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- EMDB-49626: Cryo-EM structure of AdnA(D934A)-AdnB(D1014A) in complex with AMP... -

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Basic information

Entry
Database: EMDB / ID: EMD-49626
TitleCryo-EM structure of AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and blunt end DNA
Map data
Sample
  • Complex: AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and blunt end DNA
    • Protein or peptide: DNA 3'-5' helicase
    • Protein or peptide: DNA 3'-5' helicase
    • DNA: DNA (30-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: IRON/SULFUR CLUSTER
KeywordsATPase / helicase / DNA / ISOMERASE-DNA complex
Function / homology
Function and homology information


DNA helicase complex / recombinational repair / exonuclease activity / 3'-5' DNA helicase activity / DNA 3'-5' helicase / DNA binding / ATP binding / cytosol
Similarity search - Function
PD-(D/E)XK endonuclease-like domain, AddAB-type / PD-(D/E)XK nuclease superfamily / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / PD-(D/E)XK endonuclease-like domain superfamily / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type ...PD-(D/E)XK endonuclease-like domain, AddAB-type / PD-(D/E)XK nuclease superfamily / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / PD-(D/E)XK endonuclease-like domain superfamily / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / Restriction endonuclease type II-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA 3'-5' helicase / DNA 3'-5' helicase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria) / Mycolicibacterium smegmatis MC2 155 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWarren GM / De la Cruz MJ / Goldgur Y / Shuman S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structure of an initiation complex of mycobacterial helicase-nuclease AdnAB at a blunt double-strand break reveals local melting that engages the 3' tracking strand at the ratchet pawl of the helicase motor.
Authors: Garrett M Warren / M Jason de la Cruz / Yehuda Goldgur / Stewart Shuman /
Abstract: Mycobacterial AdnAB is a heterodimeric helicase-nuclease that initiates homologous recombination by resecting double-strand breaks. The AdnB subunit hydrolyzes ATP to drive single-nucleotide steps of ...Mycobacterial AdnAB is a heterodimeric helicase-nuclease that initiates homologous recombination by resecting double-strand breaks. The AdnB subunit hydrolyzes ATP to drive single-nucleotide steps of 3'-to-5' translocation of AdnAB on the tracking DNA strand via a ratchet-like mechanism. AdnB Trp325, which makes a π stack on a nucleobase 5' of a flipped-out nucleoside, is the ratchet pawl without which ATP hydrolysis is mechanically futile. Here we report a cryo-EM (cryogenic electron microscopy) structure of AdnAB in complex with a blunt-ended DNA. AdnAB forms an initiation complex by melting five terminal base pairs and threading the splayed out 5' and 3' single strands into the AdnA nuclease domain and the AdnB motor domain, respectively. The melted 5-nucleotide 3' tracking strand is in-gear with respect to the ratchet and pawl of the AdnB motor. An analogous π-stacking aromatic pawl is present in the motor subunit of the bacterial end-resection enzymes Bacillus AddAB and Escherichia coli RecBCD. Our results highlight a common theme whereby binding of the motor-nuclease to a blunt DSB end, in the absence of ATP hydrolysis, is coupled to local melting of the terminal base pairs that suffices to engage the "clutch" of the motor on the tracking strand.
History
DepositionMar 11, 2025-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49626.png

Downloads & links

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Map

FileDownload / File: emd_49626.map.gz / Format: CCP4 / Size: 6.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 101 pix.
= 107.464 Å		1.06 Å/pix.
x 116 pix.
= 123.424 Å		1.06 Å/pix.
x 142 pix.
= 151.088 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.8572354 - 5.336732
Average (Standard dev.)0.042834274 (±0.27347732)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin938096
Dimensions116142101
Spacing101116142
CellA: 107.464005 Å / B: 123.424 Å / C: 151.088 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49626_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49626_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and blunt end DNA

