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- PDB-9ffb: ss-dsDNA-FANCD2-FANCI complex -

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Basic information

Entry
Database: PDB / ID: 9ffb
Titless-dsDNA-FANCD2-FANCI complex
Components
  • DNA (5'-D(P*CP*GP*AP*TP*GP*TP*CP*TP*CP*TP*AP*GP*AP*CP*AP*GP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*AP*GP*CP*TP*GP*TP*CP*TP*AP*GP*AP*GP*AP*CP*AP*TP*CP*GP*AP*T)-3')
  • Fanconi anemia complementation group I
  • Fanconi anemia protein FANCD2
KeywordsDNA BINDING PROTEIN / ss-dsDNA-FANCD2-FANCI / Fanconi Anemia / D2-I complex
Function / homology
Function and homology information


Fanconi Anemia Pathway in DNA repair / DNA repair / nucleoplasm
Similarity search - Function
Fanconi anemia group I protein / FANCI solenoid 1 cap / FANCI solenoid 1 domain / FANCI helical domain 1 / FANCI helical domain 2 / FANCI solenoid 3 domain / FANCI solenoid 4 domain / FANCI solenoid 2 domain / FANCI solenoid 1 cap / FANCI solenoid 1 ...Fanconi anemia group I protein / FANCI solenoid 1 cap / FANCI solenoid 1 domain / FANCI helical domain 1 / FANCI helical domain 2 / FANCI solenoid 3 domain / FANCI solenoid 4 domain / FANCI solenoid 2 domain / FANCI solenoid 1 cap / FANCI solenoid 1 / FANCI solenoid 2 / FANCI solenoid 3 / FANCI solenoid 4 / FANCI helical domain 1 / FANCI helical domain 2 / Fanconi anaemia protein FANCD2 / Fanconi anaemia protein FancD2 nuclease
Similarity search - Domain/homology
DNA / DNA (> 10) / Fanconi anemia complementation group I / Fanconi anemia protein FANCD2
Similarity search - Component
Biological speciesGallus gallus (chicken)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsAlcon, P. / Passmore, L.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_U105192715 United Kingdom
CitationJournal: Nature / Year: 2024
Title: FANCD2-FANCI surveys DNA and recognizes double- to single-stranded junctions.
Authors: Pablo Alcón / Artur P Kaczmarczyk / Korak Kumar Ray / Themistoklis Liolios / Guillaume Guilbaud / Tamara Sijacki / Yichao Shen / Stephen H McLaughlin / Julian E Sale / Puck Knipscheer / ...Authors: Pablo Alcón / Artur P Kaczmarczyk / Korak Kumar Ray / Themistoklis Liolios / Guillaume Guilbaud / Tamara Sijacki / Yichao Shen / Stephen H McLaughlin / Julian E Sale / Puck Knipscheer / David S Rueda / Lori A Passmore /
Abstract: DNA crosslinks block DNA replication and are repaired by the Fanconi anaemia pathway. The FANCD2-FANCI (D2-I) protein complex is central to this process as it initiates repair by coordinating DNA ...DNA crosslinks block DNA replication and are repaired by the Fanconi anaemia pathway. The FANCD2-FANCI (D2-I) protein complex is central to this process as it initiates repair by coordinating DNA incisions around the lesion. However, D2-I is also known to have a more general role in DNA repair and in protecting stalled replication forks from unscheduled degradation. At present, it is unclear how DNA crosslinks are recognized and how D2-I functions in replication fork protection. Here, using single-molecule imaging, we show that D2-I is a sliding clamp that binds to and diffuses on double-stranded DNA. Notably, sliding D2-I stalls on encountering single-stranded-double-stranded (ss-ds) DNA junctions, structures that are generated when replication forks stall at DNA lesions. Using cryogenic electron microscopy, we determined structures of D2-I on DNA that show that stalled D2-I makes specific interactions with the ss-dsDNA junction that are distinct from those made by sliding D2-I. Thus, D2-I surveys dsDNA and, when it reaches an ssDNA gap, it specifically clamps onto ss-dsDNA junctions. Because ss-dsDNA junctions are found at stalled replication forks, D2-I can identify sites of DNA damage. Therefore, our data provide a unified molecular mechanism that reconciles the roles of D2-I in the recognition and protection of stalled replication forks in several DNA repair pathways.
History
DepositionMay 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Oct 2, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: DNA (5'-D(P*GP*CP*AP*GP*CP*TP*GP*TP*CP*TP*AP*GP*AP*GP*AP*CP*AP*TP*CP*GP*AP*T)-3')
T: DNA (5'-D(P*CP*GP*AP*TP*GP*TP*CP*TP*CP*TP*AP*GP*AP*CP*AP*GP*CP*TP*GP*C)-3')
A: Fanconi anemia protein FANCD2
B: Fanconi anemia complementation group I


Theoretical massNumber of molelcules
Total (without water)327,0764
Polymers327,0764
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: DNA chain DNA (5'-D(P*GP*CP*AP*GP*CP*TP*GP*TP*CP*TP*AP*GP*AP*GP*AP*CP*AP*TP*CP*GP*AP*T)-3')


Mass: 6776.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*GP*AP*TP*GP*TP*CP*TP*CP*TP*AP*GP*AP*CP*AP*GP*CP*TP*GP*C)-3')


Mass: 6109.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Fanconi anemia protein FANCD2


Mass: 164731.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: fancd2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q68Y81
#4: Protein Fanconi anemia complementation group I


Mass: 149458.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: FANCI / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B0I564

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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: ss-dsDNA-FANCD2-FANCI complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 310 MDa / Experimental value: YES
Source (natural)Organism: Gallus gallus (chicken)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 319378 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01317686
ELECTRON MICROSCOPYf_angle_d0.80224060
ELECTRON MICROSCOPYf_dihedral_angle_d16.3132608
ELECTRON MICROSCOPYf_chiral_restr0.072811
ELECTRON MICROSCOPYf_plane_restr0.0062898

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