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- EMDB-15803: RecBCD in complex with the phage protein gp5.9 -

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Basic information

Entry
Database: EMDB / ID: EMD-15803
TitleRecBCD in complex with the phage protein gp5.9
Map dataFinal cryoEM map of the RecBCD-gp5.9 complex
Sample
  • Complex: Complex of gp5.9 bound to RecBCD
    • Complex: RecBCD enzyme subunit RecB, RecC and RecD
      • Protein or peptide: RecBCD enzyme subunit RecB
      • Protein or peptide: RecBCD enzyme subunit RecC
      • Protein or peptide: RecBCD enzyme subunit RecD
    • Complex: Probable RecBCD inhibitor gp5.9
      • Protein or peptide: Probable RecBCD inhibitor gp5.9
  • Ligand: MAGNESIUM ION
KeywordsHomologous recombination / DNA repair / phage / Helicase / Nuclease / Inhibitor / Protein complex / Enzyme / DNA mimic / DNA BINDING PROTEIN
Function / homology
Function and homology information


exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / clearance of foreign intracellular DNA / DNA 5'-3' helicase / single-stranded DNA helicase activity / recombinational repair / DNA 3'-5' helicase / 3'-5' DNA helicase activity / DNA helicase activity ...exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / clearance of foreign intracellular DNA / DNA 5'-3' helicase / single-stranded DNA helicase activity / recombinational repair / DNA 3'-5' helicase / 3'-5' DNA helicase activity / DNA helicase activity / isomerase 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 / virus-mediated perturbation of host defense response / DNA damage response / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding
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 RecB / RecBCD enzyme subunit RecD / RecBCD enzyme subunit RecC / Probable RecBCD inhibitor gp5.9
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWilkinson M / Wilkinson OJ / Feyerherm C / Fletcher EE / Wigley DB / Dillingham MS
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust100401/Z/12/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S007261/1 United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Elife / Year: 2022
Title: Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub.
Authors: Martin Wilkinson / Oliver J Wilkinson / Connie Feyerherm / Emma E Fletcher / Dale B Wigley / Mark S Dillingham /
Abstract: Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, ...Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, we present biochemical and structural analysis of two phage proteins, gp5.9 and Abc2, which target the DNA break resection complex RecBCD. These exemplify two contrasting mechanisms for control of DNA break repair in which the RecBCD complex is either inhibited or co-opted for the benefit of the invading phage. Gp5.9 completely inhibits RecBCD by preventing it from binding to DNA. The RecBCD-gp5.9 structure shows that gp5.9 acts by substrate mimicry, binding predominantly to the RecB arm domain and competing sterically for the DNA binding site. Gp5.9 adopts a parallel coiled-coil architecture that is unprecedented for a natural DNA mimic protein. In contrast, binding of Abc2 does not substantially affect the biochemical activities of isolated RecBCD. The RecBCD-Abc2 structure shows that Abc2 binds to the Chi-recognition domains of the RecC subunit in a position that might enable it to mediate the loading of phage recombinases onto its single-stranded DNA products.
History
DepositionSep 12, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15803.png

Downloads & links

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Map

FileDownload / File: emd_15803.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal cryoEM map of the RecBCD-gp5.9 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 224 pix.
= 246.4 Å		1.1 Å/pix.
x 224 pix.
= 246.4 Å		1.1 Å/pix.
x 224 pix.
= 246.4 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: 0.017
Minimum - Maximum-0.05141241 - 0.11767499
Average (Standard dev.)0.0000053935914 (±0.004575231)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 246.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional map from focus refinement around the phage...

Fileemd_15803_additional_1.map
AnnotationAdditional map from focus refinement around the phage protein, used to help model building
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap1

Fileemd_15803_half_map_1.map
Annotationhalfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap2

Fileemd_15803_half_map_2.map
Annotationhalfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of gp5.9 bound to RecBCD

EntireName: Complex of gp5.9 bound to RecBCD
Components
  • Complex: Complex of gp5.9 bound to RecBCD
    • Complex: RecBCD enzyme subunit RecB, RecC and RecD
      • Protein or peptide: RecBCD enzyme subunit RecB
      • Protein or peptide: RecBCD enzyme subunit RecC
      • Protein or peptide: RecBCD enzyme subunit RecD
    • Complex: Probable RecBCD inhibitor gp5.9
      • Protein or peptide: Probable RecBCD inhibitor gp5.9
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of gp5.9 bound to RecBCD

SupramoleculeName: Complex of gp5.9 bound to RecBCD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: t7 gp5.9 purified separately and then mixed with RecBCD complex

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Supramolecule #2: RecBCD enzyme subunit RecB, RecC and RecD

SupramoleculeName: RecBCD enzyme subunit RecB, RecC and RecD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Probable RecBCD inhibitor gp5.9

SupramoleculeName: Probable RecBCD inhibitor gp5.9 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Escherichia phage T7 (virus)

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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: 134.110641 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
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 (E. coli)
Molecular weightTheoretical: 128.974102 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (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: 66.990367 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
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: Probable RecBCD inhibitor gp5.9

MacromoleculeName: Probable RecBCD inhibitor gp5.9 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 6.049601 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MSRDLVTIPR DVWNDIQGYI DSLERENDSL KNQLMEADEY VAELEEKLNG TS

UniProtKB: Probable RecBCD inhibitor gp5.9

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / 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

Concentration0.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMTris-HCl
100.0 mMSodium chlorideNaCl
0.5 mMTCEP
5.0 mMMagnesium chlorideMgCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE
Details: Mixture of graphene oxide with 0.3 mM DDM detergent applied directly to grids twice before application of sample
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV / Details: 1.5s blot time.
DetailsRecBCD mixed with T7 gp5.9 protein prior to making grids

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5064 / Average exposure time: 4.3 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1458124
Startup modelType of model: INSILICO MODEL
In silico model: Generated using Cryosparc2 ab initio classification
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 141458
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)

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Atomic model buiding 1

Initial modelPDB ID:

5mbv


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 89.5 / Target criteria: Correlation coefficient
Output model

PDB-8b1r:
RecBCD in complex with the phage protein gp5.9

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