EntireName: AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and blunt end DNA
Components
  • Complex: AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and blunt end DNA
    • Protein or peptide: DNA 3'-5' helicase
    • Protein or peptide: DNA 3'-5' helicase
    • DNA: DNA (30-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and blunt end DNA

SupramoleculeName: AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and blunt end DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: MC2 155

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Macromolecule #1: DNA 3'-5' helicase

MacromoleculeName: DNA 3'-5' helicase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA 3'-5' helicase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 110.986648 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: SMTTRPAESA PQTASTLLEP GSNGVVRLLG GPGTGKSSLL VDTAVQHILA GADPESVLLL TGSARLRTAA RAAITARLLG AGTVGVVRE PLVRTVHSYA FAVLRLAAQR NGDPPPRLIT SAEQDGIIRE LLAGDLEDGH RSPVGWPEQL WPALTTAGFA T ELRDLMAR ...String:
SMTTRPAESA PQTASTLLEP GSNGVVRLLG GPGTGKSSLL VDTAVQHILA GADPESVLLL TGSARLRTAA RAAITARLLG AGTVGVVRE PLVRTVHSYA FAVLRLAAQR NGDPPPRLIT SAEQDGIIRE LLAGDLEDGH RSPVGWPEQL WPALTTAGFA T ELRDLMAR CTERGVDPIA LQRLGRTAKR PEWLAAGRFA QAYEQIMLLR SAVGMAAPQA TVPALGAAEL VGAALEALGA DD ELLDTER NRIKLLLVDD AQHLDPQAAR LVRALAAGTG LTVIAGDPDQ SVFGYRGADP VLLRDDTHPA ITLTQSYRCA PEI ASAITG LGQRLPGVSD TRHWTGNPQR EGTVTVRLAA STHAEGTMIA DALRRAHLVD GIPWSQMAVI VRSVPRVGTA LARA LTAAG VPVQDNGTDV PVGRQPAAAA LLTVLDVTAT GHLDADSAVA LLTGPIGRVD PVTLRQLRRA LRRADGSQPP RDFGD LLVD AIEREPKGLS AEHARTLRRL RAVLTAARRS DASGADPRYT LWQAWHASGL QRRWLAASER GGSVGAQADR DLDAVT TLF DVADQYVNRT AGASLRGLVD HVTRLGAAVA RTEPETAAEA VAVLSVHGAL AGEWDFVVIA GVQEGLWPNM IPRGGVL GT QHLVDVLDGV ADMTDRTVST RAPLVAEERR LLMAAMGRAR TRVMITAVDS DTGDESLLPS PFCAEISAWA TEPVAEPP L VAPRVLAPSA LVGRLRAVVC APDGAVDDDA RACAAAQLAR LAAAGVPGAD PSQWHAMTSL TTEEPLWSEP GHVVTLSPS TLQMLTDCPL RWLLERHGGD DGRDVRSTVG SLVHALVSEP GKTESQLVNE LEKVWDDLPY DAKWYSDNEL ARHRAMLETF TRWREDTRR QLTEVATEIP VEGIVVEPGE NTPGVRVRGR LDRLERDEAG RLVVVALKTG KSPVTKDDAQ NHAQLAMYQL A VAAGLLDD GDEPGGGKLV YLGKAGAAGA TEREQDPLTP DKRAEWLETV GEAAAATAGP RFVARVNNGC ANCPVRSSCP AQ ANGDRP

UniProtKB: DNA 3'-5' helicase

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Macromolecule #2: DNA 3'-5' helicase

