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- EMDB-4038: Cryo-EM structure of RecBCD+DNA complex revealing activated nucle... -

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Basic information

Entry
Database: EMDB / ID: EMD-4038
TitleCryo-EM structure of RecBCD+DNA complex revealing activated nuclease domain
Map data
Sample
  • Complex: Ternary complex of RecBCD with forked DNA substrate and ADPNP
    • Protein or peptide: RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB
    • Protein or peptide: RecBCD enzyme subunit RecC
    • Protein or peptide: RecBCD enzyme subunit RecD
    • DNA: Fork-Hairpin DNA (70-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / clearance of foreign intracellular DNA / DNA translocase activity / single-stranded DNA helicase activity / recombinational repair / 3'-5' DNA helicase activity / ATP-dependent activity, acting on DNA / DNA helicase activity ...exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / clearance of foreign intracellular DNA / DNA translocase activity / single-stranded DNA helicase activity / recombinational repair / 3'-5' DNA helicase activity / ATP-dependent activity, acting on DNA / DNA helicase activity / DNA endonuclease activity / helicase activity / double-strand break repair via homologous recombination / response to radiation / 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 / PD-(D/E)XK nuclease superfamily ...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 / UvrD-like helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / PD-(D/E)XK endonuclease-like domain superfamily / 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) / Endothia gyrosa (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsWilkinson M / Chaban Y / Wigley DB
CitationJournal: Elife / Year: 2016
Title: Mechanism for nuclease regulation in RecBCD.
Authors: Martin Wilkinson / Yuriy Chaban / Dale B Wigley /
Abstract: In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is catalysed by AddAB, AdnAB or RecBCD-type helicase-nucleases. These enzyme complexes are highly ...In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is catalysed by AddAB, AdnAB or RecBCD-type helicase-nucleases. These enzyme complexes are highly processive, duplex unwinding and degrading machines that require tight regulation. Here, we report the structure of E.coli RecBCD, determined by cryoEM at 3.8 Å resolution, with a DNA substrate that reveals how the nuclease activity of the complex is activated once unwinding progresses. Extension of the 5'-tail of the unwound duplex induces a large conformational change in the RecD subunit, that is transferred through the RecC subunit to activate the nuclease domain of the RecB subunit. The process involves a SH3 domain that binds to a region of the RecB subunit in a binding mode that is distinct from others observed previously in SH3 domains and, to our knowledge, this is the first example of peptide-binding of an SH3 domain in a bacterial system.
History
DepositionJun 23, 2016-
Header (metadata) releaseOct 5, 2016-
Map releaseOct 5, 2016-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5ld2
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4038.png

Downloads & links

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Map

FileDownload / File: emd_4038.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy ANNOTATOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.05896135 - 0.14512563
Average (Standard dev.)0.00002842575 (±0.008563512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 241.20001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z241.200241.200241.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0590.1450.000

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Supplemental data

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Sample components

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Entire : Ternary complex of RecBCD with forked DNA substrate and ADPNP

EntireName: Ternary complex of RecBCD with forked DNA substrate and ADPNP
Components
  • Complex: Ternary complex of RecBCD with forked DNA substrate and ADPNP
    • Protein or peptide: RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB
    • Protein or peptide: RecBCD enzyme subunit RecC
    • Protein or peptide: RecBCD enzyme subunit RecD
    • DNA: Fork-Hairpin DNA (70-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Ternary complex of RecBCD with forked DNA substrate and ADPNP

SupramoleculeName: Ternary complex of RecBCD with forked DNA substrate and ADPNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli K12 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: B834 / Recombinant plasmid: 3 plasmids
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB,RecBCD enzy...

MacromoleculeName: RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB
type: protein_or_peptide / ID: 1
Details: Residues 913-932 modelled as poly-Alanine in model to reflect uncertainty of the exact position of this loop due to weak density.
Number of copies: 1 / Enantiomer: LEVO / EC number: exodeoxyribonuclease V
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 133.717391 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GMSDVAETLD PLRLPLQGER LIEASAGTGK TFTIAALYLR LLLGLGGSAA FPRPLTVEEL LVVTFTEAAT AELRGRIRSN IHELRIACL RETTDNPLYE RLLEEIDDKA QAAQWLLLAE RQMDEAAVFT IHGFCQRMLN LNAFESGMLF EQQLIEDESL L RYQACADF ...String:
GMSDVAETLD PLRLPLQGER LIEASAGTGK TFTIAALYLR LLLGLGGSAA FPRPLTVEEL LVVTFTEAAT AELRGRIRSN IHELRIACL RETTDNPLYE RLLEEIDDKA QAAQWLLLAE RQMDEAAVFT IHGFCQRMLN LNAFESGMLF EQQLIEDESL L RYQACADF WRRHCYPLPR EIAQVVFETW KGPQALLRDI NRYLQGEAPV IKAPPPDDET LASRHAQIVA RIDTVKQQWR DA VGELDAL IESSGIDRRK FNRSNQAKWI DKISAWAEEE TNSYQLPESL EKFSQRFLED RTKAGGETPR HPLFEAIDQL LAE PLSIRD LVITRALAEI RETVAREKRR RGELGFDDML SRLDSALRSE SGEVLAAAIR TRFPVAMIDE FQDTDPQQYR IFRR IWHHQ PETALLLIGD PKQAIYAFRG ADIFTYMKAR SEVHAHYTLD TNWRSAPGMV NSVNKLFSQT DDAFMFREIP FIPVK SAGK NQALRFVFKG ETQPAMKMWL MEGESCGVGD YQSTMAQVCA AQIRDWLQAG QRGEALLMNG DDARPVRASD ISVLVR SRQ EAAQVRDALT LLEIPSVYLS NRDSVFETLE AQEMLWLLQA VMTPERENTL RSALATSMMG LNALDIETLN NDEHAWD VV VEEFDGYRQI WRKRGVMPML RALMSARNIA ENLLATAGGE RRLTDILHIS ELLQEAGTQL ESEHALVRWL SQHILEPD S NASSQQMRLE SDKHLVQIVT IHKSKGLEYP LVWLPFITNF RVQEQAFYHD RHSFEAVLDL NAAPESVDLA EAERLAEDL RLLYVALTRS VWHCSLGVAP LVRRRGDKKG DTDVHQSALG RLLQKGEPQD AAGLRTCIEA LCDDDIAWQT AQTGDNQPWQ VNDVSTAEL NAKTLQRLPG DNWRVTSYSG LQQR(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) PTLTPHQFP RGASPGTFLH SLFEDLDFTQ PVDPNWVREK LELGGFESQW EPVLTEWITA VLQAPLNETG VSLSQLSARN K QVEMEFYL PISEPLIASQ LDTLIRQFDP LSAGCPPLEF MQVRGMLKGF IDLVFRHEGR YYLLAYKSNW LGEDSSAYTQ QA MAAAMQA HRYDLQYQLY TLALHRYLRH RIADYDYEHH FGGVIYLFLR GVDKEHPQQG IYTTRPNAGL IALMDEMFAG MTL EEA

