Chemical | ChemComp-ZN / #14: Chemical | #15: Chemical | #16: Chemical | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 57.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213527 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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