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- EMDB-65859: Open state of A8 gpJ 713 central tail fiber with OmpC G17 from E.... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-65859
TitleOpen state of A8 gpJ 713 central tail fiber with OmpC G17 from E. coli EDL933
Map data
Sample
  • Complex: Closed state of central tail fiber of bacteriophage lambda A8
    • Protein or peptide: A8 gpJ 713
    • Protein or peptide: Outer membrane porin C
KeywordsPhage Tail / VIRAL PROTEIN
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
Outer membrane porin C
Similarity search - Component
Biological speciesLambdavirus / Escherichia phage Lambda (virus) / Escherichia coli O157:H7 str. EDL933 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsDeng TY / Ge XF / Wang JW
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254, 32171190 China
CitationJournal: To Be Published
Title: Closed state of A8 gpJ 713 central tail fiber
Authors: Deng TY / Ge XF / Wang JW
History
DepositionAug 16, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65859.png

Downloads & links

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Map

FileDownload / File: emd_65859.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.463
Minimum - Maximum-1.7281213 - 2.819902
Average (Standard dev.)0.0021999015 (±0.054192577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65859_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65859_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Closed state of central tail fiber of bacteriophage lambda A8

EntireName: Closed state of central tail fiber of bacteriophage lambda A8
Components
  • Complex: Closed state of central tail fiber of bacteriophage lambda A8
    • Protein or peptide: A8 gpJ 713
    • Protein or peptide: Outer membrane porin C

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Supramolecule #1: Closed state of central tail fiber of bacteriophage lambda A8

SupramoleculeName: Closed state of central tail fiber of bacteriophage lambda A8
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Lambdavirus

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Macromolecule #1: A8 gpJ 713

MacromoleculeName: A8 gpJ 713 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 47.315691 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: HHHHHHHHAP AAPSRIELTP GYFQITATPH LAVYDPTVQF EFWFSEKQIA DIRQVETSTR YLGTALYWIA ASINIKPGHD YYFYIRSVN TVGKSAFVEA VGRASDDAEG YLDFFKGKIT ESHLGKELLE KVELTEDNAS RLEEFSKEWK DASDKWNAMW A VKIEQTKD ...String:
HHHHHHHHAP AAPSRIELTP GYFQITATPH LAVYDPTVQF EFWFSEKQIA DIRQVETSTR YLGTALYWIA ASINIKPGHD YYFYIRSVN TVGKSAFVEA VGRASDDAEG YLDFFKGKIT ESHLGKELLE KVELTEDNAS RLEEFSKEWK DASDKWNAMW A VKIEQTKD GKHYVAGIGL SMEDTEEGKL SQFLVAANRI AFIDPANGNE TPMFVAQGNQ IFMNDVFLKR LTAPTITSGG NP PAFSLTP DGKLTAKNAD ISGSVNANSG TLNNVTINEN CQIKGKLSAN QIEGDIVKTV SKSFPRTNSY ASGTITVRIS DDQ KFDRQV MIPPVLFRGG KHENFNSNNQ QSYWYSTCRL RVTRNGQEIF NQSTTDAQGV FSSVIDMPAG QGTLTLTFTV SSSG ANNWT PTTSISDLLV VVMKKSTAGI SIS

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Macromolecule #2: Outer membrane porin C

MacromoleculeName: Outer membrane porin C / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O157:H7 str. EDL933 (bacteria)
Molecular weightTheoretical: 38.476484 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AEVYNKDGNK LDLYGKVDGL HYFSDDKSVD GDQTYMRLGF KGETQVTDQL TGYGQWEYQI QGNSAENENN SWTRVAFAGL KFQDVGSFD YGRNYGVVYD VTSWTDVLPE FGGDTYGSDN FMQQRGNGFA TYRNTDFFGL VDGLNFAVQY QGKNGSVSGE G MTNNGREA ...String:
AEVYNKDGNK LDLYGKVDGL HYFSDDKSVD GDQTYMRLGF KGETQVTDQL TGYGQWEYQI QGNSAENENN SWTRVAFAGL KFQDVGSFD YGRNYGVVYD VTSWTDVLPE FGGDTYGSDN FMQQRGNGFA TYRNTDFFGL VDGLNFAVQY QGKNGSVSGE G MTNNGREA LRQNGDGVGG SITYDYEGFG IGAAVSSSKR TDDQNSPLYI GNGDRAETYT GGLKYDANNI YLAAQYTQTY NA TRVGSLG WANKAQNFEA VAQYQFDFGL RPSLAYLQSK GKNLGVINGR NYDDEDILKY VDVGATYYFN KNMSTYVDYK INL LDDNQF TRDAGINTDN IVALGLVYQF

UniProtKB: Outer membrane porin C

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 168284
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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