+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25127 | ||||||||||||
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Title | Structure of Xenopus laevis CRL2Lrr1 (State 1) | ||||||||||||
Map data | It's a composite map made with State1-map1, State1-map2 and State1-map3. | ||||||||||||
Sample |
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Keywords | Cullin RING E3 ubiquitin ligase / DNA replication termination / LIGASE | ||||||||||||
Function / homology | Function and homology information cullin-RING ubiquitin ligase complex / elongin complex / VCB complex / transcription elongation by RNA polymerase II / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Zhou H / Brown A | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nucleic Acids Res / Year: 2021 Title: Structure of CRL2Lrr1, the E3 ubiquitin ligase that promotes DNA replication termination in vertebrates. Authors: Haixia Zhou / Manal S Zaher / Johannes C Walter / Alan Brown / Abstract: When vertebrate replisomes from neighboring origins converge, the Mcm7 subunit of the replicative helicase, CMG, is ubiquitylated by the E3 ubiquitin ligase, CRL2Lrr1. Polyubiquitylated CMG is then ...When vertebrate replisomes from neighboring origins converge, the Mcm7 subunit of the replicative helicase, CMG, is ubiquitylated by the E3 ubiquitin ligase, CRL2Lrr1. Polyubiquitylated CMG is then disassembled by the p97 ATPase, leading to replication termination. To avoid premature replisome disassembly, CRL2Lrr1 is only recruited to CMGs after they converge, but the underlying mechanism is unclear. Here, we use cryogenic electron microscopy to determine structures of recombinant Xenopus laevis CRL2Lrr1 with and without neddylation. The structures reveal that CRL2Lrr1 adopts an unusually open architecture, in which the putative substrate-recognition subunit, Lrr1, is located far from the catalytic module that catalyzes ubiquitin transfer. We further demonstrate that a predicted, flexible pleckstrin homology domain at the N-terminus of Lrr1 is essential to target CRL2Lrr1 to terminated CMGs. We propose a hypothetical model that explains how CRL2Lrr1's catalytic module is positioned next to the ubiquitylation site on Mcm7, and why CRL2Lrr1 binds CMG only after replisomes converge. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25127.map.gz | 113.1 MB | EMDB map data format | |
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Header (meta data) | emd-25127-v30.xml emd-25127.xml | 23.8 KB 23.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25127_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_25127.png | 75.7 KB | ||
Masks | emd_25127_msk_1.map emd_25127_msk_2.map emd_25127_msk_3.map | 125 MB 125 MB 125 MB | Mask map | |
Filedesc metadata | emd-25127.cif.gz | 7 KB | ||
Others | emd_25127_additional_1.map.gz emd_25127_additional_2.map.gz emd_25127_additional_3.map.gz | 4.4 MB 113.9 MB 3.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25127 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25127 | HTTPS FTP |
-Validation report
Summary document | emd_25127_validation.pdf.gz | 537.4 KB | Display | EMDB validaton report |
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Full document | emd_25127_full_validation.pdf.gz | 536.9 KB | Display | |
Data in XML | emd_25127_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_25127_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25127 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25127 | HTTPS FTP |
-Related structure data
Related structure data | 7shkMC 7shlC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25127.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | It's a composite map made with State1-map1, State1-map2 and State1-map3. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_25127_msk_1.map | ||||||||||||
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-Mask #2
File | emd_25127_msk_2.map | ||||||||||||
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-Mask #3
File | emd_25127_msk_3.map | ||||||||||||
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-Additional map: #3
File | emd_25127_additional_1.map | ||||||||||||
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-Additional map: #2
