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- EMDB-52522: Agrobacterium phage 7-7-1 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-52522
TitleAgrobacterium phage 7-7-1 capsid
Map dataCapsid of Agrobacterium phage 7-7-1
Sample
  • Virus: Agrobacterium phage 7-7-1 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Structural protein
    • Protein or peptide: Structural protein
    • Protein or peptide: Structural protein
KeywordsFlagella phage / Agrobacterium sp. H13-3 / Capsid / VIRAL PROTEIN
Function / homology: / Phage capsid / Phage capsid family / virion component / Structural protein / Structural protein / Major capsid protein / Structural protein
Function and homology information
Biological speciesAgrobacterium phage 7-7-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNoteborn WEM / Hoeksma T / Rouchen OY / Briegel A
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
History
DepositionJan 13, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52522.png

Downloads & links

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Map

FileDownload / File: emd_52522.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCapsid of Agrobacterium phage 7-7-1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 800 pix.
= 1096. Å		1.37 Å/pix.
x 800 pix.
= 1096. Å		1.37 Å/pix.
x 800 pix.
= 1096. 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: 0.129
Minimum - Maximum-0.39829126 - 0.76752406
Average (Standard dev.)0.001359863 (±0.038374033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1096.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Capsid of Agrobacterium phage 7-7-1 half map A

Fileemd_52522_half_map_1.map
AnnotationCapsid of Agrobacterium phage 7-7-1 half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Capsid of Agrobacterium phage 7-7-1 half map B

Fileemd_52522_half_map_2.map
AnnotationCapsid of Agrobacterium phage 7-7-1 half map B
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: Major capsid protein
    • Protein or peptide: Structural protein
    • Protein or peptide: Structural 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: all / 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: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 52.592863 KDa
SequenceString: MANKESEQNG LEAISGDIEK LSSNVDLFSK AMDDKYKELT ARFDGQKSDS EEIRKAAEQA TKEYAELSAK HQFFTEELVA MKARLDSPI MRSQADLDDH DRKTAIQLQR NMHEFRGGDP KEFVADESNL VDLKAYRSAV RKMLKVGIES KERVISSMTD V ERKAFEAS ...String:
MANKESEQNG LEAISGDIEK LSSNVDLFSK AMDDKYKELT ARFDGQKSDS EEIRKAAEQA TKEYAELSAK HQFFTEELVA MKARLDSPI MRSQADLDDH DRKTAIQLQR NMHEFRGGDP KEFVADESNL VDLKAYRSAV RKMLKVGIES KERVISSMTD V ERKAFEAS TIGPAFFTPQ VLALEVDCNI ECASLLDLYG QIEVSRSTFT YMKIADYGQL GEYTCDAKCD AEFGEPGNIR HL EGKTYDY RGVFCFNRKN LQEANYDFLS FMIGAAQRSH RINRNRALMV GDGINEPKGW LKEDCFPTFL TLPVNTGTPE NPV QTPAFL AQDWRRFVTS FPAEYGDARS VMHQNVFGYL AAMVDANGRF LFGDGDLTFS PDLVRERIRI SNCLPDPTEG NTKG GTGQD AFAAGSFIAA QAAWKTAYYA VEKRPMFFEQ YEGGSSAWCV KYQFGAEDGG FVGCCEHGRV LRIG

UniProtKB: Major capsid protein

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Macromolecule #2: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 2 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 14.286115 KDa
SequenceString:
MNFNVGVDFP SFIAWDGTTS FPVKIDGFNQ FGFTFKVIEE LTADVPFNIF YHEASEADPC VPGPAIRVPD VPFCDGVATA DGLATVVIP EAVAVDSFCA GSVPCFNGPW ISIAPVTVNA DSAKVQVTVT MKGATR

UniProtKB: Structural protein

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Macromolecule #3: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 23.077988 KDa
SequenceString: MVSLDCRNTC APAPASRLVQ PPCFVCRDVF PLPVAPNPPG PVSAIIGTTP STFSLKPDGT FITGTGISSS GSAVATDGSL ELFLAPLVA HVTGSEMSPP YAVELQEGQE LAIVFGATLK SGFGVRITDY YDVVFNIVSS EGTKQLKLVP GNTPSGYIWT D GEGYNIVD ...String:
MVSLDCRNTC APAPASRLVQ PPCFVCRDVF PLPVAPNPPG PVSAIIGTTP STFSLKPDGT FITGTGISSS GSAVATDGSL ELFLAPLVA HVTGSEMSPP YAVELQEGQE LAIVFGATLK SGFGVRITDY YDVVFNIVSS EGTKQLKLVP GNTPSGYIWT D GEGYNIVD SNGDFHSVQN VTRPSFLGIT DTGVLWQLVG YLKGTTQAEL AIAIEVTVTH AN

UniProtKB: Structural protein

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Macromolecule #4: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 3.209962 KDa
SequenceString:
MIKLNCRPLC QTPTASRLVS PPCFICRR

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 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
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: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 6975
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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