MacromoleculeName: DNA 3'-5' helicase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA 3'-5' helicase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 118.084531 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MTQVASPVVQ ARYSPVELSA ALGLFPPTDE QAAVIAAPPG PLVVIAGAGA GKTETMAARV VWLVANGFAT PSQVLGLTFT RKAAGQLLR RVRTRLARLA GAGLAPGSGA SDESATVSTY HAFAGTLLRE HGLLLPVEPD TRLLSETELW QLAYDVVCAH P GHLDTEKT ...String:
MTQVASPVVQ ARYSPVELSA ALGLFPPTDE QAAVIAAPPG PLVVIAGAGA GKTETMAARV VWLVANGFAT PSQVLGLTFT RKAAGQLLR RVRTRLARLA GAGLAPGSGA SDESATVSTY HAFAGTLLRE HGLLLPVEPD TRLLSETELW QLAYDVVCAH P GHLDTEKT PAAVTAMVLR LSGALAEHLV DTDQLRDTHV ELERLVHTLP AGPYQRDRGP SQWLLRMLAT QTERTELVPL ID ALHQRMR AEKVMDFGMQ MAAAARLAAR FPQVGEQLRQ RFRVVLLDEY QDTGHAQRIA LSSLFGGGAD DGLALTAVGD PIQ SIYGWR GASATNLPRF TTDFPYSDGT PAPTLELRTS WRNPPSTLHV ANAVSEEARR RSVAVRALRP RPDAEPGTIR CALL NNVAA ERDWVADHLA RAYHGAIGRG EAAPTAAVLV RRNADAAPMA EALTARGVPV EVVGVAGLLA VPEVADLVAM LRLIA DPTA GSAVMRILTG PRWRFGARDI AALWRRAVEL DDRPKGELGT ADIVAQAAPD ADTACVADAI CDPGDAERYS PAGYER IVA LGRELTMLRA HLGHPLPELV AEVRRVLGLD AEARAARPVA AGWAGTENLD RFSDLVSDFA GHAGASVSAL LAYLDAA VE VENGLAPAEL TVSHDRVQIL TVHAAKGLEW QVVAVPHLSA RVFPSTTQAR TWLTDASDLP PLLRGDRATE SEIGVPVL D TSDIYDRKIL SDKISDHKKS LDQRRVDEER RLLYVAITRA EDTLLLSGHH WGATESKPRG PSEFLCELKT ILEEATAAG TPCGEIEHWA PDPAPGETNP LRDQVVEALW PPVASADDHV HRGAQLVAAA MAGEVSAEAD QEGWAADVDA LLAERERPPQ QEDTELPGQ LSVSTLVELS RDPKAALTRL RRRLPQRPDP HALLGTTFHE WVQRYFHAER LFDLDDLPGA VDSDSGRAVE E SLAELQDA FVKSPWAART PVEVEVPFDM VLGETVVRGR IDAVFAEPDG TTMVLAWKTG DPPETPEAKE HAAVQLAVYR LA WAAMRGC PPESVRAAFH YVRSGQTVIP ETLPGAEELV KLLAAAPTET AEEADRIT

UniProtKB: DNA 3'-5' helicase

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Macromolecule #3: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 18.112617 KDa
SequenceString: (DT)(DC)(DA)(DT)(DA)(DT)(DC)(DC)(DT)(DC) (DT)(DA)(DA)(DT)(DG)(DC)(DG)(DA)(DG)(DC) (DA)(DC)(DT)(DG)(DC)(DT)(DA)(DT)(DT) (DC)(DC)(DC)(DT)(DA)(DG)(DC)(DA)(DG)(DT) (DG) (DC)(DT)(DC)(DG)(DC)(DA) ...String:
(DT)(DC)(DA)(DT)(DA)(DT)(DC)(DC)(DT)(DC) (DT)(DA)(DA)(DT)(DG)(DC)(DG)(DA)(DG)(DC) (DA)(DC)(DT)(DG)(DC)(DT)(DA)(DT)(DT) (DC)(DC)(DC)(DT)(DA)(DG)(DC)(DA)(DG)(DT) (DG) (DC)(DT)(DC)(DG)(DC)(DA)(DT)(DT) (DA)(DG)(DA)(DG)(DG)(DA)(DT)(DA)(DT)(DG) (DA)

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Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 2 / 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 #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ppr

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104148
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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