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- EMDB-56178: RAD51-ssDNA filament in complex with magnesium and ATP bound by t... -

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Entry
Database: EMDB / ID: EMD-56178
TitleRAD51-ssDNA filament in complex with magnesium and ATP bound by the RAD54B N-terminus (beta-barrel)
Map data
Sample
  • Complex: RAD51 filament in complex with magnesium and ATP bound by the RAD54B N-terminus (beta-barrel)
    • Protein or peptide: DNA repair protein RAD51 homolog 1
    • Protein or peptide: DNA repair and recombination protein RAD54B
    • DNA: DNA
  • Protein or peptide: DNA repair and recombination protein RAD54B
  • Ligand: POTASSIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsRAD51 recombinase / RAD54B / filament modulation / homologous recombination / DNA BINDING PROTEIN
Function / homology
Function and homology information


presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / cellular response to cisplatin / DNA translocase activity ...presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / cellular response to cisplatin / DNA translocase activity / homologous recombination / DNA strand invasion / cellular response to hydroxyurea / mitotic recombination / cellular response to camptothecin / replication-born double-strand break repair via sister chromatid exchange / lateral element / regulation of DNA damage checkpoint / DNA strand exchange activity / Impaired BRCA2 binding to PALB2 / telomere maintenance via recombination / reciprocal meiotic recombination / single-stranded DNA helicase activity / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / HDR through Single Strand Annealing (SSA) / ATP-dependent DNA damage sensor activity / Resolution of D-loop Structures through Holliday Junction Intermediates / regulation of double-strand break repair via homologous recombination / response to ionizing radiation / nuclear chromosome / Impaired BRCA2 binding to RAD51 / Transcriptional Regulation by E2F6 / negative regulation of signal transduction by p53 class mediator / replication fork processing / Presynaptic phase of homologous DNA pairing and strand exchange / response to X-ray / ATP-dependent activity, acting on DNA / interstrand cross-link repair / condensed chromosome / DNA polymerase binding / helicase activity / condensed nuclear chromosome / determination of adult lifespan / cellular response to ionizing radiation / male germ cell nucleus / meiotic cell cycle / cellular response to gamma radiation / protein-DNA complex / PML body / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / Meiotic recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to toxic substance / single-stranded DNA binding / site of double-strand break / double-stranded DNA binding / DNA recombination / protein-macromolecule adaptor activity / chromosome, telomeric region / response to xenobiotic stimulus / mitochondrial matrix / DNA repair / hydrolase activity / DNA damage response / chromatin binding / centrosome / chromatin / nucleolus / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical ...: / DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / : / SNF2-like, N-terminal domain superfamily / Helix-hairpin-helix domain / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / 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
DNA repair protein RAD51 homolog 1 / DNA repair and recombination protein RAD54B
Similarity search - Component
Biological speciesHomo sapiens (human) / Homo (humans) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLiang P / Zhang X
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: bioRxiv / Year: 2026
Title: Structures and molecular mechanisms of RAD54B in modulating homologous recombination.
Abstract: Genome stability is essential for cellular viability yet constantly threatened by endogenous and exogenous DNA-damaging agents. Among these, DNA double-strand breaks (DSBs) are particularly harmful ...Genome stability is essential for cellular viability yet constantly threatened by endogenous and exogenous DNA-damaging agents. Among these, DNA double-strand breaks (DSBs) are particularly harmful and in S/G2 phases are faithfully repaired through homologous recombination (HR), a high-fidelity pathway utilising homologous sequences in sister chromatin. The RAD51 recombinase forms nucleoprotein filaments on single-stranded DNA (ssDNA) to mediate homology search, strand invasion and subsequent D-loop formation that leads to DNA synthesis and repair. The efficiency of HR depends on precise regulation of RAD51 filament dynamics by accessory factors, including RAD54 and RAD54B, which belong to the SWI2/SNF2-family DNA translocases. While RAD54 is well-characterized, RAD54B's molecular functions remain poorly understood. Here, we define RAD54B's role in HR using cryo-electron microscopy, mutagenesis, biochemical and cellular assays. We show that RAD54B stabilizes RAD51-DNA filaments, inhibits RAD51 ATPase activity, and promotes strand invasion, D-loop formation and strand exchange. The N-terminal domain (NTD) alone supports filament stabilization and strand exchange, while the C-terminal ATPase domain is required for D-loop formation. Structural and biochemical analyses reveal three RAD51-interacting sites within the NTD and a unique domain (β-domain) that bridges RAD51 protomers and contacts donor dsDNA. This β-domain also regulates RAD54B's ATPase activity and higher-order oligomer organization on dsDNA. Cellular assays reveal that the NTD RAD51-interacting sites as well as the β-domain are required for repairing camptothecin-induced DSBs by HR in human cells. Our findings uncover a modular architecture and mechanistic framework for RAD54B function in HR, highlighting its critical role in genome maintenance.
HIGHLIGHTS: cryoEM structure of RAD54B in complex with RAD51-DNA complexRAD54B uses three sites to interact with RAD51, including a previously unrecognised β-domain that bridges distal RAD51 ...HIGHLIGHTS: cryoEM structure of RAD54B in complex with RAD51-DNA complexRAD54B uses three sites to interact with RAD51, including a previously unrecognised β-domain that bridges distal RAD51 protomers.The β-domain plays multiple crucial roles including regulating filament stability, RAD54B ATPase activity and RAD54B higher order assembly on DNA.RAD54B employs a modular mechanism, with the N-terminal region engaing and stabilising RAD51 filaments, capturing of the homologous strands, whereas the ATPase motor domainrequired for homology search and strand invasion.RAD54B N-terminus and β-domain are essential for HR-mediated repair of camptothecin-induced breaks in human cells.
History
DepositionDec 25, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56178.png

Downloads & links

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Map

FileDownload / File: emd_56178.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.5984645 - 3.3320007
Average (Standard dev.)0.0018131249 (±0.08614319)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_56178_additional_1.map
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Half map: #2

Fileemd_56178_half_map_1.map
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Half map: #1

Fileemd_56178_half_map_2.map
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Sample components

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Entire : RAD51 filament in complex with magnesium and ATP bound by the RAD...

