[English] 日本語
Yorodumi
- EMDB-51172: MtUvrA2UvrB2 bound to damaged oligonucleotide (half 2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51172
TitleMtUvrA2UvrB2 bound to damaged oligonucleotide (half 2)
Map dataunsharped map
Sample
  • Complex: MtUvrA2UvrB2-DNA complex
    • Protein or peptide: UvrA
    • Protein or peptide: UvrB
    • DNA: DNA
    • DNA: 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: 3.7 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: To Be Published
Title: MtUvrA2UvrB2 bound to damaged oligonucleotide (half 2)
Authors: Genta M / Capelli R / Ferrara G / Rizzi M / Rossi F / Jeruzalmi D / Bolognesi M / Chaves-Sanjuan A / Miggiano R
History
DepositionJul 26, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51172.png

Downloads & links

-
Map

FileDownload / File: emd_51172.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharped map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.42836088 - 0.8356461
Average (Standard dev.)0.0013320628 (±0.022878649)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51172_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: sharped map

Fileemd_51172_additional_1.map
Annotationsharped map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_51172_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51172_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MtUvrA2UvrB2-DNA complex

EntireName: MtUvrA2UvrB2-DNA complex
Components
  • Complex: MtUvrA2UvrB2-DNA complex
    • Protein or peptide: UvrA
    • Protein or peptide: UvrB
    • DNA: DNA
    • DNA: DNA

-
Supramolecule #1: MtUvrA2UvrB2-DNA complex

SupramoleculeName: MtUvrA2UvrB2-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Heterotetrameric MtUvrA2UvrB2 in complex with DNA
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 400 KDa

-
Macromolecule #1: UvrA

MacromoleculeName: UvrA / 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: UvrB

MacromoleculeName: UvrB / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
SequenceString: MGHHHHHHHH HHSSGHIEGR HMVRAGGHFE VVSPHAPAGD QPAAIDELER RINAGERDVV LLGATGTGKS ATTAWLIERL QRPTLVMAPN KTLAAQLANE LREMLPHNAV EYFVSYYDYY QPEAYIAQTD TYIEKDSSIN DDVERLRHSA TSALLSRRDV VVVASVSCIY ...String:
MGHHHHHHHH HHSSGHIEGR HMVRAGGHFE VVSPHAPAGD QPAAIDELER RINAGERDVV LLGATGTGKS ATTAWLIERL QRPTLVMAPN KTLAAQLANE LREMLPHNAV EYFVSYYDYY QPEAYIAQTD TYIEKDSSIN DDVERLRHSA TSALLSRRDV VVVASVSCIY GLGTPQSYLD RSVELKVGEE VPRDGLLRLL VDVQYTRNDM SFTRGSFRVR GDTVEIIPSY EELAVRIEFF GDEIEALYYL HPLTGEVIRQ VDSLRIFPAT HYVAGPERMA HAVSAIEEEL AERLAELESQ GKLLEAQRLR MRTNYDIEMM RQVGFCSGIE NYSRHIDGRG PGTPPATLLD YFPEDFLLVI DESHVTVPQI GGMYEGDISR KRNLVEYGFR LPSACDNRPL TWEEFADRIG QTVYLSATPG PYELSQTGGE FVEQVIRPTG LVDPKVVVKP TKGQIDDLIG EIRTRADADQ RVLVTTLTKK MAEDLTDYLL EMGIRVRYLH SEVDTLRRVE LLRQLRLGDY DVLVGINLLR EGLDLPEVSL VAILDADKEG FLRSSRSLIQ TIGRAARNVS GEVHMYADKI TDSMREAIDE TERRRAKQIA YNEANGIDPQ PLRKKIADIL DQVYREADDT AVVEVGGSGR NASRGRRAQG EPGRAVSAGV FEGRDTSAMP RAELADLIKD LTAQMMAAAR DLQFELAARF RDEIADLKRE LRGMDAAGLK

-
Macromolecule #3: DNA

MacromoleculeName: DNA / type: dna / ID: 3 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString:
TAGTCACATC AGTGATCAGT GGTtCCGGAA CCACTGATCA CT

-
Macromolecule #4: DNA

MacromoleculeName: DNA / type: dna / ID: 4 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString:
TAGTCACATC AGTGATCAGT GGTtCCGGAA CCACTGATCA CT

-
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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 21232 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 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: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 666671
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 110916
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