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- EMDB-51691: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein ... -

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Basic information

Entry
Database: EMDB / ID: EMD-51691
TitleC. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP (composite map)
Map datacomposite map created by combining consensus map with two copies of focused UvrB map
Sample
  • Complex: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP
    • Protein or peptide: UvrABC system protein A
    • DNA: DNA (50-MER) with a fluorescein modification - (random sequence built in model)
    • Protein or peptide: UvrABC system protein B
  • Ligand: ZINC ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsDNA binding protein / DNA Repair pathway / Nucleotide excision repair pathway / NER
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / UVR domain superfamily / UvrA, interaction domain / UvrB/uvrC motif / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain ...UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / UVR domain superfamily / UvrA, interaction domain / UvrB/uvrC motif / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / UvrB, interaction domain / UvrB interaction domain / UVR domain / UVR domain profile. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / ATP-grasp fold, subdomain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / Helicase conserved C-terminal domain / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
UvrABC system protein B / UvrABC system protein A
Similarity search - Component
Biological speciesAcetivibrio thermocellus (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsNirwal S / Czarnocki-Cieciura M / Nowotny M
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/A/NZ1/01098 Poland
CitationJournal: Nat Commun / Year: 2025
Title: Structural snapshots of the mechanism of ATP-dependent DNA damage recognition by UvrA.
Authors: Shivlee Nirwal / Mariusz Czarnocki-Cieciura / Weronika Zajko / Krzysztof Skowronek / Roman H Szczepanowski / Marcin Nowotny /
Abstract: Nucleotide excision repair is a DNA repair pathway which detects and fixes various DNA lesions that distort the structure of DNA. In bacteria, the pathway starts with the UvrA protein which has two ...Nucleotide excision repair is a DNA repair pathway which detects and fixes various DNA lesions that distort the structure of DNA. In bacteria, the pathway starts with the UvrA protein which has two adenosine triphosphatase modules and forms dimers. The DNA is handed over from UvrA to UvrB, which is a weak helicase that verifies the presence of damage. Despite intense studies, the role of the ATPase activity of UvrA in damage recognition is unclear. Here, we present a series of cryo-electron microscopy structures of UvrA in complex with three different DNAs and in the presence and absence of nucleotides. We also present a structure of UvrA:UvrB:DNA complex. These structures reveal a major rearrangement of the UvrA dimer upon ATP binding. We propose that these conformational changes are used to mechanically probe the integrity of DNA for damage localization. Collectively, our results present snapshots of UvrA's ATP-dependent DNA damage detection.
History
DepositionOct 1, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51691.png

Downloads & links

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Map

FileDownload / File: emd_51691.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map created by combining consensus map with two copies of focused UvrB map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 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: 0.35
Minimum - Maximum0.0 - 3.2519114
Average (Standard dev.)0.0029505368 (±0.03691102)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein ...

EntireName: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP
Components
  • Complex: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP
    • Protein or peptide: UvrABC system protein A
    • DNA: DNA (50-MER) with a fluorescein modification - (random sequence built in model)
    • Protein or peptide: UvrABC system protein B
  • Ligand: ZINC ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein ...

SupramoleculeName: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Acetivibrio thermocellus (bacteria)
Molecular weightTheoretical: 398 KDa

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Macromolecule #1: UvrABC system protein A

MacromoleculeName: UvrABC system protein A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetivibrio thermocellus (bacteria)
Molecular weightTheoretical: 107.144773 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MKKDYIVVKG AREHNLKNID VKIPRDKFVV ITGLSGSGKS SLAFDTIYAE GQRRYVESLS SYARQFLGQ MEKPDVDYID GLSPAIAIDQ KTTSRNPRST VGTVTEIYDY LRLLFARIGT PHCYLCGREI SQQTVDQMVD R IMEFEEGT ...String:
MGSSHHHHHH SSGLVPRGSH MKKDYIVVKG AREHNLKNID VKIPRDKFVV ITGLSGSGKS SLAFDTIYAE GQRRYVESLS SYARQFLGQ MEKPDVDYID GLSPAIAIDQ KTTSRNPRST VGTVTEIYDY LRLLFARIGT PHCYLCGREI SQQTVDQMVD R IMEFEEGT RIQLLAPVVR GRKGEYHKLI EDIKKEGYVR IRVDGEVVDV NDPVNLDKNK KHNIEIVVDR LIVRPGIQKR LT DSIETVL RLSNGILVVD VIGGKEMLLS QNFACTECNV SMEEITPRMF SFNNPYGACP ECTGLGSLMR IDPDLVIPDK KLS LAQGAV RASGWNIAND ESYARMYIDA LAKHYNFSVD TPVEELPPHI LDIILYGTNG EKIKIEYERE NEKGTFMASF PGII NSMER RYKETTSEVM KQYYENFMSN IPCPVCKGAR LKKESLAVTI GGKNIYEVCC LSIGEAKEFF ANLNLTERQQ LIARQ ILKE INARLGFLVD VGLDYLTLAR AAGTLSGGEA QRIRLATQIG SGLMGVIYIL DEPSIGLHQR DNDRLLRSLK KLRDLG NTL LVVEHDEDTM YASDYIIDLG PGAGSHGGQI VAEGTVEEIK QNPNSVTGEY LSGRKKIEVP KERRKPNGKW LEIIGAR EN NLKNINVRIP LGVFTCITGV SGSGKSSLIN EILYKRLAAE LNRASVKPGE HDLIKGIEYL DKVIDIDQSP IGRTPRSN P ATYTGVFDFI REIFANTTEA KTRGYKAGRF SFNVKGGRCE ACAGDGINKI EMHFLPDIYV PCEVCKGKRY NRETLEVRY KGKNIAEVLD MTVEEALEFF KNIPRIHKKI ETLYDVGLGY IKLGQSSTTL SGGEAQRVKL ATELSRKSTG KTMYILDEPT TGLHMADVH RLVGILHRLV EAGNSVVVIE HNLDVIKTAD YIIDLGPEGG SGGGLVVAEG TPEEVAKVEN SYTGQFLKKV L ST

