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- EMDB-23956: Cryo-EM structure of RecBCD-DNA complex with undocked RecBNuc and... -

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Basic information

Entry
Database: EMDB / ID: EMD-23956
TitleCryo-EM structure of RecBCD-DNA complex with undocked RecBNuc and flexible RecD
Map data
Sample
  • Complex: RecBCD heterotrimer in complex with 60bp blunt-ended dsDNA
    • Protein or peptide: RecBCD enzyme subunit RecB
    • Protein or peptide: RecBCD enzyme subunit RecC
    • Protein or peptide: RecBCD enzyme subunit RecD
  • DNA: DNA (60-MER)
  • DNA: DNA (60-MER)
KeywordsSF1 helicase / complex / DNA repair / motor protein / HYDROLASE-DNA complex
Function / homology
Function and homology information


exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / clearance of foreign intracellular DNA / DNA translocase activity / DNA 5'-3' helicase / single-stranded DNA helicase activity / recombinational repair / DNA 3'-5' helicase / 3'-5' DNA helicase activity ...exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / clearance of foreign intracellular DNA / DNA translocase activity / DNA 5'-3' helicase / single-stranded DNA helicase activity / recombinational repair / DNA 3'-5' helicase / 3'-5' DNA helicase activity / ATP-dependent activity, acting on DNA / DNA helicase activity / DNA endonuclease activity / isomerase activity / helicase activity / double-strand break repair via homologous recombination / response to radiation / 5'-3' DNA helicase activity / DNA recombination / DNA damage response / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / cytosol
Similarity search - Function
RecBCD enzyme subunit RecB / RecBCD enzyme subunit RecD / RecBCD enzyme subunit RecC / RecC, C-terminal / RecBCD enzyme subunit RecD, N-terminal domain / : / Exodeoxyribonuclease V, gamma subunit / RecC C-terminal domain / RecBCD enzyme subunit RecD, N-terminal domain / PD-(D/E)XK endonuclease-like domain, AddAB-type ...RecBCD enzyme subunit RecB / RecBCD enzyme subunit RecD / RecBCD enzyme subunit RecC / RecC, C-terminal / RecBCD enzyme subunit RecD, N-terminal domain / : / Exodeoxyribonuclease V, gamma subunit / RecC C-terminal domain / RecBCD enzyme subunit RecD, N-terminal domain / PD-(D/E)XK endonuclease-like domain, AddAB-type / PD-(D/E)XK nuclease superfamily / DExx box DNA helicase domain superfamily / AAA domain / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / PD-(D/E)XK endonuclease-like domain superfamily / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / Restriction endonuclease type II-like / : / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RecBCD enzyme subunit RecD / RecBCD enzyme subunit RecC / RecBCD enzyme subunit RecB
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria) / Escherichia coli (strain K12) (bacteria) / Synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsHao L / Zhang R
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM045948 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136632 United States
CitationJournal: J Mol Biol / Year: 2021
Title: Heterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting.
Authors: Linxuan Hao / Rui Zhang / Timothy M Lohman /
Abstract: E. coli RecBCD, a helicase/nuclease involved in double stranded (ds) DNA break repair, binds to a dsDNA end and melts out several DNA base pairs (bp) using only its binding free energy. We examined ...E. coli RecBCD, a helicase/nuclease involved in double stranded (ds) DNA break repair, binds to a dsDNA end and melts out several DNA base pairs (bp) using only its binding free energy. We examined RecBCD-DNA initiation complexes using thermodynamic and structural approaches. Measurements of enthalpy changes for RecBCD binding to DNA ends possessing pre-melted ssDNA tails of increasing length suggest that RecBCD interacts with ssDNA as long as 17-18 nucleotides and can melt at least 10-11 bp upon binding a blunt DNA end. Cryo-EM structures of RecBCD alone and in complex with a blunt-ended dsDNA show significant conformational heterogeneities associated with the RecB nuclease domain (RecB) and the RecD subunit. In the absence of DNA, 56% of RecBCD molecules show no density for the RecB nuclease domain, RecB, and all RecBCD molecules show only partial density for RecD. DNA binding reduces these conformational heterogeneities, with 63% of the molecules showing density for both RecD and RecB. This suggests that the RecB domain is dynamic and influenced by DNA binding. The major RecBCD-DNA structural class in which RecB is docked onto RecC shows melting of at least 11 bp from a blunt DNA end, much larger than previously observed. A second structural class in which RecB is not docked shows only four bp melted suggesting that RecBCD complexes transition between states with different extents of DNA melting and that the extent of melting regulates initiation of helicase activity.
History
DepositionMay 7, 2021-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mr4
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23956.png

