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

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Database: PDB / ID: 5mbv
TitleCryo-EM structure of Lambda Phage protein GamS bound to RecBCD
DescriptorRecBCD enzyme subunit RecB
RecBCD enzyme subunit RecC
RecBCD enzyme subunit RecD
Host-nuclease inhibitor protein gam
KeywordsDNA BINDING PROTEIN / Inhibitor / Complex / DNA repair / Helicase/Nuclease / DNA binding protein
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Enterobacteria phage lambda / virus
MethodElectron microscopy (3.8 A resolution / Single particle)
AuthorsWilkinson, M. / Chaban, Y. / Wigley, D.B.
CitationElife, 2016, 5

Elife, 2016, 5 StrPapers
Structural basis for the inhibition of RecBCD by Gam and its synergistic antibacterial effect with quinolones.
Martin Wilkinson / Lucy Troman / Wan Ak Wan Nur Ismah / Yuriy Chaban / Matthew B Avison / Mark S Dillingham / Dale B Wigley

DateDeposition: Nov 8, 2016 / Release: Jan 11, 2017

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Deposited unit
B: RecBCD enzyme subunit RecB
C: RecBCD enzyme subunit RecC
D: RecBCD enzyme subunit RecD
A: Host-nuclease inhibitor protein gam
E: Host-nuclease inhibitor protein gam

Theoretical massNumber of molelcules
Total (without water)353,5135

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (A2)25710
ΔGint (kcal/M)-97
Surface area (A2)129280


#1: Polypeptide(L)RecBCD enzyme subunit RecB / Exodeoxyribonuclease V 135 kDa polypeptide / Exodeoxyribonuclease V beta chain / Exonuclease V subunit RecB / ExoV subunit RecB / Helicase/nuclease RecBCD subunit RecB

Mass: 134167.703 Da / Num. of mol.: 1
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P08394, EC:
#2: Polypeptide(L)RecBCD enzyme subunit RecC / Exodeoxyribonuclease V 125 kDa polypeptide / Exodeoxyribonuclease V gamma chain / Exonuclease V subunit RecC / ExoV subunit RecC

Mass: 128974.102 Da / Num. of mol.: 1
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P07648, EC:
#3: Polypeptide(L)RecBCD enzyme subunit RecD / Exodeoxyribonuclease V 67 kDa polypeptide / Exodeoxyribonuclease V alpha chain / Exonuclease V subunit RecD / ExoV subunit RecD / Helicase/nuclease RecBCD subunit RecD

Mass: 67047.422 Da / Num. of mol.: 1
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P04993, EC:
#4: Polypeptide(L)Host-nuclease inhibitor protein gam

Mass: 11661.924 Da / Num. of mol.: 2
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.
Mutation: L79I same as crystal structure / Source: (gene. exp.) Enterobacteria phage lambda / virus / References: UniProt: P03702

Experimental details


EM experimentReconstruction method: SINGLE PARTICLE

Sample preparation

Assembly of specimen
IDNameDetailsTypeAssembly id
1RecBCD complex bound to inhibitory protein lambda GamSRecBCD 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.COMPLEX1
2RecBCD helicase/nuclease complexCOMPLEX2
3Lambda GamSCOMPLEX3
Specimen supportDetails: 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.
Grid mesh size: 400 /inch. / Grid type: EMS C-Flat 1/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 / Details: 3 ul sample applied Blot force of -4 for 1 s

Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 37313 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
EM image scansSampling size: 5 microns


SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
ComputingStructure refinement: PHENIX (1.10.1_2155: phenix.real_space_refine)
3D reconstructionResolution: 3.8 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 122796
Atomic model building
IDRef protocolTarget criteria
1RIGID BODY FITCorrelation coefficient
2RIGID BODY FITCorrelation coefficient
Atomic model building
PDB-ID 3D fitting idID
Refine LS restraints
Refine idTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00124635
ELECTRON MICROSCOPYf_angle_d0.42733407
ELECTRON MICROSCOPYf_dihedral_angle_d15.51414917
ELECTRON MICROSCOPYf_chiral_restr0.0363657
ELECTRON MICROSCOPYf_plane_restr0.0034402

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