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- EMDB-54021: Agrobacterium phage 7-7-1 baseplate -

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Basic information

Entry
Database: EMDB / ID: EMD-54021
TitleAgrobacterium phage 7-7-1 baseplate
Map dataAgrobacterium phage 7-7-1 baseplate
Sample
  • Virus: Agrobacterium phage 7-7-1 (virus)
    • Protein or peptide: Baseplate protein
    • Protein or peptide: Putative tail biosynthetic protein
    • Protein or peptide: Structural protein
    • Protein or peptide: Baseplate protein
  • Protein or peptide: Putative tail biosynthetic protein
  • Protein or peptide: Putative structural protein
  • Protein or peptide: Tail sheath protein
  • Protein or peptide: Structural protein
KeywordsFlagella phage / Agrobacterium sp. H13-3 / Baseplate / VIRUS
Function / homology
Function and homology information


Bacteriophage Mu, Baseplate protein gp46 / Phage protein GP46 / DNA circulation, N-terminal / DNA circularisation protein N-terminus / Baseplate protein J-like / Baseplate J-like protein barrel domain
Similarity search - Domain/homology
Baseplate protein / Structural protein / Putative tail biosynthetic protein / Putative structural protein / Tail sheath protein / Putative tail biosynthetic protein / Structural protein / Baseplate protein
Similarity search - Component
Biological speciesAgrobacterium phage 7-7-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsNoteborn WEM / Hoeksma T / Briegel A
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
CitationJournal: To Be Published
Title: Using cryogenic electron micrography methods to gain insight into structure and initial host attachment of the fagellotrophic bacteriophage 7-7-1
Authors: Noteborn WEM / Hoeksma T / Briegel A
History
DepositionJun 14, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54021.png

Downloads & links

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Map

FileDownload / File: emd_54021.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAgrobacterium phage 7-7-1 baseplate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 560 pix.
= 767.2 Å		1.37 Å/pix.
x 560 pix.
= 767.2 Å		1.37 Å/pix.
x 560 pix.
= 767.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.2083775 - 2.3039947
Average (Standard dev.)0.0014392035 (±0.08766101)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 767.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Agrobacterium phage 7-7-1 baseplate

Fileemd_54021_half_map_1.map
AnnotationAgrobacterium phage 7-7-1 baseplate
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Agrobacterium phage 7-7-1 baseplate

Fileemd_54021_half_map_2.map
AnnotationAgrobacterium phage 7-7-1 baseplate
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Agrobacterium phage 7-7-1

EntireName: Agrobacterium phage 7-7-1 (virus)
Components
  • Virus: Agrobacterium phage 7-7-1 (virus)
    • Protein or peptide: Baseplate protein
    • Protein or peptide: Putative tail biosynthetic protein
    • Protein or peptide: Structural protein
    • Protein or peptide: Baseplate protein
  • Protein or peptide: Putative tail biosynthetic protein
  • Protein or peptide: Putative structural protein
  • Protein or peptide: Tail sheath protein
  • Protein or peptide: Structural protein

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Supramolecule #1: Agrobacterium phage 7-7-1

SupramoleculeName: Agrobacterium phage 7-7-1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 1161931 / Sci species name: Agrobacterium phage 7-7-1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Baseplate protein

MacromoleculeName: Baseplate protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 20.893727 KDa
SequenceString:
MTTTKTFDER NRDTQDGFER HVFRKLDHTD TGAIVTVEGS GTMDEDVPVI NSGYGFNPED DEELEVFLLS DGSDASGKFG VMTIPRNKQ RKWPKKTGGI QHPFNADKFV QLDDDSIWLK DGKFTLGDNR SLSITVEGNN VVIDTGGGEL DIRSSKLMHN G VNIGDSHV HPQQADSDGD TEADTDPPKR D

UniProtKB: Baseplate protein

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Macromolecule #2: Putative tail biosynthetic protein