UniProtKB: UvrABC system protein A

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Macromolecule #3: UvrABC system protein B

MacromoleculeName: UvrABC system protein B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetivibrio thermocellus (bacteria)
Molecular weightTheoretical: 75.703227 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMHKFKLVSD YKPCGDQPEA IDKLVEGINR GYRGQTLLGV TGSGKTFTMA NVIERVQKPT LVIAHNKTLA AQLCSEFKEF FPNNCVEYF VSYYDYYQPE AYIPATDTYI EKDSSINDEI DKLRHSATAA LFERRDVIIV ASVSCIYGLG DPEDYTDLML S LRPGMIKD ...String:
SMHKFKLVSD YKPCGDQPEA IDKLVEGINR GYRGQTLLGV TGSGKTFTMA NVIERVQKPT LVIAHNKTLA AQLCSEFKEF FPNNCVEYF VSYYDYYQPE AYIPATDTYI EKDSSINDEI DKLRHSATAA LFERRDVIIV ASVSCIYGLG DPEDYTDLML S LRPGMIKD RDEIIRKLVD IQYERNEIDF KRGKFRVRGD ILEIFPASSS DKVIRVEFFG EEIDRITEVD SLTGEITGVC SH VAIFPAS HYATTKAKMQ RAIASIEQEL EERVRELKSQ GKLLEAQRLE QRTRYDLEMM QEIGFCQGIE NYSRHISGRA PGS PPFTLI DYFPKDFLLI IDESHVTIPQ IGAMYNGDRS RKESLVEYGF RLPSAFDNRP LTFEEFEKKI NQVIFVSATP AKYE REHSQ QIVEQIIRPT GLLDPEIVVK PVKGQIDDLI GEISERVQKN QRVMITTLTK KMAEDLTDYL RELDFKVEYL HSDID TIER MEIIRNLRLG VFDVLVGINL LREGLDIPEV SLVAILDADK EGFLRSETSL IQTIGRAARN VEGKVIMYAD TITDSM RRA IDETNRRRKI QSEYNQKHGI TPKSVQKGIR DVIEITKVAE EDAKYFIRGD EDSMDKDEVL DLIEKLTNEM KAAAAEL QF ERAAELRDKI AELKKKIGA

UniProtKB: UvrABC system protein B

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Macromolecule #2: DNA (50-MER) with a fluorescein modification - (random sequence b...

MacromoleculeName: DNA (50-MER) with a fluorescein modification - (random sequence built in model)
type: dna / ID: 2 / Details: Random sequence built in model. / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.411887 KDa
SequenceString:
(DG)(DC)(DA)(DT)(DC)(DG)(DT)(DA)(DC)(DT) (DG)(DT)(DT)(DA)(DC)(DG)(DG)(DC)(DT)(DC) (DC)(DA)(DT)(DC)(DA)(DG)(DA)(DT)(DG) (DG)(DA)(DG)(DC)(DC)(DG)(DT)(DA)(DA)(DC) (DA) (DG)(DT)(DA)(DC)(DG)(DA)(DT)(DG) (DC)(DA)

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 4 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE OXIDE / Support film - #1 - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsSample fixed by GraFix with 0.1% glutaraldehyde and concentrated prior to vitrification; exact concentration cannot be estimated accurately.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: EPU (ver. 2.10.0.1941REL)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9695 / Average electron dose: 40.73 e/Å2 / Details: 6326 images were collected with 30 deg stage tilt.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2702429
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-intio model in cryoSPARC
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: OTHER / Software - Name: cryoSPARC (ver. 4.5)
Details: Composite map Resolution of the focused map is 3.18 Resolution of the global map is 2.97
Number images used: 136850
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9gy7:
C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP

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