EntireName: RAD51 filament in complex with magnesium and ATP bound by the RAD54B N-terminus (beta-barrel)
Components
  • Complex: RAD51 filament in complex with magnesium and ATP bound by the RAD54B N-terminus (beta-barrel)
    • Protein or peptide: DNA repair protein RAD51 homolog 1
    • Protein or peptide: DNA repair and recombination protein RAD54B
    • DNA: DNA
  • Protein or peptide: DNA repair and recombination protein RAD54B
  • Ligand: POTASSIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RAD51 filament in complex with magnesium and ATP bound by the RAD...

SupramoleculeName: RAD51 filament in complex with magnesium and ATP bound by the RAD54B N-terminus (beta-barrel)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA repair protein RAD51 homolog 1

MacromoleculeName: DNA repair protein RAD51 homolog 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo (humans)
Molecular weightTheoretical: 37.009125 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAMQMQLEAN ADTSVEEESF GPQPISRLEQ CGINANDVKK LEEAGFHTVE AVAYAPKKEL INIKGISEAK ADKILAEAAK LVPMGFTTA TEFHQRRSEI IQITTGSKEL DKLLQGGIET GSITEMFGEF RTGKTQICHT LAVTCQLPID RGGGEGKAMY I DTEGTFRP ...String:
MAMQMQLEAN ADTSVEEESF GPQPISRLEQ CGINANDVKK LEEAGFHTVE AVAYAPKKEL INIKGISEAK ADKILAEAAK LVPMGFTTA TEFHQRRSEI IQITTGSKEL DKLLQGGIET GSITEMFGEF RTGKTQICHT LAVTCQLPID RGGGEGKAMY I DTEGTFRP ERLLAVAERY GLSGSDVLDN VAYARAFNTD HQTQLLYQAS AMMVESRYAL LIVDSATALY RTDYSGRGEL SA RQMHLAR FLRMLLRLAD EFGVAVVITN QVVAQVDGAA MFAADPKKPI GGNIIAHAST TRLYLRKGRG ETRICKIYDS PCL PEAEAM FAINADGVGD AKD

UniProtKB: DNA repair protein RAD51 homolog 1

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Macromolecule #2: DNA repair and recombination protein RAD54B

MacromoleculeName: DNA repair and recombination protein RAD54B / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.036555 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: (ACE)MRRSAAPSQ LQGNSFKKPK FIPPGRSNPG LNEEITKLNP DIKLFEGVAI NNTFLPSQND LRICSLNLPS EESTRE INN RDNCSGKYCF EAPTLATLDP PHTVHSAPKE VAVSKEQEEK SDSLVKYFSV VWCKPSKKKH KKWEGDAVLI VKGKSFI LK NLEGKDIGRG ...String:
(ACE)MRRSAAPSQ LQGNSFKKPK FIPPGRSNPG LNEEITKLNP DIKLFEGVAI NNTFLPSQND LRICSLNLPS EESTRE INN RDNCSGKYCF EAPTLATLDP PHTVHSAPKE VAVSKEQEEK SDSLVKYFSV VWCKPSKKKH KKWEGDAVLI VKGKSFI LK NLEGKDIGRG IGYKFKELEK IEEGQTLMIC GKEIEVMGVI SPDDFSSGRC FQLGGGSTAI SHSSQVARKC FSNPFKSV C KPSSKENRQN DFQNCKPRHD PYTPNSLVMP RPDKNHQWVF NKNCFPLVD

UniProtKB: DNA repair and recombination protein RAD54B

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Macromolecule #3: DNA repair and recombination protein RAD54B

MacromoleculeName: DNA repair and recombination protein RAD54B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.052555 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: (AME)RRSAAPSQL QGNSFKKPKF IPPGRSNPGL NEEITKLNPD IKLFEGVAIN NTFLPSQNDL RICSLNLPSE ESTREI NNR DNCSGKYCFE APTLATLDPP HTVHSAPKEV AVSKEQEEKS DSLVKYFSVV WCKPSKKKHK KWEGDAVLIV KGKSFIL KN LEGKDIGRGI ...String:
(AME)RRSAAPSQL QGNSFKKPKF IPPGRSNPGL NEEITKLNPD IKLFEGVAIN NTFLPSQNDL RICSLNLPSE ESTREI NNR DNCSGKYCFE APTLATLDPP HTVHSAPKEV AVSKEQEEKS DSLVKYFSVV WCKPSKKKHK KWEGDAVLIV KGKSFIL KN LEGKDIGRGI GYKFKELEKI EEGQTLMICG KEIEVMGVIS PDDFSSGRCF QLGGGSTAIS HSSQVARKCF SNPFKSVC K PSSKENRQND FQNCKPRHDP YTPNSLVMPR PDKNHQWVFN KNCFPLVD

UniProtKB: DNA repair and recombination protein RAD54B

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Macromolecule #4: DNA

MacromoleculeName: DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.051004 KDa
SequenceString:
(DC)(DA)(DA)(DC)(DA)(DA)(DC)(DA)(DA)(DC) (DA)(DA)(DC)(DA)(DA)(DC)(DA)(DA)(DC)(DA)

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 7 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 5 / 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 statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 148633
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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