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- EMDB-14694: Structure of ubiquitinated FANCI in complex with FANCD2 and doubl... -

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Entry
Database: EMDB / ID: EMD-14694
TitleStructure of ubiquitinated FANCI in complex with FANCD2 and double-stranded DNA
Map data
Sample
  • Complex: Complex of ubiquitinated FANCI with FANCD2 and double-stranded DNA.
    • Protein or peptide: Fanconi anemia group I protein
    • Protein or peptide: Fanconi anemia group D2 protein
    • Protein or peptide: Ubiquitin-60S ribosomal protein L40
    • DNA: DNA (61-MER)
    • DNA: DNA (61-MER)
KeywordsFanconi anemia / DNA repair / ubiquitination / ID2 complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


regulation of CD40 signaling pathway / regulation of regulatory T cell differentiation / double-strand break repair involved in meiotic recombination / gamete generation / homologous chromosome pairing at meiosis / neuronal stem cell population maintenance / brain morphogenesis / mitotic intra-S DNA damage checkpoint signaling / DNA repair complex / Peptide chain elongation ...regulation of CD40 signaling pathway / regulation of regulatory T cell differentiation / double-strand break repair involved in meiotic recombination / gamete generation / homologous chromosome pairing at meiosis / neuronal stem cell population maintenance / brain morphogenesis / mitotic intra-S DNA damage checkpoint signaling / DNA repair complex / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / interstrand cross-link repair / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / DNA polymerase binding / condensed chromosome / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / cytosolic ribosome / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / positive regulation of protein ubiquitination / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / response to gamma radiation / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex
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 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eL40 fusion protein / Fanconi anemia group D2 protein / Fanconi anemia group I protein
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.14 Å
AuthorsLemonidis K / Rennie ML / Arkinson C / Streetley J / Clarke M / Chaugule VK / Walden H
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC- 2015-CoG-681582 ICLUbEuropean Union
CitationJournal: EMBO J / Year: 2023
Title: Structural and biochemical basis of interdependent FANCI-FANCD2 ubiquitination.
Authors: Kimon Lemonidis / Martin L Rennie / Connor Arkinson / Viduth K Chaugule / Mairi Clarke / James Streetley / Helen Walden /
Abstract: Di-monoubiquitination of the FANCI-FANCD2 (ID2) complex is a central and crucial step for the repair of DNA interstrand crosslinks via the Fanconi anaemia pathway. While FANCD2 ubiquitination ...Di-monoubiquitination of the FANCI-FANCD2 (ID2) complex is a central and crucial step for the repair of DNA interstrand crosslinks via the Fanconi anaemia pathway. While FANCD2 ubiquitination precedes FANCI ubiquitination, FANCD2 is also deubiquitinated at a faster rate than FANCI, which can result in a FANCI-ubiquitinated ID2 complex (I D2). Here, we present a 4.1 Å cryo-EM structure of I D2 complex bound to double-stranded DNA. We show that this complex, like ID2 and I D2 , is also in the closed ID2 conformation and clamps on DNA. The target lysine of FANCD2 (K561) becomes fully exposed in the I D2-DNA structure and is thus primed for ubiquitination. Similarly, FANCI's target lysine (K523) is also primed for ubiquitination in the ID2 -DNA complex. The I D2-DNA complex exhibits deubiquitination resistance, conferred by the presence of DNA and FANCD2. ID2 -DNA, on the other hand, can be efficiently deubiquitinated by USP1-UAF1, unless further ubiquitination on FANCI occurs. Therefore, FANCI ubiquitination effectively maintains FANCD2 ubiquitination in two ways: it prevents excessive FANCD2 deubiquitination within an I D2 -DNA complex, and it enables re-ubiquitination of FANCD2 within a transient, closed-on-DNA, I D2 complex.
History
DepositionMar 31, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14694.png

Downloads & links

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Map

FileDownload / File: emd_14694.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 320 pix.
= 327.36 Å		1.02 Å/pix.
x 320 pix.
= 327.36 Å		1.02 Å/pix.
x 320 pix.
= 327.36 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.023 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.9912983 - 1.4648827
Average (Standard dev.)0.0022898978 (±0.03240899)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 327.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_14694_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_14694_half_map_1.map
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Half map: #1

Fileemd_14694_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex of ubiquitinated FANCI with FANCD2 and double-stranded DNA.

EntireName: Complex of ubiquitinated FANCI with FANCD2 and double-stranded DNA.
Components
  • Complex: Complex of ubiquitinated FANCI with FANCD2 and double-stranded DNA.
    • Protein or peptide: Fanconi anemia group I protein
    • Protein or peptide: Fanconi anemia group D2 protein
    • Protein or peptide: Ubiquitin-60S ribosomal protein L40
    • DNA: DNA (61-MER)
    • DNA: DNA (61-MER)

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Supramolecule #1: Complex of ubiquitinated FANCI with FANCD2 and double-stranded DNA.