MacromoleculeName: Putative tail biosynthetic protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 49.30443 KDa
SequenceString: MIKPMRIFIG GEELETYTSA RLQRTKKQLT GSLTVEIFLN YVPSKPVIVN AVRGKEILVY VMGELAFTGI IDKRKGKTVA GSQPRDASG RFAYSGGPGS MSDEGGSDVT VNFAKGQGYS VTLTARGRTK YLVDSSHSHP TGSFKDTSDR KVIEALVKEH K VVLDWQGT ...String:
MIKPMRIFIG GEELETYTSA RLQRTKKQLT GSLTVEIFLN YVPSKPVIVN AVRGKEILVY VMGELAFTGI IDKRKGKTVA GSQPRDASG RFAYSGGPGS MSDEGGSDVT VNFAKGQGYS VTLTARGRTK YLVDSSHSHP TGSFKDTSDR KVIEALVKEH K VVLDWQGT EVKEPKITLR DGNRIFNEIF ERCNQNCHFA YETRDGKLLV TDGTTGVVGE DIVLGQNILD FSAEQSEDRA NS EITVKGH RVAKDVWGKN AIVQPVQSVA DSWVGANIPL TIQHYGDATN ESLQRRAKFE ADRRAAESKS VNVTVFHVAQ QGG IPWDIG NIHYVEIPPE GIFDVMECVS LTYSVDAKST LETQLELAPP PSESISGASS GLLSSISNSL ADISTKGVAR RVQA GIKLI AGQYPSTWTS AALSAITTPV NVIASVVNSL LLNEDESTPK QPPLRLPPE

UniProtKB: Putative tail biosynthetic protein

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Macromolecule #3: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 31.473984 KDa
SequenceString: MNVLVPGIDG MVSAGKFEYS GCCPPDFADM DECTLATSYV GLLPSGPLWD RAKYEAITTI TATGNCAACW TEDHCPTLVD YAVNVGARL ASVIDMTLWP AVRESDPFTA VTSTADWLER FKWVNCFETS CRSKALGEIT PIEYMTECGP VYVAINYPPS I KQAFESAL ...String:
MNVLVPGIDG MVSAGKFEYS GCCPPDFADM DECTLATSYV GLLPSGPLWD RAKYEAITTI TATGNCAACW TEDHCPTLVD YAVNVGARL ASVIDMTLWP AVRESDPFTA VTSTADWLER FKWVNCFETS CRSKALGEIT PIEYMTECGP VYVAINYPPS I KQAFESAL IKSLERLSMG IIKNLASINF VIEPLKVRVV PLDTTNACEN ETLCVTFEKT SDFFDGVNQN PCGIPSPVAA YI DRDVMQL PSELPKYIWP GHMAAECVVR SLLSHVSRFC VVRTDQTPD

UniProtKB: Structural protein

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Macromolecule #4: Baseplate protein

MacromoleculeName: Baseplate protein / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 43.428816 KDa
SequenceString: MACTIQRPEP QALRDKIATR FSTNVLGGAE IIPESNEFYV VTLEYAMQEE FFAFAEQMWR EQDPRYACCE NLVKMAARRG VYPKPAQFA QGYVRMTGVP GSALNQNLRF QFENQTYEAA SVVPDQLPAT GVLVLRVSAV TPGPSGNIRV TEGSLVTPVP G ISSAVTAY ...String:
MACTIQRPEP QALRDKIATR FSTNVLGGAE IIPESNEFYV VTLEYAMQEE FFAFAEQMWR EQDPRYACCE NLVKMAARRG VYPKPAQFA QGYVRMTGVP GSALNQNLRF QFENQTYEAA SVVPDQLPAT GVLVLRVSAV TPGPSGNIRV TEGSLVTPVP G ISSAVTAY GGNFCGGDDA EECEPFRTRY LQRLQYEPRL TVEWLKSKAM EWPCVTDVFD LGPNCCSVNA LGEVECPNNI EF YVLFRDT FDCGLAPQCV VDEITDWLFG SPQGLGQGEA EFGICGKVRT ATAVNLDIYL NGLSCATPAQ ARVVEQRITD FIN RHPPST NLTVEQLRFI GLQVLGSSFA FDVAIRSPGD ASQSGLRFNA CGDAEIDCDY KACLNSVQVI NNNVTTSGCL

UniProtKB: Baseplate protein

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Macromolecule #5: Putative tail biosynthetic protein

