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- EMDB-10369: Cryo-EM structure of the RecBCD in complex with Chi-minus2 substrate -

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Basic information

Entry
Database: EMDB / ID: EMD-10369
TitleCryo-EM structure of the RecBCD in complex with Chi-minus2 substrate
Map dataRecBdCD complex with Chi-minus2 substrate
Sample
  • Complex: RecBCD bound to a forked DNA substrate that contain Chi-minus2
    • Complex: RecBCD
      • Protein or peptide: RecBCD enzyme subunit RecB
      • Protein or peptide: RecBCD enzyme subunit RecC
      • Protein or peptide: RecBCD enzyme subunit RecD
    • Complex: Chi-minus2
      • DNA: DNA (Chi-minus2)
KeywordsDNA repair / Homologous recombination / ATP hydrolysis / Helicase / Nuclease / translocation / HYDROLASE
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 (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsCheng K / Wilkinson M
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair.
Authors: Kaiying Cheng / Martin Wilkinson / Yuriy Chaban / Dale B Wigley /
Abstract: The RecBCD complex plays key roles in phage DNA degradation, CRISPR array acquisition (adaptation) and host DNA repair. The switch between these roles is regulated by a DNA sequence called Chi. We ...The RecBCD complex plays key roles in phage DNA degradation, CRISPR array acquisition (adaptation) and host DNA repair. The switch between these roles is regulated by a DNA sequence called Chi. We report cryo-EM structures of the Escherichia coli RecBCD complex bound to several different DNA forks containing a Chi sequence, including one in which Chi is recognized and others in which it is not. The Chi-recognized structure shows conformational changes in regions of the protein that contact Chi and reveals a tortuous path taken by the DNA. Sequence specificity arises from interactions with both the RecC subunit and the sequence itself. These structures provide molecular details for how Chi is recognized and insights into the changes that occur in response to Chi binding that switch RecBCD from bacteriophage destruction and CRISPR spacer acquisition to constructive host DNA repair.
History
DepositionOct 9, 2019-
Header (metadata) releaseJan 1, 2020-
Map releaseJan 1, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing 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-6t2u
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10369.png

Downloads & links

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Map

FileDownload / File: emd_10369.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRecBdCD complex with Chi-minus2 substrate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 224 pix.
= 243.04 Å		1.09 Å/pix.
x 224 pix.
= 243.04 Å		1.09 Å/pix.
x 224 pix.
= 243.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.085 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.05899796 - 0.13680856
Average (Standard dev.)0.000028020664 (±0.0065017277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 243.04001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0851.0851.085
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z243.040243.040243.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0590.1370.000

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Supplemental data

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Sample components

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Entire : RecBCD bound to a forked DNA substrate that contain Chi-minus2

EntireName: RecBCD bound to a forked DNA substrate that contain Chi-minus2
Components
  • Complex: RecBCD bound to a forked DNA substrate that contain Chi-minus2
    • Complex: RecBCD
      • Protein or peptide: RecBCD enzyme subunit RecB
      • Protein or peptide: RecBCD enzyme subunit RecC
      • Protein or peptide: RecBCD enzyme subunit RecD
    • Complex: Chi-minus2
      • DNA: DNA (Chi-minus2)

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Supramolecule #1: RecBCD bound to a forked DNA substrate that contain Chi-minus2

SupramoleculeName: RecBCD bound to a forked DNA substrate that contain Chi-minus2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 355 KDa

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Supramolecule #2: RecBCD

SupramoleculeName: RecBCD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Chi-minus2

SupramoleculeName: Chi-minus2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: synthetic construct (others)

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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 (E. coli)
Molecular weightTheoretical: 134.123688 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 LQQRGHGIAQ DLMPRLDVDA AGVASVVEEP TLTPHQFPRG ASPGTFLHSL F EDLDFTQP VDPNWVREKL ELGGFESQWE PVLTEWITAV LQAPLNETGV SLSQLSARNK QVEMEFYLPI SEPLIASQLD TL IRQFDPL SAGCPPLEFM QVRGMLKGFI DLVFRHEGRY YLLAYKSNWL GEDSSAYTQQ AMAAAMQAHR YDLQYQLYTL ALH RYLRHR IADYDYEHHF GGVIYLFLRG VDKEHPQQGI YTTRPNAGLI ALMDEMFAGM TLEEA

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 (E. coli)
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 (E. coli)
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 (Chi-minus2)

MacromoleculeName: DNA (Chi-minus2) / type: dna / ID: 4
Details: We generated a forked DNA substrate with single-stranded overhangs by annealing two synthesised oligonucleotides
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.551277 KDa
SequenceString: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DG)(DA)(DG)(DC)(DG) (DA)(DC)(DT)(DG)(DC)(DA)(DC)(DT)(DA) (DC)(DA)(DA)(DC)(DA)(DG)(DA)(DA)(DC)(DC) (DA) (DT)(DG)(DG)(DT)(DT)(DC) ...String:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DG)(DA)(DG)(DC)(DG) (DA)(DC)(DT)(DG)(DC)(DA)(DC)(DT)(DA) (DC)(DA)(DA)(DC)(DA)(DG)(DA)(DA)(DC)(DC) (DA) (DT)(DG)(DG)(DT)(DT)(DC)(DT)(DG) (DT)(DT)(DG)(DT)(DA)(DG)(DT)(DG)(DC)(DA) (DG)(DT) (DC)(DG)(DC)(DT)(DC)(DT)(DT) (DT)(DT)(DT)(DT)(DG)(DC)(DT)(DG)(DG)(DT) (DG)(DG)(DT) (DT)(DT)(DT)

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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

Concentration0.2 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTRIS-HCl
50.0 mMNaCl
0.5 mMTCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 1s blot before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 4013 / Average exposure time: 1.0 sec. / Average electron dose: 75.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 754150
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ld2


Details: Initially low-pass filtered to 30 Angstrom
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 379790
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5ld2


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsRounds of manual structure editing in coot and real-space refinement with Phenix
RefinementSpace: REAL
Output model

PDB-6t2u:
Cryo-EM structure of the RecBCD in complex with Chi-minus2 substrate

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