SupramoleculeName: Complex of ubiquitinated FANCI with FANCD2 and double-stranded DNA.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fanconi anemia group I protein

MacromoleculeName: Fanconi anemia group I protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 152.658594 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHENL YFQGKPIPNP LLGLDSTMDQ KILSLAAEKT ADKLQEFLQT LREGDLTNLL QNQAVKGKVA GALLRAIFKG SPCSEEAGT LRRRKIYTCC IQLVESGDLQ KEIASEIIGL LMLEAHHFPG PLLVELANEF ISAVREGSLV NGKSLELLPI I LTALATKK ...String:
MHHHHHHENL YFQGKPIPNP LLGLDSTMDQ KILSLAAEKT ADKLQEFLQT LREGDLTNLL QNQAVKGKVA GALLRAIFKG SPCSEEAGT LRRRKIYTCC IQLVESGDLQ KEIASEIIGL LMLEAHHFPG PLLVELANEF ISAVREGSLV NGKSLELLPI I LTALATKK ENLAYGKGVL SGEECKKQLI NTLCSGRWDQ QYVIQLTSMF KDVPLTAEEV EFVVEKALSM FSKMNLQEIP PL VYQLLVL SSKGSRKSVL EGIIAFFSAL DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHL KVGQQG DSNNNLSPFS IALLLSVTRI QRFQDQVLDL LKTSVVKSFK DLQLLQGSKF LQNLVPHRSY VSTMILEVVK NSVH SWDHV TQGLVELGFI LMDSYGPKKV LDGKTIETSP SLSRMPNQHA CKLGANILLE TFKIHEMIRQ EILEQVLNRV VTRAS SPIS HFLDLLSNIV MYAPLVLQSC SSKVTEAFDY LSFLPLQTVQ RLLKAVQPLL KVSMSMRDCL ILVLRKAMFA NQLDAR KSA VAGFLLLLKN FKVLGSLSSS QCSQSLSVSQ VHVDVHSHYN SVANETFCLE IMDSLRRCLS QQADVRLMLY EGFYDVL RR NSQLANSVMQ TLLSQLKQFY EPKPDLLPPL KLEACILTQG DKISLQEPLD YLLCCIQHCL AWYKNTVIPL QQGEEEEE E EEAFYEDLDD ILESITNRMI KSELEDFELD KSADFSQSTS IGIKNNICAF LVMGVCEVLI EYNFSISSFS KNRFEDILS LFMCYKKLSD ILNEKAGKAK TKMANKTSDS LLSMKFVSSL LTALFRDSIQ SHQESLSVLR SSNEFMRYAV NVALQKVQQL KETGHVSGP DGQNPEKIFQ NLCDITRVLL WRYTSIPTSV EESGKKEKGK SISLLCLEGL QKIFSAVQQF YQPKIQQFLR A LDVTDKEG EEREDADVSV TQRTAFQIRQ FQRSLLNLLS SQEEDFNSKE ALLLVTVLTS LSKLLEPSSP QFVQMLSWTS KI CKENSRE DALFCKSLMN LLFSLHVSYK SPVILLRDLS QDIHGHLGDI DQDVEVEKTN HFAIVNLRTA APTVCLLVLS QAE KVLEEV DWLITKLKGQ VSQETLSEEA SSQATLPNQP VEKAIIMQLG TLLTFFHELV QTALPSGSCV DTLLKDLCKM YTTL TALVR YYLQVCQSSG GIPKNMEKLV KLSGSHLTPL CYSFISYVQN KSKSLNYTGE KKEKPAAVAT AMARVLRETK PIPNL IFAI EQYEKFLIHL SKKSKVNLMQ HMKLSTSRDF KIKGNILDMV LREDGEDENE EGTASEHGGQ NKEPAKKKRK K

UniProtKB: Fanconi anemia group I protein

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Macromolecule #2: Fanconi anemia group D2 protein

