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- EMDB-51171: MtUvrA2UvrB2 bound to damaged oligonucleotide (half 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-51171
TitleMtUvrA2UvrB2 bound to damaged oligonucleotide (half 1)
Map data
Sample
  • Complex: MtUvrA2UvrB2-DNA complex
    • Protein or peptide: MtUvrA
    • Protein or peptide: MtUvrA
    • Protein or peptide: MtUvrB
    • Protein or peptide: MtUvrB
    • 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: 3.6 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-DNA half 1 reconstruction
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

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Structure visualization

Supplemental images

emd_51171.png

Downloads & links

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Map

FileDownload / File: emd_51171.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.)
0.84 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: 0.2
Minimum - Maximum-0.43749622 - 0.9279842
Average (Standard dev.)0.0015863726 (±0.024539622)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Mask #1

Fileemd_51171_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharp

Fileemd_51171_additional_1.map
Annotationsharp
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51171_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51171_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MtUvrA2UvrB2-DNA complex

EntireName: MtUvrA2UvrB2-DNA complex
Components
  • Complex: MtUvrA2UvrB2-DNA complex
    • Protein or peptide: MtUvrA
    • Protein or peptide: MtUvrA
    • Protein or peptide: MtUvrB
    • Protein or peptide: MtUvrB
    • DNA: DNA
    • DNA: DNA

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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

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Macromolecule #1: MtUvrA

MacromoleculeName: MtUvrA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
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

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Macromolecule #2: MtUvrA

MacromoleculeName: MtUvrA / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
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

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Macromolecule #3: MtUvrB

MacromoleculeName: MtUvrB / type: protein_or_peptide / ID: 3 / 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

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Macromolecule #4: MtUvrB

MacromoleculeName: MtUvrB / type: protein_or_peptide / ID: 4 / 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

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Macromolecule #5: DNA

MacromoleculeName: DNA / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString:
TAGTCACATC AGTGATCAGT GGTtCCGGAA CCACTGATCA CT

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Macromolecule #6: DNA

MacromoleculeName: DNA / type: dna / ID: 6 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString:
TAGTCACATC AGTGATCAGT GGTtCCGGAA CCACTGATCA CT

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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

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
300.0 mMNaClNaCl
20.0 mMTris HCl
GridModel: Quantifoil R1.2/1.3 / 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

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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

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Image processing

Particle selectionNumber selected: 666671
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 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

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