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- PDB-6vaa: Structure of the Fanconi Anemia ID complex bound to ICL DNA -

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Basic information

Entry
Database: PDB / ID: 6vaa
TitleStructure of the Fanconi Anemia ID complex bound to ICL DNA
Components
  • DNA (26-MER)
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Fanconi anemia group D2 protein
  • Fanconi anemia, complementation group I
KeywordsDNA BINDING PROTEIN/DNA / DNA repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of CD40 signaling pathway / regulation of regulatory T cell differentiation / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / gamete generation / neuronal stem cell population maintenance / brain morphogenesis / DNA repair complex / mitotic intra-S DNA damage checkpoint signaling / interstrand cross-link repair ...regulation of CD40 signaling pathway / regulation of regulatory T cell differentiation / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / gamete generation / neuronal stem cell population maintenance / brain morphogenesis / DNA repair complex / mitotic intra-S DNA damage checkpoint signaling / interstrand cross-link repair / DNA polymerase binding / condensed chromosome / positive regulation of protein ubiquitination / response to gamma radiation / TP53 Regulates Transcription of DNA Repair Genes / Fanconi Anemia Pathway / cellular response to oxidative stress / regulation of inflammatory response / nuclear body / DNA repair / chromatin / nucleolus / DNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
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 group D2 protein / Fanconi anemia group I protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPavletich, N.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2020
Title: DNA clamp function of the monoubiquitinated Fanconi anaemia ID complex.
Authors: Renjing Wang / Shengliu Wang / Ankita Dhar / Christopher Peralta / Nikola P Pavletich /
Abstract: The ID complex, involving the proteins FANCI and FANCD2, is required for the repair of DNA interstrand crosslinks (ICL) and related lesions. These proteins are mutated in Fanconi anaemia, a disease ...The ID complex, involving the proteins FANCI and FANCD2, is required for the repair of DNA interstrand crosslinks (ICL) and related lesions. These proteins are mutated in Fanconi anaemia, a disease in which patients are predisposed to cancer. The Fanconi anaemia pathway of ICL repair is activated when a replication fork stalls at an ICL; this triggers monoubiquitination of the ID complex, in which one ubiquitin molecule is conjugated to each of FANCI and FANCD2. Monoubiquitination of ID is essential for ICL repair by excision, translesion synthesis and homologous recombination; however, its function remains unknown. Here we report a cryo-electron microscopy structure of the monoubiquitinated human ID complex bound to DNA, and reveal that it forms a closed ring that encircles the DNA. By comparison with the structure of the non-ubiquitinated ID complex bound to ICL DNA-which we also report here-we show that monoubiquitination triggers a complete rearrangement of the open, trough-like ID structure through the ubiquitin of one protomer binding to the other protomer in a reciprocal fashion. These structures-together with biochemical data-indicate that the monoubiquitinated ID complex loses its preference for ICL and related branched DNA structures, and becomes a sliding DNA clamp that can coordinate the subsequent repair reactions. Our findings also reveal how monoubiquitination in general can induce an alternative protein structure with a new function.
History
DepositionDec 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _refine.ls_d_res_high / _refine.ls_d_res_low

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-21134
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fanconi anemia, complementation group I
B: Fanconi anemia group D2 protein
W: DNA (26-MER)
X: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
Y: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Z: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)337,1986
Polymers337,1986
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Fanconi anemia, complementation group I


Mass: 149566.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCI / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B7ZMF2, UniProt: Q9NVI1*PLUS
#2: Protein Fanconi anemia group D2 protein / Protein FACD2


Mass: 164314.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCD2, FACD / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BXW9

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DNA chain , 4 types, 4 molecules WXYZ

#3: DNA chain DNA (26-MER)


Mass: 8411.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 5430.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 4653.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 4822.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: FANCI-FANCD2-DNA complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
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
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0238 / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4CTF correction
7Omodel fitting
9RELION3initial Euler assignment
13REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 231943 / Symmetry type: POINT
Atomic model buildingB value: 169 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: Rfactor
Atomic model buildingPDB-ID: 3S4W