MacromoleculeName: Fanconi anemia group D2 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 166.313719 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHLEV LFQGPGSMVS KRRLSKSEDK ESLTEDASKT RKQPLSKKTK KSHIANEVEE NDSIFVKLLK ISGIILKTGE SQNQLAVDQ IAFQKKLFQT LRRHPSYPKI IEEFVSGLES YIEDEDSFRN CLLSCERLQD EEASMGASYS KSLIKLLLGI D ILQPAIIK ...String:
MHHHHHHLEV LFQGPGSMVS KRRLSKSEDK ESLTEDASKT RKQPLSKKTK KSHIANEVEE NDSIFVKLLK ISGIILKTGE SQNQLAVDQ IAFQKKLFQT LRRHPSYPKI IEEFVSGLES YIEDEDSFRN CLLSCERLQD EEASMGASYS KSLIKLLLGI D ILQPAIIK TLFEKLPEYF FENKNSDEIN IPRLIVSQLK WLDRVVDGKD LTTKIMQLIS IAPENLQHDI ITSLPEILGD SQ HADVGKE LSDLLIENTS LTVPILDVLS SLRLDPNFLL KVRQLVMDKL SSIRLEDLPV IIKFILHSVT AMDTLEVISE LRE KLDLQH CVLPSRLQAS QVKLKSKGRA SSSGNQESSG QSCIILLFDV IKSAIRYEKT ISEAWIKAIE NTASVSEHKV FDLV MLFII YSTNTQTKKY IDRVLRNKIR SGCIQEQLLQ STFSVHYLVL KDMCSSILSL AQSLLHSLDQ SIISFGSLLY KYAFK FFDT YCQQEVVGAL VTHICSGNEA EVDTALDVLL ELVVLNPSAM MMNAVFVKGI LDYLDNISPQ QIRKLFYVLS TLAFSK QNE ASSHIQDDMH LVIRKQLSST VFKYKLIGII GAVTMAGIMA ADRSESPSLT QERANLSDEQ CTQVTSLLQL VHSCSEQ SP QASALYYDEF ANLIQHEKLD PKALEWVGHT ICNDFQDAFV VDSCVVPEGD FPFPVKALYG LEEYDTQDGI AINLLPLL F SQDFAKDGGP VTSQESGQKL VSPLCLAPYF RLLRLCVERQ HNGNLEEIDG LLDCPIFLTD LEPGEKLESM SAKERSFMC SLIFLTLNWF REIVNAFCQE TSPEMKGKVL TRLKHIVELQ IILEKYLAVT PDYVPPLGNF DVETLDITPH TVTAISAKIR KKGKIERKQ KTDGSKTSSS DTLSEEKNSE CDPTPSHRGQ LNKEFTGKEE KTSLLLHNSH AFFRELDIEV FSILHCGLVT K FILDTEMH TEATEVVQLG PPELLFLLED LSQKLESMLT PPIARRVPFL KNKGSRNIGF SHLQQRSAQE IVHCVFQLLT PM CNHLENI HNYFQCLAAE NHGVVDGPGV KVQEYHIMSS CYQRLLQIFH GLFAWSGFSQ PENQNLLYSA LHVLSSRLKQ GEH SQPLEE LLSQSVHYLQ NFHQSIPSFQ CALYLIRLLM VILEKSTASA QNKEKIASLA RQFLCRVWPS GDKEKSNISN DQLH ALLCI YLEHTESILK AIEEIAGVGV PELINSPKDA SSSTFPTLTR HTFVVFFRVM MAELEKTVKK IEPGTAADSQ QIHEE KLLY WNMAVRDFSI LINLIKVFDS HPVLHVCLKY GRLFVEAFLK QCMPLLDFSF RKHREDVLSL LETFQLDTRL LHHLCG HSK IHQDTRLTQH VPLLKKTLEL LVCRVKAMLT LNNCREAFWL GNLKNRDLQG EEIKSQNSQE STADESEDDM SSQASKS KA TEDGEEDEVS AGEKEQDSDE SYDDSD

UniProtKB: Fanconi anemia group D2 protein

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Macromolecule #3: Ubiquitin-60S ribosomal protein L40

MacromoleculeName: Ubiquitin-60S ribosomal protein L40 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.875125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGSMQIFVK TLTGKTITLE VEPSDTIENV KAKIQDKEGI PPDQQRLIFA GKQLEDGRTL SDYNIQKEST LHLVLRLRGG

UniProtKB: Ubiquitin-ribosomal protein eL40 fusion protein

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Macromolecule #4: DNA (61-MER)

MacromoleculeName: DNA (61-MER) / type: dna / ID: 4
Details: 61-MER DNA modelled using chain S of PDB entry 6VAE as initial model for refinement. Complementary to chain S.
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.951746 KDa
SequenceString:
(DG)(DG)(DC)(DA)(DC)(DA)(DG)(DG)(DT)(DT) (DC)(DA)(DG)(DA)(DG)(DC)(DA)(DG)(DG)(DC) (DG)(DT)(DT)(DC)(DC)(DG)(DT)(DT)(DC)

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Macromolecule #5: DNA (61-MER)

MacromoleculeName: DNA (61-MER) / type: dna / ID: 5
Details: 61-MER DNA modelled using chain T of PDB entry 6VAE as initial model for refinement. Complementary to chain S.
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.880711 KDa
SequenceString:
(DG)(DA)(DA)(DC)(DG)(DG)(DA)(DA)(DC)(DG) (DC)(DC)(DT)(DG)(DC)(DT)(DC)(DT)(DG)(DA) (DA)(DC)(DC)(DT)(DG)(DT)(DG)(DC)(DC)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: COUNTING / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 0.5 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139601
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6vae

chain_id: A, source_name: PDB, initial_model_type: experimental model

6vae

chain_id: B, source_name: PDB, initial_model_type: experimental model

6vae

chain_id: C, source_name: PDB, initial_model_type: experimental model

6vae

chain_id: S, source_name: PDB, initial_model_type: experimental model

6vae

chain_id: T, source_name: PDB, initial_model_type: experimental model
Output model

PDB-7zf1:
Structure of ubiquitinated FANCI in complex with FANCD2 and double-stranded DNA

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