[English] 日本語
Yorodumi
- EMDB-14719: FANCD2 Middle and C-terminal domains with USP1-NTE (focused refin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14719
TitleFANCD2 Middle and C-terminal domains with USP1-NTE (focused refinement)
Map dataLocally refined, globally sharpened map
Sample
  • Complex: FANCD2 mono-ubiquitinated on K561
    • Protein or peptide: Fanconi anemia group D2 protein
KeywordsComplex / Enzyme-Substrate / HYDROLASE
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 / Fanconi Anemia Pathway / response to gamma radiation / TP53 Regulates Transcription of DNA Repair Genes / cellular response to oxidative stress / regulation of inflammatory response / nuclear body / chromatin / nucleolus / nucleoplasm / nucleus / cytosol
Similarity search - Function
Fanconi anaemia protein FANCD2 / Fanconi anaemia protein FancD2 nuclease
Similarity search - Domain/homology
Fanconi anemia group D2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsRennie ML / Walden H
Funding supportEuropean Union, United Kingdom, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2015-CoG-681582European Union
Medical Research Council (MRC, United Kingdom)MC_UU_12016/12 United Kingdom
CitationJournal: Sci Adv / Year: 2022
Title: Cryo-EM reveals a mechanism of USP1 inhibition through a cryptic binding site.
Authors: Martin L Rennie / Connor Arkinson / Viduth K Chaugule / Helen Walden /
Abstract: Repair of DNA damage is critical to genomic integrity and frequently disrupted in cancers. Ubiquitin-specific protease 1 (USP1), a nucleus-localized deubiquitinase, lies at the interface of multiple ...Repair of DNA damage is critical to genomic integrity and frequently disrupted in cancers. Ubiquitin-specific protease 1 (USP1), a nucleus-localized deubiquitinase, lies at the interface of multiple DNA repair pathways and is a promising drug target for certain cancers. Although multiple inhibitors of this enzyme, including one in phase 1 clinical trials, have been established, their binding mode is unknown. Here, we use cryo-electron microscopy to study an assembled enzyme-substrate-inhibitor complex of USP1 and the well-established inhibitor, ML323. Achieving 2.5-Å resolution, with and without ML323, we find an unusual binding mode in which the inhibitor disrupts part of the hydrophobic core of USP1. The consequent conformational changes in the secondary structure lead to subtle rearrangements in the active site that underlie the mechanism of inhibition. These structures provide a platform for structure-based drug design targeting USP1.
History
DepositionApr 5, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14719.png

Downloads & links

-
Map

FileDownload / File: emd_14719.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally refined, globally sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-6.333053 - 9.242692999999999
Average (Standard dev.)-0.000025321668 (±0.1463915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_14719_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: LocSpiral processed map

Fileemd_14719_additional_1.map
AnnotationLocSpiral processed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_14719_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_14719_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FANCD2 mono-ubiquitinated on K561

EntireName: FANCD2 mono-ubiquitinated on K561
Components
  • Complex: FANCD2 mono-ubiquitinated on K561
    • Protein or peptide: Fanconi anemia group D2 protein

-
Supramolecule #1: FANCD2 mono-ubiquitinated on K561

SupramoleculeName: FANCD2 mono-ubiquitinated on K561 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Fanconi anemia group D2 protein

MacromoleculeName: Fanconi anemia group D2 protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: GPGSMVSKRR LSKSEDKESL TEDASKTRKQ PLSKKTKKSH IANEVEENDS IFVKLLKISG IILKTGESQN QLAVDQIAFQ KKLFQTLRRH PSYPKIIEEF VSGLESYIED EDSFRNCLLS CERLQDEEAS MGASYSKSLI KLLLGIDILQ PAIIKTLFEK LPEYFFENKN ...String:
GPGSMVSKRR LSKSEDKESL TEDASKTRKQ PLSKKTKKSH IANEVEENDS IFVKLLKISG IILKTGESQN QLAVDQIAFQ KKLFQTLRRH PSYPKIIEEF VSGLESYIED EDSFRNCLLS CERLQDEEAS MGASYSKSLI KLLLGIDILQ PAIIKTLFEK LPEYFFENKN SDEINIPRLI VSQLKWLDRV VDGKDLTTKI MQLISIAPEN LQHDIITSLP EILGDSQHAD VGKELSDLLI ENTSLTVPIL DVLSSLRLDP NFLLKVRQLV MDKLSSIRLE DLPVIIKFIL HSVTAMDTLE VISELREKLD LQHCVLPSRL QASQVKLKSK GRASSSGNQE SSGQSCIILL FDVIKSAIRY EKTISEAWIK AIENTASVSE HKVFDLVMLF IIYSTNTQTK KYIDRVLRNK IRSGCIQEQL LQSTFSVHYL VLKDMCSSIL SLAQSLLHSL DQSIISFGSL LYKYAFKFFD TYCQQEVVGA LVTHICSGNE AEVDTALDVL LELVVLNPSA MMMNAVFVKG ILDYLDNISP QQIRKLFYVL STLAFSKQNE ASSHIQDDMH LVIRKQLSST VFKYKLIGII GAVTMAGIMA ADRSESPSLT QERANLSDEQ CTQVTSLLQL VHSCSEQSPQ ASALYYDEFA NLIQHEKLDP KALEWVGHTI CNDFQDAFVV DSCVVPEGDF PFPVKALYGL EEYDTQDGIA INLLPLLFSQ DFAKDGGPVT SQESGQKLVS PLCLAPYFRL LRLCVERQHN GNLEEIDGLL DCPIFLTDLE PGEKLESMSA KERSFMCSLI FLTLNWFREI VNAFCQETSP EMKGKVLTRL KHIVELQIIL EKYLAVTPDY VPPLGNFDVE TLDITPHTVT AISAKIRKKG KIERKQKTDG SKTSSSDTLS EEKNSECDPT PSHRGQLNKE FTGKEEKTSL LLHNSHAFFR ELDIEVFSIL HCGLVTKFIL DTEMHTEATE VVQLGPPELL FLLEDLSQKL ESMLTPPIAR RVPFLKNKGS RNIGFSHLQQ RSAQEIVHCV FQLLTPMCNH LENIHNYFQC LAAENHGVVD GPGVKVQEYH IMSSCYQRLL QIFHGLFAWS GFSQPENQNL LYSALHVLSS RLKQGEHSQP LEELLSQSVH YLQNFHQSIP SFQCALYLIR LLMVILEKST ASAQNKEKIA SLARQFLCRV WPSGDKEKSN ISNDQLHALL CIYLEHTESI LKAIEEIAGV GVPELINSPK DASSSTFPTL TRHTFVVFFR VMMAELEKTV KKIEPGTAAD SQQIHEEKLL YWNMAVRDFS ILINLIKVFD SHPVLHVCLK YGRLFVEAFL KQCMPLLDFS FRKHREDVLS LLETFQLDTR LLHHLCGHSK IHQDTRLTQH VPLLKKTLEL LVCRVKAMLT LNNCREAFWL GNLKNRDLQG EEIKSQNSQE STADESEDDM SSQASKSKAT EDGEEDEVSA GEKEQDSDES YDDSD

UniProtKB: Fanconi anemia group D2 protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: UltrAuFoil R1.2/1.3 / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV / Details: blotting for 3.0 seconds.
Details9.3 uM USP1-UAF1, 1.8 uM FANCI-FANCD2Ub, 2.2 uM dsDNA (61 base-pairs), 18 uM ML323

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 6716868
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1154740
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more