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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

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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: 67.047422 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGKLQKQLLE AVEHKQLRPL DVQFALTVAG DEHPAVTLAA ALLSHDAGEG HVCLPLSRLE NNEASHPLLA TCVSEIGELQ NWEECLLAS QAVSRGDEPT PMILCGDRLY LNRMWCNERT VARFFNEVNH AIEVDEALLA QTLDKLFPVS DEINWQKVAA A VALTRRIS ...String:
MGKLQKQLLE AVEHKQLRPL DVQFALTVAG DEHPAVTLAA ALLSHDAGEG HVCLPLSRLE NNEASHPLLA TCVSEIGELQ NWEECLLAS QAVSRGDEPT PMILCGDRLY LNRMWCNERT VARFFNEVNH AIEVDEALLA QTLDKLFPVS DEINWQKVAA A VALTRRIS VISGGPGTGK TTTVAKLLAA LIQMADGERC RIRLAAPTGK AAARLTESLG KALRQLPLTD EQKKRIPEDA ST LHRLLGA QPGSQRLRHH AGNPLHLDVL VVDEASMIDL PMMSRLIDAL PDHARVIFLG DRDQLASVEA GAVLGDICAY ANA GFTAER ARQLSRLTGT HVPAGTGTEA ASLRDSLCLL QKSYRFGSDS GIGQLAAAIN RGDKTAVKTV FQQDFTDIEK RLLQ SGEDY IAMLEEALAG YGRYLDLLQA RAEPDLIIQA FNEYQLLCAL REGPFGVAGL NERIEQFMQQ KRKIHRHPHS RWYEG RPVM IARNDSALGL FNGDIGIALD RGQGTRVWFA MPDGNIKSVQ PSRLPEHETT WAMTVHKSQG SEFDHAALIL PSQRTP VVT RELVYTAVTR ARRRLSLYAD ERILSAAIAT RTERRSGLAA LFSSRE

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Macromolecule #4: Fork-Hairpin DNA (70-MER)

MacromoleculeName: Fork-Hairpin DNA (70-MER) / type: dna / ID: 4
Details: Hairpin=38-42 Duplex=13-37&43-67 5'Tail=1-12 3'Tail=68-70
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Endothia gyrosa (fungus)
Molecular weightTheoretical: 21.440707 KDa
SequenceString: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DC)(DT)(DA)(DA)(DT)(DG)(DC) (DG)(DA)(DG)(DC)(DA)(DC)(DT)(DG)(DC) (DT)(DA)(DC)(DA)(DG)(DC)(DA)(DT)(DT)(DT) (DC) (DC)(DC)(DA)(DT)(DG)(DC) ...String:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DC)(DT)(DA)(DA)(DT)(DG)(DC) (DG)(DA)(DG)(DC)(DA)(DC)(DT)(DG)(DC) (DT)(DA)(DC)(DA)(DG)(DC)(DA)(DT)(DT)(DT) (DC) (DC)(DC)(DA)(DT)(DG)(DC)(DT)(DG) (DT)(DA)(DG)(DC)(DA)(DG)(DT)(DG)(DC)(DT) (DC)(DG) (DC)(DA)(DT)(DT)(DA)(DG)(DA) (DT)(DT)(DT)

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Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 1 / 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: 1 / 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

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris-HClTris
50.0 mMSodium ChlorideNaClSodium chloride
1.0 mMTCEP
4.0 mMMagnesium ChlorideMgCl2
GridModel: C-flat / Support film - Material: CARBON / Support film - topology: HOLEY
Details: Glow discharge was used to thin the carbon film, but allowed to dissipate prior to use. Detergent or amphipols treatment was used to render carbon hydrophilic. See article for details.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.8 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 37313 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specialist opticsEnergy filter - Name: GIF
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 1674 / Average exposure time: 0.4 sec. / Average electron dose: 1.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4)
Gctf (ver. 0.50)Used at the end to apply local CTF corrections for individual particles
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1w36

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 74656

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