Downloads & links

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Map

FileDownload / File: emd_23956.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 250 pix.
= 275. Å		1.1 Å/pix.
x 250 pix.
= 275. Å		1.1 Å/pix.
x 250 pix.
= 275. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.03575014 - 0.08114886
Average (Standard dev.)0.00045328104 (±0.0036402657)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 275.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z275.000275.000275.000
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0360.0810.000

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Supplemental data

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Sample components

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Entire : RecBCD heterotrimer in complex with 60bp blunt-ended dsDNA

EntireName: RecBCD heterotrimer in complex with 60bp blunt-ended dsDNA
Components
  • Complex: RecBCD heterotrimer in complex with 60bp blunt-ended dsDNA
    • Protein or peptide: RecBCD enzyme subunit RecB
    • Protein or peptide: RecBCD enzyme subunit RecC
    • Protein or peptide: RecBCD enzyme subunit RecD
  • DNA: DNA (60-MER)
  • DNA: DNA (60-MER)

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Supramolecule #1: RecBCD heterotrimer in complex with 60bp blunt-ended dsDNA

SupramoleculeName: RecBCD heterotrimer in complex with 60bp blunt-ended dsDNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli K12 (bacteria) / Strain: K12

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Macromolecule #1: RecBCD enzyme subunit RecB

MacromoleculeName: RecBCD enzyme subunit RecB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: exodeoxyribonuclease V
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 134.110641 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDVAETLDP LRLPLQGERL IEASAGTGKT FTIAALYLRL LLGLGGSAAF PRPLTVEELL VVTFTEAATA ELRGRIRSNI HELRIACLR ETTDNPLYER LLEEIDDKAQ AAQWLLLAER QMDEAAVFTI HGFCQRMLNL NAFESGMLFE QQLIEDESLL R YQACADFW ...String:
MSDVAETLDP LRLPLQGERL IEASAGTGKT FTIAALYLRL LLGLGGSAAF PRPLTVEELL VVTFTEAATA ELRGRIRSNI HELRIACLR ETTDNPLYER LLEEIDDKAQ AAQWLLLAER QMDEAAVFTI HGFCQRMLNL NAFESGMLFE QQLIEDESLL R YQACADFW RRHCYPLPRE IAQVVFETWK GPQALLRDIN RYLQGEAPVI KAPPPDDETL ASRHAQIVAR IDTVKQQWRD AV GELDALI ESSGIDRRKF NRSNQAKWID KISAWAEEET NSYQLPESLE KFSQRFLEDR TKAGGETPRH PLFEAIDQLL AEP LSIRDL VITRALAEIR ETVAREKRRR GELGFDDMLS RLDSALRSES GEVLAAAIRT RFPVAMIDEF QDTDPQQYRI FRRI WHHQP ETALLLIGDP KQAIYAFRGA DIFTYMKARS EVHAHYTLDT NWRSAPGMVN SVNKLFSQTD DAFMFREIPF IPVKS AGKN QALRFVFKGE TQPAMKMWLM EGESCGVGDY QSTMAQVCAA QIRDWLQAGQ RGEALLMNGD DARPVRASDI SVLVRS RQE AAQVRDALTL LEIPSVYLSN RDSVFETLEA QEMLWLLQAV MTPERENTLR SALATSMMGL NALDIETLNN DEHAWDV VV EEFDGYRQIW RKRGVMPMLR ALMSARNIAE NLLATAGGER RLTDILHISE LLQEAGTQLE SEHALVRWLS QHILEPDS N ASSQQMRLES DKHLVQIVTI HKSKGLEYPL VWLPFITNFR VQEQAFYHDR HSFEAVLDLN AAPESVDLAE AERLAEDLR LLYVALTRSV WHCSLGVAPL VRRRGDKKGD TDVHQSALGR LLQKGEPQDA AGLRTCIEAL CDDDIAWQTA QTGDNQPWQV NDVSTAELN AKTLQRLPGD NWRVTSYSGL QQRGHGIAQD LMPRLDVDAA GVASVVEEPT LTPHQFPRGA SPGTFLHSLF E DLDFTQPV DPNWVREKLE LGGFESQWEP VLTEWITAVL QAPLNETGVS LSQLSARNKQ VEMEFYLPIS EPLIASQLDT LI RQFDPLS AGCPPLEFMQ VRGMLKGFID LVFRHEGRYY LLDYKSNWLG EDSSAYTQQA MAAAMQAHRY DLQYQLYTLA LHR YLRHRI ADYDYEHHFG GVIYLFLRGV DKEHPQQGIY TTRPNAGLIA LMDEMFAGMT LEEA