File | emd_25127_additional_2.map | ||||||||||||
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-Additional map: #1
File | emd_25127_additional_3.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CRL2Lrr1
Entire | Name: CRL2Lrr1 |
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Components |
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-Supramolecule #1: CRL2Lrr1
Supramolecule | Name: CRL2Lrr1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
-Macromolecule #1: CULLIN_2 domain-containing protein
Macromolecule | Name: CULLIN_2 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 87.244117 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSLKPRVVDF DETWNKLLTT IKAVVMLDYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHVQ QLHTRVLDSA EQVLVMYFR YWEEYSRGAD YMDCLYRYLN TQYIKKNKLT EADLQYGYGG VDMNEPLMEI GELALDLWRK LMIEPLQDTL L IMLLREIK ...String: MSLKPRVVDF DETWNKLLTT IKAVVMLDYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHVQ QLHTRVLDSA EQVLVMYFR YWEEYSRGAD YMDCLYRYLN TQYIKKNKLT EADLQYGYGG VDMNEPLMEI GELALDLWRK LMIEPLQDTL L IMLLREIK RDRCGEDPNQ KVIHGVINSF VHVEQYKKKF PLKFYQEIFE SPFLAETGEY YKQEASNLLQ ESNCSQYMEK IL GRLKDEE IRCRKYLHPS SYNKVIHECQ QRMVADHLQF LHAECHNIIR QERRNDMANM YTLLRAVSSG LPHMIQELQN HIH DEGLRA ISNLSQENMP TQFVESVLEV HSKFVQLVNC VLNGDQHFMS ALDKALTCVV NYREPKSVCK APELLAKYCD NMLK KSAKG MTENEVEDKL TSFITVFKYI DDKDVFQKFY ARMLAKRLIH GLSMSMDSEE TMINKLKQAC GYEFTSKLHR MYTDM SVSA DLNNKFNNFI KSQDTVIDLG ISFQIYVLQA GAWPLTQAPS STFAIPQELE KSVQMFELFY NQHFSGRKLT WLHYLC TGE VKMNYLCKPY VAMVTTYQMA VLLAFNNSEI ITYKELQDST QMNEKELTKT IKSLLDVKMI NHDSDKEDIE GESTFSL NM NFSSKRTKFK ITTPMQKDTP QEVEQTRSAV DEDRKMYLQA AIVRIMKARK VLRHNALIQE VISQSRARFN PSISMIKK C IEVLIDKQYI ERSQASADEY SYVA UniProtKB: CULLIN_2 domain-containing protein |
-Macromolecule #2: Tceb2-prov protein
Macromolecule | Name: Tceb2-prov protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 13.325927 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MDVFLMIRHH KTTIFTDAKE NTTVYELKRI VEGILKRPPE DQKLYKDDQL LDDNKTLGDC GFTSQTARPQ APATVGLAFR SSGDSFEPL RVEPFSSPPE LPDVMKPQET SGSANEQAVQ UniProtKB: Elongin B L homeolog |
-Macromolecule #3: Elongin-C
Macromolecule | Name: Elongin-C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 12.485135 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MDGEEKTYGG CEGPDAMYVK LISSDGHEFI VKREHALTSG TIKAMLSGPG QFAENETNEV NFREIPSHVL SKVCMYFTYK VRYTNSSTE IPEFPIAPEI ALELLMAANF LDC UniProtKB: Elongin-C |
-Macromolecule #4: Lrr1
Macromolecule | Name: Lrr1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 46.882258 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MKLQCEVEVI NRMLPTFGLK NRGKGTRAVL SVGRQEGKRG AAYLMICTLK DKSGSRYKLE NNIEQLFTRF VGEGKATLRL KEPALDICL SKAEICGLRN FISTVGLANK GTDIGTVSLP RLTPAKTSEI EKPRSKLFIT TKKDYPITKS FPYSLEHLQV S YCKLARVD ...String: MKLQCEVEVI NRMLPTFGLK NRGKGTRAVL SVGRQEGKRG AAYLMICTLK DKSGSRYKLE NNIEQLFTRF VGEGKATLRL KEPALDICL SKAEICGLRN FISTVGLANK GTDIGTVSLP RLTPAKTSEI EKPRSKLFIT TKKDYPITKS FPYSLEHLQV S YCKLARVD MRMLCLKKLQ KLDLSNNHIK KLPKTIGDLV CLQELILNHN FLESFEVVLC STTLRDTLKS LDLSANKLKA LP VQICNFK ELVSLKLDEN ELLQLPFPIG QLSKLRFLSA TKNNLQCLPN TFKKLTLENL DLFGNPFMQA TPLVPDIQLK IPL PLLETA ARATLKYRIP YGPHLIPATL CQDLSLAKTC DCGLPCLNSF IQTIVLMNLH QVSQTVVLVD TMGGTDGPIV CYFC SLTCY SQFLDKYLQS TRV UniProtKB: Leucine rich repeat protein 1 L homeolog isoform X1 |
-Macromolecule #5: RING-type domain-containing protein
Macromolecule | Name: RING-type domain-containing protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 12.277985 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAAAMDVDTP SGANNSAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYVG UniProtKB: RING-type domain-containing protein |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: TCEP is freshly added. | ||||||||||||
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa | ||||||||||||
Vitrification | Cryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 281.2 K / Instrument: FEI VITROBOT MARK IV / Details: Blot 6 seconds with the force 12. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Target criteria: Correlation coefficient |
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Output model | PDB-7shk: |