MacromoleculeName: Putative tail biosynthetic protein / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 43.729598 KDa
SequenceString: MAGPCYNPNE HYLPASFKGV PFDADSSDSE HGRNGAEAEF VFGERTGYAD LGIKIRSYSI RARFQTNDHV ALSNAFIAVL ESTGPGLLV HPTRGPVMAA CRSARVTDSK VDAAGVTYID IDFVEANDTV TGFGLVGSLI ALALSPIITA TEESFKRYYS P ENVRYYNS ...String:
MAGPCYNPNE HYLPASFKGV PFDADSSDSE HGRNGAEAEF VFGERTGYAD LGIKIRSYSI RARFQTNDHV ALSNAFIAVL ESTGPGLLV HPTRGPVMAA CRSARVTDSK VDAAGVTYID IDFVEANDTV TGFGLVGSLI ALALSPIITA TEESFKRYYS P ENVRYYNS ETVIATMAEA VQQVQTGYLA LSGNDTSQEK WTIVRDFRNV LIDEFTFFDP ANSWNVLRNG FSYLDSAAVG QD KFTILRN IINWSSSHSE LDGESADAQN AIFSAVRVLA TAYLSKAYME TVASTVNEGL AQYDQIAAIL EQEAQIAQED CHD NEFFLS IREFSVSVAR VMVNRAYNSP ALIVYSFPGT MHSLVVAWEI FGDAKRSREL EGRNTGAPWA IGPKVIAERV RA

UniProtKB: Putative tail biosynthetic protein

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Macromolecule #6: Putative structural protein

MacromoleculeName: Putative structural protein / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 19.32174 KDa
SequenceString:
MTCNFETADR RKRFWTTQVA ACGQSSDDCG DCARPGLQLL CNGEGRITIA TDNYVAGLAL NILLTDASKA DTGCGWTPGN RGGFWGDSF RSDNMRSGSK IRQVTARGSM RETVALIRAY AIDDLKKLVA YGVAKSVDVD LTYQGSNKID MTIMIQGVDG N ESRVGLTG ERIANAWVWS

UniProtKB: Putative structural protein

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Macromolecule #7: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 7 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 54.120355 KDa
SequenceString: MAQDALSDGF VRLCIDPSLN FFGEGCKILV EGQITDDATA AENVVTCVNS ELDLVERFGQ GSVLTESLRK VFCMCKSGVS VYALPRADA AAAVSAVYTL TVTGTALTDG RVQLYMGEAE YSLDIGVDEG DTPTQIAAKI VAAISPDFPY EATAAAGVIT L TARNGGTI ...String:
MAQDALSDGF VRLCIDPSLN FFGEGCKILV EGQITDDATA AENVVTCVNS ELDLVERFGQ GSVLTESLRK VFCMCKSGVS VYALPRADA AAAVSAVYTL TVTGTALTDG RVQLYMGEAE YSLDIGVDEG DTPTQIAAKI VAAISPDFPY EATAAAGVIT L TARNGGTI GNHLSVIYTN LGSCTSVTPE GVTVAFAQTT PGSVNPEPND YASVVNECCF AVYVLSSDDT DWQENLRDWI RS AWDCSKP QCFGHGYVFN KGTLGQVLAD GDNSAELSRL ALPTTYPVLP YLTNAAYGAL SACSTCENPE LNVQGQTYGL LSC INMPES CTPGWEFTEV TQLQNNGFVV SGPATTSGQG NFTSPYIYND VTNYLRDEKN RPNATFRDAS SRRLAAATGV ALAT FLQQF NGLAVFTKNT NIKTGIIGTN LRLMLGKIRK WASDNVGVLF SEFDNINEDI QLVSDFDVQP KCVGQPGVFH LNMRY RPPV RGARINVNLV PALFDNCDR

UniProtKB: Tail sheath protein

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Macromolecule #8: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 8 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 14.503347 KDa
SequenceString:
MACNKQNGVK NILITFTHCD TGEVIGPISH EQPDDTLPTY KTCAWTNTAL TNGAVMRSAS NATMTLPVVR DPRVPLAWYQ GCAQIDAQV EKFDGTVMTL TEGAVTEPEE SDGRAVTMTI IAAEIDELLP PGSLAAA

UniProtKB: Structural protein

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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

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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: 64000
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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 8161
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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