3s4w


Accession code: 3S4W / Source name: PDB / Type: experimental model
RefinementResolution: 3.4→3.4 Å / Cor.coef. Fo:Fc: 0.847 / SU B: 55.551 / SU ML: 0.389 / ESU R: 0.646
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.34249 --
obs0.34249 143563 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 174.481 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-1.01 Å2-0.62 Å2
2---1.3 Å2-1.98 Å2
3---1.79 Å2
Refinement stepCycle: 1 / Total: 20055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0110.01320620
ELECTRON MICROSCOPYr_bond_other_d0.0060.01718997
ELECTRON MICROSCOPYr_angle_refined_deg1.4151.58628075
ELECTRON MICROSCOPYr_angle_other_deg1.5671.63444257
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.9515.1212679
ELECTRON MICROSCOPYr_dihedral_angle_2_deg37.43623.674890
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.443153585
ELECTRON MICROSCOPYr_dihedral_angle_4_deg17.4991579
ELECTRON MICROSCOPYr_chiral_restr0.2290.2072786
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0221196
ELECTRON MICROSCOPYr_gen_planes_other0.0040.023928
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.8850.2339259
ELECTRON MICROSCOPYr_mcbond_other2.8850.2339258
ELECTRON MICROSCOPYr_mcangle_it4.7340.33911530
ELECTRON MICROSCOPYr_mcangle_other4.7330.33911531
ELECTRON MICROSCOPYr_scbond_it0.7630.19211361
ELECTRON MICROSCOPYr_scbond_other0.7630.19211360
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other1.2230.28816546
ELECTRON MICROSCOPYr_long_range_B_refined3.6652.6553015
ELECTRON MICROSCOPYr_long_range_B_other3.6652.6553014
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.35→3.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.587 10623 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON MICROSCOPY