UniProtKB: RecBCD enzyme subunit RecB

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Macromolecule #2: RecBCD enzyme subunit RecC

MacromoleculeName: RecBCD enzyme subunit RecC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: exodeoxyribonuclease V
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 128.974102 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLRVYHSNRL DVLEALMEFI VERERLDDPF EPEMILVQST GMAQWLQMTL SQKFGIAANI DFPLPASFIW DMFVRVLPEI PKESAFNKQ SMSWKLMTLL PQLLEREDFT LLRHYLTDDS DKRKLFQLSS KAADLFDQYL VYRPDWLAQW ETGHLVEGLG E AQAWQAPL ...String:
MLRVYHSNRL DVLEALMEFI VERERLDDPF EPEMILVQST GMAQWLQMTL SQKFGIAANI DFPLPASFIW DMFVRVLPEI PKESAFNKQ SMSWKLMTLL PQLLEREDFT LLRHYLTDDS DKRKLFQLSS KAADLFDQYL VYRPDWLAQW ETGHLVEGLG E AQAWQAPL WKALVEYTHQ LGQPRWHRAN LYQRFIETLE SATTCPPGLP SRVFICGISA LPPVYLQALQ ALGKHIEIHL LF TNPCRYY WGDIKDPAYL AKLLTRQRRH SFEDRELPLF RDSENAGQLF NSDGEQDVGN PLLASWGKLG RDYIYLLSDL ESS QELDAF VDVTPDNLLH NIQSDILELE NRAVAGVNIE EFSRSDNKRP LDPLDSSITF HVCHSPQREV EVLHDRLLAM LEED PTLTP RDIIVMVADI DSYSPFIQAV FGSAPADRYL PYAISDRRAR QSHPVLEAFI SLLSLPDSRF VSEDVLALLD VPVLA ARFD ITEEGLRYLR QWVNESGIRW GIDDDNVREL ELPATGQHTW RFGLTRMLLG YAMESAQGEW QSVLPYDESS GLIAEL VGH LASLLMQLNI WRRGLAQERP LEEWLPVCRD MLNAFFLPDA ETEAAMTLIE QQWQAIIAEG LGAQYGDAVP LSLLRDE LA QRLDQERISQ RFLAGPVNIC TLMPMRSIPF KVVCLLGMND GVYPRQLAPL GFDLMSQKPK RGDRSRRDDD RYLFLEAL I SAQQKLYISY IGRSIQDNSE RFPSVLVQEL IDYIGQSHYL PGDEALNCDE SEARVKAHLT CLHTRMPFDP QNYQPGERQ SYAREWLPAA SQAGKAHSEF VQPLPFTLPE TVPLETLQRF WAHPVRAFFQ MRLQVNFRTE DSEIPDTEPF ILEGLSRYQI NQQLLNALV EQDDAERLFR RFRAAGDLPY GAFGEIFWET QCQEMQQLAD RVIACRQPGQ SMEIDLACNG VQITGWLPQV Q PDGLLRWR PSLLSVAQGM QLWLEHLVYC ASGGNGESRL FLRKDGEWRF PPLAAEQALH YLSQLIEGYR EGMSAPLLVL PE SGGAWLK TCYDAQNDAM LDDDSTLQKA RTKFLQAYEG NMMVRGEGDD IWYQRLWRQL TPETMEAIVE QSQRFLLPLF RFN QS

UniProtKB: RecBCD enzyme subunit RecC

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Macromolecule #3: RecBCD enzyme subunit RecD

