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- EMDB-3460: Cryo-EM structure of Lambda Phage protein GamS bound to RecBCD -

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Basic information

Entry
Database: EMDB / ID: EMD-3460
TitleCryo-EM structure of Lambda Phage protein GamS bound to RecBCD
Map data
Sample
  • Complex: RecBCD complex bound to inhibitory protein lambda GamS
    • Complex: RecBCD helicase/nuclease complex
      • Protein or peptide: RecBCD enzyme subunit RecB
      • Protein or peptide: RecBCD enzyme subunit RecC
      • Protein or peptide: RecBCD enzyme subunit RecD
    • Complex: Lambda GamS
      • Protein or peptide: Host-nuclease inhibitor protein gam
KeywordsInhibitor / Complex / DNA repair / Helicase/Nuclease / DNA binding protein
Function / homology
Function and homology information


symbiont-mediated evasion of DNA end degradation by host / exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / deoxyribonuclease inhibitor activity / clearance of foreign intracellular DNA / DNA translocase activity / DNA 5'-3' helicase / single-stranded DNA helicase activity / recombinational repair ...symbiont-mediated evasion of DNA end degradation by host / exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / deoxyribonuclease inhibitor activity / clearance of foreign intracellular DNA / DNA translocase activity / DNA 5'-3' helicase / single-stranded DNA helicase activity / recombinational repair / 3'-5' DNA helicase activity / DNA 3'-5' helicase / ATP-dependent activity, acting on DNA / DNA helicase activity / isomerase activity / DNA endonuclease activity / helicase activity / double-strand break repair via homologous recombination / response to radiation / 5'-3' DNA helicase activity / DNA recombination / symbiont-mediated suppression of host innate immune response / DNA damage response / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / cytosol
Similarity search - Function
Host-nuclease inhibitor Gam / Host-nuclease inhibitor Gam superfamily / Host-nuclease inhibitor protein Gam / 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 ...Host-nuclease inhibitor Gam / Host-nuclease inhibitor Gam superfamily / Host-nuclease inhibitor protein Gam / 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 / AAA domain / DExx box DNA helicase domain superfamily / UvrD-like helicase C-terminal 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/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
Host-nuclease inhibitor protein gam / RecBCD enzyme subunit RecD / RecBCD enzyme subunit RecC / RecBCD enzyme subunit RecB
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Enterobacteria phage lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWilkinson M / Chaban Y
CitationJournal: Elife / Year: 2016
Title: Structural basis for the inhibition of RecBCD by Gam and its synergistic antibacterial effect with quinolones.
Authors: Martin Wilkinson / Luca Troman / Wan Ak Wan Nur Ismah / Yuriy Chaban / Matthew B Avison / Mark S Dillingham / Dale B Wigley /
Abstract: Our previous paper (Wilkinson , 2016) used high-resolution cryo-electron microscopy to solve the structure of the RecBCD complex, which acts in both the repair of double-stranded DNA breaks and the ...Our previous paper (Wilkinson , 2016) used high-resolution cryo-electron microscopy to solve the structure of the RecBCD complex, which acts in both the repair of double-stranded DNA breaks and the degradation of bacteriophage DNA. To counteract the latter activity, bacteriophage λ encodes a small protein inhibitor called Gam that binds to RecBCD and inactivates the complex. Here, we show that Gam inhibits RecBCD by competing at the DNA-binding site. The interaction surface is extensive and involves molecular mimicry of the DNA substrate. We also show that expression of Gam in or increases sensitivity to fluoroquinolones; antibacterials that kill cells by inhibiting topoisomerases and inducing double-stranded DNA breaks. Furthermore, fluoroquinolone-resistance in clinical isolates is reversed by expression of Gam. Together, our data explain the synthetic lethality observed between topoisomerase-induced DNA breaks and the RecBCD gene products, suggesting a new co-antibacterial strategy.
History
DepositionNov 8, 2016-
Header (metadata) releaseNov 16, 2016-
Map releaseJan 11, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5mbv
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3460.png