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.5654-1.738-1.29422.93520.65172.6728-0.07230.12820.1921-0.13240.0567-0.6438-0.01921.10920.01562.0941-0.17290.23051.7430.14872.5691132.665596.185745.9998
217.99111.8441-1.33748.8455-1.16796.65240.005-0.46321.7502-0.1397-0.0653-0.6458-0.98680.1060.06020.88340.03620.01370.5559-0.02351.492898.092292.175652.1535
315.6107-3.2274-2.72312.19763.87436.9806-0.0849-0.26790.74130.13020.0913-0.0943-0.8775-0.4066-0.00640.4494-0.00350.00330.35970.0110.894276.780586.295556.2756
412.51664.22082.9434.97412.13851.25160.11910.2059-0.059-0.1314-0.32350.7310.1109-0.43090.20440.94520.05430.03450.8040.0321.12748.471763.133744.4485
58.1957-0.1678-0.41766.3371-0.9521.596-0.1514-0.832-0.33880.6088-0.33811.0160.5315-1.31950.48951.7692-0.11870.16611.7717-0.33072.217420.223665.822456.67
613.05221.69450.84878.80941.02355.68480.0455-0.36370.79840.1636-0.50581.3619-0.7163-0.93370.46031.28750.1469-0.1670.9855-0.30741.595831.334986.731354.8689
79.49041.02211.57917.62072.50554.4292-0.0332-0.12881.11580.1426-0.36320.8821-0.8146-0.98930.39641.72960.0759-0.3331.3677-0.0921.855441.8297103.816365.5598
86.5006-2.5552-1.5015.0863.475.49830.1175-1.230.64660.87820.07920.0529-0.50090.0664-0.19671.76950.0789-0.26451.8132-0.18221.853559.4055107.461280.5093
91.3953-1.26030.18772.63022.85117.8829-0.2026-1.02630.47730.71380.7517-0.7752-0.33420.8892-0.54912.45350.0279-0.55962.8745-0.16712.525973.2489105.796388.3997
105.97731.63586.95596.24563.93429.69330.08360.9875-0.5507-1.1852-0.06621.07770.1985-0.3071-0.01742.32740.0905-0.21432.69020.00642.206335.008740.852922.9417
115.8691.55876.705711.2881-0.138811.00910.52370.5728-1.4807-0.3399-0.22180.05621.6379-0.1853-0.30191.54510.0932-0.28061.50690.04992.155753.86134.391738.1183
1211.84385.01227.901311.6707-0.17746.98640.8604-0.182-1.57990.1158-0.4984-0.51360.81720.4711-0.3621.35080.0108-0.09881.23560.32321.962271.311640.047447.9777
1319.69254.34660.55029.40950.41253.1404-0.027-0.5446-1.40620.2286-0.2392-0.40730.35050.31840.26620.8363-0.0037-0.11460.67520.40771.368888.533353.168850.9828
1421.80046.8842-5.76246.8732-0.80712.3004-0.21451.2012-0.5341-0.94050.333-1.4196-0.02910.43-0.11851.0370.05820.12471.14670.28782.0469115.892372.612544.9401
156.7710.1645-0.02074.07780.32675.38350.07580.080.23810.10830.0232-0.5121-0.46320.7488-0.0991.95690.09250.07041.62630.38682.6026147.245461.674455.0738
167.39580.7178-0.8127.0775-1.29623.9522-0.12330.3499-0.8198-0.11110.04140.06730.8301-0.15710.08191.9355-0.07610.24531.63810.42662.7177131.639235.872960.0547
177.31460.89920.16273.18971.34825.5177-0.0481-2.1837-0.56971.103-0.00880.1388-0.2607-0.54110.05692.88820.07040.34592.520.61383.0053120.697826.749483.1098
180.08650.0142-0.03450.0183-0.01210.01660.1356-0.41540.3970.11070.09880.225-0.06070.0971-0.23433.79890.0668-0.03313.7044-0.15994.1719100.03426.839294.3324
197.69750.2275-1.29080.9521-0.06721.2575-3.39980.72710.27250.49661.652-0.0430.5313-0.09531.74783.47610.0134-0.04173.170.00573.09759.194377.652180.9911
201.084-3.9131.052518.5718-1.19763.35540.61450.2298-0.0139-0.9978-1.22010.2323-0.0129-0.14990.60563.1918-0.3520.14983.3142-0.16293.228293.416891.352285.1842
219.9069-3.84924.31552.4218-1.51923.5175-3.06110.9604-2.13591.59741.6020.8421-2.32260.9561.45923.9050.0376-0.18834.22450.01374.0869112.790452.554886.4998
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1ELECTRON MICROSCOPY1A1 - 169
2ELECTRON MICROSCOPY2A170 - 305
3ELECTRON MICROSCOPY3A306 - 398
4ELECTRON MICROSCOPY4A411 - 684
5ELECTRON MICROSCOPY5A696 - 791
6ELECTRON MICROSCOPY6A801 - 934
7ELECTRON MICROSCOPY7A949 - 1039
8ELECTRON MICROSCOPY8A1040 - 1154
9ELECTRON MICROSCOPY9A1155 - 1280
10ELECTRON MICROSCOPY10B45 - 187
11ELECTRON MICROSCOPY11B188 - 254
12ELECTRON MICROSCOPY12B255 - 311
13ELECTRON MICROSCOPY13B337 - 465
14ELECTRON MICROSCOPY14B466 - 623
15ELECTRON MICROSCOPY15B624 - 839
16ELECTRON MICROSCOPY16B916 - 1145
17ELECTRON MICROSCOPY17B1150 - 1250
18ELECTRON MICROSCOPY18B1251 - 1376
19ELECTRON MICROSCOPY19X2 - 19
20ELECTRON MICROSCOPY19W30 - 48
21ELECTRON MICROSCOPY20W22 - 28
22ELECTRON MICROSCOPY21Y14 - 28
23ELECTRON MICROSCOPY21Z21 - 36

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