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- EMDB-25182: Procapsid of bacteriophage lambda -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-25182
TitleProcapsid of bacteriophage lambda
Map dataLow resolution phage lambda procapsid map.
Sample
  • Complex: Procapsid of bacteriophage lambda
    • Protein or peptide: Major Capsid Protein
Biological speciesEscherichia virus Lambda
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsMaruthi K / Prokhorov NS / Morais MC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Assembly Incompetent Major Capsid Protein Reveals Elementary and Transient Interactions with Scaffolding Chaparone that Nucleate Viral Shell Assembly
Authors: Davis CR / Churchill ME / Backos D / Maruthi K / Prokhorov NS / Morais MC / Catalano CE
History
DepositionOct 21, 2021-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateNov 9, 2022-
Current statusNov 9, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25182.png

Downloads & links

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Map

FileDownload / File: emd_25182.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLow resolution phage lambda procapsid map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 384 pix.
= 1075.2 Å		2.8 Å/pix.
x 384 pix.
= 1075.2 Å		2.8 Å/pix.
x 384 pix.
= 1075.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.035653997 - 0.075861655
Average (Standard dev.)0.00040838923 (±0.0049743284)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 1075.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Procapsid of bacteriophage lambda

EntireName: Procapsid of bacteriophage lambda
Components
  • Complex: Procapsid of bacteriophage lambda
    • Protein or peptide: Major Capsid Protein

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Supramolecule #1: Procapsid of bacteriophage lambda

SupramoleculeName: Procapsid of bacteriophage lambda / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia virus Lambda

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Macromolecule #1: Major Capsid Protein

MacromoleculeName: Major Capsid Protein / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
SequenceString: MSMYTTAQLL AANEQKFKFD PLFLRLFFRE SYPFTTEKVY LSQIPGLVNM ALYVSPIVSG EVIRSRGGS TSEFTPGYVK PKHEVNPQMT LRRLPDEDPQ NLADPAYRRR RIIMQNMRDE E LAIAQVEE MQAVSAVLKG KYTMTGEAFD PVEVDMGRSE ENNITQSGGT ...String:
MSMYTTAQLL AANEQKFKFD PLFLRLFFRE SYPFTTEKVY LSQIPGLVNM ALYVSPIVSG EVIRSRGGS TSEFTPGYVK PKHEVNPQMT LRRLPDEDPQ NLADPAYRRR RIIMQNMRDE E LAIAQVEE MQAVSAVLKG KYTMTGEAFD PVEVDMGRSE ENNITQSGGT EWSKRDKSTY DP TDDIEAY ALNASGVVNI IVFDPKGWAL FRSFKAVKEK LDTRRGSNSE LETAVKDLGK AVS YKGMYG DVAIVVYSGQ YVENGVKKNF LPDNTMVLGN TQARGLRTYG CIQDADAQRE GINA SARYP KNWVTTGDPA REFTMIQSAP LMLLADPDEF VSVQLA

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 2200FS
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1253
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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