[English] 日本語
Yorodumi
- EMDB-51168: MtUvrA2 bound to endogenous E. coli DNA at low resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51168
TitleMtUvrA2 bound to endogenous E. coli DNA at low resolution
Map data
Sample
  • Complex: MtUvrA2-DNA complex
    • Protein or peptide: MtUvrA
    • DNA: Endogenous E. coli DNA
KeywordsDNA repair / NER / UVRA / UVRB / UVR / MTB / DNA BINDING PROTEIN
Biological speciesMycobacterium tuberculosis (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsGenta M / Capelli R / Ferrara G / Rizzi M / Rossi F / Jeruzalmi D / Bolognesi M / Chaves-Sanjuan A / Miggiano R
Funding support Italy, 1 items
OrganizationGrant numberCountry
Ministero dell Universita e della RicercaP2022P8KMF Italy
CitationJournal: Nat Commun / Year: 2025
Title: Mechanistic understanding of UvrA damage detection and lesion hand-off to UvrB in Nucleotide Excision Repair.
Authors: Marianna Genta / Giulia Ferrara / Riccardo Capelli / Diego Rondelli / Sarah Sertic / Martino Bolognesi / Menico Rizzi / Franca Rossi / David Jeruzalmi / Antonio Chaves-Sanjuan / Riccardo Miggiano /
Abstract: Nucleotide excision repair (NER) represents one of the major molecular machineries that control chromosome stability in all living species. In Eubacteria, the initial stages of the repair process are ...Nucleotide excision repair (NER) represents one of the major molecular machineries that control chromosome stability in all living species. In Eubacteria, the initial stages of the repair process are carried out by the UvrABC excinuclease complex. Despite the wealth of structural data available, some crucial details of the pathway remain elusive. In this study, we present a structural investigation of the Mycobacterium tuberculosis UvrAUvrB complex and of the UvrA dimer, both in complex with damaged DNA. Our analyses yield insights into the DNA binding mode of UvrA, showing an unexplored conformation of Insertion Domains (IDs), underlying the essential role of these domains in DNA coordination. Furthermore, we observe an interplay between the ID and the UvrB Binding Domain (UBD): after the recognition of the damage, the IDs repositions with the concomitant reorganization of UBD, allowing the formation of the complex between UvrA and UvrB. These events are detected along the formation of the uncharacterized UvrAUvrB-DNA and the UvrAUvrB-DNA complexes which we interpret as hierarchical steps initiating the DNA repair cascade in the NER pathway, resulting in the formation of the pre-incision complex.
History
DepositionJul 26, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51168.png

Downloads & links

-
Map

FileDownload / File: emd_51168.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 400 pix.
= 355.6 Å		0.89 Å/pix.
x 400 pix.
= 355.6 Å		0.89 Å/pix.
x 400 pix.
= 355.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.46227485 - 1.4004056
Average (Standard dev.)0.00056575664 (±0.043904856)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 355.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51168_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: sharp

Fileemd_51168_additional_1.map
Annotationsharp
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_51168_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51168_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MtUvrA2-DNA complex

EntireName: MtUvrA2-DNA complex
Components
  • Complex: MtUvrA2-DNA complex
    • Protein or peptide: MtUvrA
    • DNA: Endogenous E. coli DNA

-
Supramolecule #1: MtUvrA2-DNA complex

SupramoleculeName: MtUvrA2-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: MtUvrA2 in complex with DNA
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 220 KDa

-
Macromolecule #1: MtUvrA

MacromoleculeName: MtUvrA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH HHSSGHIEGR HMADRLIVKG AREHNLRSVD LDLPRDALIV FTGLSGSGKS SLAFDTIFAE GQRRYVESLS AYARQFLGQM DKPDVDFIEG LSPAVSIDQK STNRNPRSTV GTITEVYDYL RLLYARAGTP HCPTCGERVA RQTPQQIVDQ VLAMPEGTRF ...String:
MGHHHHHHHH HHSSGHIEGR HMADRLIVKG AREHNLRSVD LDLPRDALIV FTGLSGSGKS SLAFDTIFAE GQRRYVESLS AYARQFLGQM DKPDVDFIEG LSPAVSIDQK STNRNPRSTV GTITEVYDYL RLLYARAGTP HCPTCGERVA RQTPQQIVDQ VLAMPEGTRF LVLAPVVRTR KGEFADLFDK LNAQGYSRVR VDGVVHPLTD PPKLKKQEKH DIEVVVDRLT VKAAAKRRLT DSVETALNLA DGIVVLEFVD HELGAPHREQ RFSEKLACPN GHALAVDDLE PRSFSFNSPY GACPECSGLG IRKEVDPELV VPDPDRTLAQ GAVAPWSNGH TAEYFTRMMA GLGEALGFDV DTPWRKLPAK ARKAILEGAD EQVHVRYRNR YGRTRSYYAD FEGVLAFLQR KMSQTESEQM KERYEGFMRD VPCPVCAGTR LKPEILAVTL AGESKGEHGA KSIAEVCELS IADCADFLNA LTLGPREQAI AGQVLKEIRS RLGFLLDVGL EYLSLSRAAA TLSGGEAQRI RLATQIGSGL VGVLYVLDEP SIGLHQRDNR RLIETLTRLR DLGNTLIVVE HDEDTIEHAD WIVDIGPGAG EHGGRIVHSG PYDELLRNKD SITGAYLSGR ESIEIPAIRR SVDPRRQLTV VGAREHNLRG IDVSFPLGVL TSVTGVSGSG KSTLVNDILA AVLANRLNGA RQVPGRHTRV TGLDYLDKLV RVDQSPIGRT PRSNPATYTG VFDKIRTLFA ATTEAKVRGY QPGRFSFNVK GGRCEACTGD GTIKIEMNFL PDVYVPCEVC QGARYNRETL EVHYKGKTVS EVLDMSIEEA AEFFEPIAGV HRYLRTLVDV GLGYVRLGQP APTLSGGEAQ RVKLASELQK RSTGRTVYIL DEPTTGLHFD DIRKLLNVIN GLVDKGNTVI VIEHNLDVIK TSDWIIDLGP EGGAGGGTVV AQGTPEDVAA VPASYTGKFL AEVVGGGASA ATSRSNRRRN VSA

-
Macromolecule #2: Endogenous E. coli DNA

MacromoleculeName: Endogenous E. coli DNA / type: dna / ID: 2 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString:
CACATGAAAA AAAAAATGAA AATGATTTCT GA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
300.0 mMNaClNaCl
20.0 mMTris HCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 30mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3642 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 240304
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 22766
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

+
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