Downloads & links

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Map

FileDownload / File: emd_3460.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 180 pix.
= 241.2 Å		1.34 Å/pix.
x 180 pix.
= 241.2 Å		1.34 Å/pix.
x 180 pix.
= 241.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.042780045 - 0.16285071
Average (Standard dev.)-0.0006984152 (±0.009656814)
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-0.0430.163-0.001

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Supplemental data

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Sample components

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Entire : RecBCD complex bound to inhibitory protein lambda GamS

EntireName: RecBCD complex bound to inhibitory protein lambda GamS
Components
  • Complex: RecBCD complex bound to inhibitory protein lambda GamS
    • Complex: RecBCD helicase/nuclease complex
      • Protein or peptide: RecBCD enzyme subunit RecB
      • Protein or peptide: RecBCD enzyme subunit RecC
      • Protein or peptide: RecBCD enzyme subunit RecD
    • Complex: Lambda GamS
      • Protein or peptide: Host-nuclease inhibitor protein gam

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Supramolecule #1: RecBCD complex bound to inhibitory protein lambda GamS

SupramoleculeName: RecBCD complex bound to inhibitory protein lambda GamS
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: RecBCD and GamS were expressed and purified separately. They were mixed with an excess of GamS then passed through a size exclusion column to separate out free GamS.
Molecular weightTheoretical: 350 KDa

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Supramolecule #2: RecBCD helicase/nuclease complex

SupramoleculeName: RecBCD helicase/nuclease complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 330 KDa

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Supramolecule #3: Lambda GamS

SupramoleculeName: Lambda GamS / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Enterobacteria phage lambda (virus)
Molecular weightTheoretical: 20 KDa

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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: 134.167703 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 YLLDYKSNWL 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 BL21(DE3) (bacteria)
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: 67.047422 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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

UniProtKB: RecBCD enzyme subunit RecD

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Macromolecule #4: Host-nuclease inhibitor protein gam

MacromoleculeName: Host-nuclease inhibitor protein gam / type: protein_or_peptide / ID: 4
Details: GamL is cleaved at position Y44 when expressed in E.coli into GamS (see paper - pubmed id 17544443). We had the GamS gene synthesised to start at M41 for this project. It purifies as a dimer.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage lambda (virus)
Molecular weightTheoretical: 11.661924 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MNAYYIQDRL EAQSWARHYQ QLAREEKEAE LADDMEKGIP QHLFESLCID HLQRHGASKK SITRAFDDDV EFQERMAEHI RYMVETIAH HQVDIDSEV

UniProtKB: Host-nuclease inhibitor protein gam

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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

Concentration1.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMTris-HCl
50.0 mMSodium chloride
0.5 mMTCEP-HCl
GridModel: C-flat-1/1 / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec.
Details: Grids were thinned by glow discharge in 30s steps with 1 minute wait in between treatments. Then left for 1-2 weeks prior to overnight treatment with 1 mM Ampiphol A8-35 to render surface ...Details: Grids were thinned by glow discharge in 30s steps with 1 minute wait in between treatments. Then left for 1-2 weeks prior to overnight treatment with 1 mM Ampiphol A8-35 to render surface hydrophilic. Grids were washed with 5 drops of water prior to use. EMS
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3 ul sample applied Blot force of -4 for 1 s.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-25 / Number grids imaged: 1 / Number real images: 334 / Average exposure time: 0.4 sec. / Average electron dose: 1.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.9 µm / Calibrated defocus min: 0.6 µm / Calibrated magnification: 37313 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
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

DetailsFrames were aligned using motioncorr prior to processing.
Particle selectionNumber selected: 134124
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3k70


Details: The DNA was removed from the model so there was nothing to bias density where the inhibitor protein Gam was thought to bind.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 122796
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 1.4)
Details: 3D classification without alignment (after running 3D refinement)

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Atomic model buiding 1

Initial modelPDB ID:

5ld2


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-5mbv:
Cryo-EM structure of Lambda Phage protein GamS bound to RecBCD.

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Atomic model buiding 2

Initial modelPDB ID:

2uuz


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-5mbv:
Cryo-EM structure of Lambda Phage protein GamS bound to RecBCD.

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