MacromoleculeName: RecBCD enzyme subunit RecD / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: exodeoxyribonuclease V
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 66.990367 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLQKQLLEA VEHKQLRPLD VQFALTVAGD EHPAVTLAAA LLSHDAGEGH VCLPLSRLEN NEASHPLLAT CVSEIGELQN WEECLLASQ AVSRGDEPTP MILCGDRLYL NRMWCNERTV ARFFNEVNHA IEVDEALLAQ TLDKLFPVSD EINWQKVAAA V ALTRRISV ...String:
MKLQKQLLEA VEHKQLRPLD VQFALTVAGD EHPAVTLAAA LLSHDAGEGH VCLPLSRLEN NEASHPLLAT CVSEIGELQN WEECLLASQ AVSRGDEPTP MILCGDRLYL NRMWCNERTV ARFFNEVNHA IEVDEALLAQ TLDKLFPVSD EINWQKVAAA V ALTRRISV ISGGPGTGKT TTVAKLLAAL IQMADGERCR IRLAAPTGKA AARLTESLGK ALRQLPLTDE QKKRIPEDAS TL HRLLGAQ PGSQRLRHHA GNPLHLDVLV VDEASMIDLP MMSRLIDALP DHARVIFLGD RDQLASVEAG AVLGDICAYA NAG FTAERA RQLSRLTGTH VPAGTGTEAA SLRDSLCLLQ KSYRFGSDSG IGQLAAAINR GDKTAVKTVF QQDFTDIEKR LLQS GEDYI AMLEEALAGY GRYLDLLQAR AEPDLIIQAF NEYQLLCALR EGPFGVAGLN ERIEQFMQQK RKIHRHPHSR WYEGR PVMI ARNDSALGLF NGDIGIALDR GQGTRVWFAM PDGNIKSVQP SRLPEHETTW AMTVHKSQGS EFDHAALILP SQRTPV VTR ELVYTAVTRA RRRLSLYADE RILSAAIATR TERRSGLAAL FSSRE

UniProtKB: RecBCD enzyme subunit RecD

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Macromolecule #4: DNA (60-MER)

MacromoleculeName: DNA (60-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Synthetic construct (others)
Molecular weightTheoretical: 18.482836 KDa
SequenceString: (DC)(DT)(DG)(DG)(DA)(DG)(DC)(DA)(DT)(DA) (DA)(DG)(DA)(DT)(DC)(DC)(DT)(DA)(DG)(DT) (DT)(DT)(DC)(DA)(DT)(DC)(DC)(DT)(DT) (DT)(DA)(DG)(DG)(DC)(DT)(DA)(DC)(DT)(DG) (DC) (DA)(DG)(DC)(DT)(DA)(DG) ...String:
(DC)(DT)(DG)(DG)(DA)(DG)(DC)(DA)(DT)(DA) (DA)(DG)(DA)(DT)(DC)(DC)(DT)(DA)(DG)(DT) (DT)(DT)(DC)(DA)(DT)(DC)(DC)(DT)(DT) (DT)(DA)(DG)(DG)(DC)(DT)(DA)(DC)(DT)(DG) (DC) (DA)(DG)(DC)(DT)(DA)(DG)(DC)(DT) (DC)(DA)(DG)(DG)(DA)(DG)(DC)(DC)(DA)(DT) (DG)(DG)

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Macromolecule #5: DNA (60-MER)

MacromoleculeName: DNA (60-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Synthetic construct (others)
Molecular weightTheoretical: 18.500861 KDa
SequenceString: (DC)(DC)(DA)(DT)(DG)(DG)(DC)(DT)(DC)(DC) (DT)(DG)(DA)(DG)(DC)(DT)(DA)(DG)(DC)(DT) (DG)(DC)(DA)(DG)(DT)(DA)(DG)(DC)(DC) (DT)(DA)(DA)(DA)(DG)(DG)(DA)(DT)(DG)(DA) (DA) (DA)(DC)(DT)(DA)(DG)(DG) ...String:
(DC)(DC)(DA)(DT)(DG)(DG)(DC)(DT)(DC)(DC) (DT)(DG)(DA)(DG)(DC)(DT)(DA)(DG)(DC)(DT) (DG)(DC)(DA)(DG)(DT)(DA)(DG)(DC)(DC) (DT)(DA)(DA)(DA)(DG)(DG)(DA)(DT)(DG)(DA) (DA) (DA)(DC)(DT)(DA)(DG)(DG)(DA)(DT) (DC)(DT)(DT)(DA)(DT)(DG)(DC)(DT)(DC)(DC) (DA)(DG)

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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: 7.4
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris-hydrochloride
50.0 mMNaClSodium chloride
4.0 mMMgCl2Magnesium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 49.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: the initial model were generated ab initio using Relion
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 26265
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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