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- EMDB-18518: Asymmetric structure of the Borrelia bacteriophage BB1 procapsid,... -

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Basic information

Entry
Database: EMDB / ID: EMD-18518
TitleAsymmetric structure of the Borrelia bacteriophage BB1 procapsid, 3D class 2
Map data
Sample
  • Complex: Procapsid of Borrelia bacteriophage BB1
    • Protein or peptide: Cytosolic proteinCytosol
    • Protein or peptide: Decoration protein P03
    • Protein or peptide: Decoration protein P04
    • Protein or peptide: DUF228 domain-containing protein
    • Protein or peptide: Scaffold protein
    • Protein or peptide: Putative phage portal protein
KeywordsPortal / capsid / procapsid / scaffold / VIRAL PROTEIN
Function / homology
Function and homology information


Protein of unknown function DUF228 / Lyme disease proteins of unknown function / Uncharacterised conserved protein UCP020357 / Protein of unknown function DUF1073 / Anti-CBASS protein Acb1-like / Protein of unknown function DUF1357 / Protein of unknown function (DUF1357)
Similarity search - Domain/homology
DUF228 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Phage portal protein / Cytosolic protein
Similarity search - Component
Biological speciesBorreliella burgdorferi B31 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.62 Å
AuthorsRumnieks J / Fuzik T / Tars K
Funding supportEuropean Union, 3 items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.2/VIAA/4/20/704European Union
iNEXT-Discovery18826European Union
iNEXT-Discovery24421European Union
CitationJournal: J Mol Biol / Year: 2023
Title: Structure of the Borrelia Bacteriophage φBB1 Procapsid.
Authors: Jānis Rūmnieks / Tibor Füzik / Kaspars Tārs /
Abstract: Bacteriophages of Borrelia burgdorferi are a biologically important but under-investigated feature of the Lyme disease-causing spirochete. No virulent borrelial viruses have been identified, but all ...Bacteriophages of Borrelia burgdorferi are a biologically important but under-investigated feature of the Lyme disease-causing spirochete. No virulent borrelial viruses have been identified, but all B. burgdorferi isolates carry a prophage φBB1 as resident circular plasmids. Like its host, the φBB1 phage is quite distinctive and shares little sequence similarity with other known bacteriophages. We expressed φBB1 head morphogenesis proteins in Escherichia coli which resulted in assembly of homogeneous prolate procapsid structures and used cryo-electron microscopy to determine the three-dimensional structure of these particles. The φBB1 procapsids consist of 415 copies of the major capsid protein and an equal combined number of three homologous capsid decoration proteins that form trimeric knobs on the outside of the particle. One of the end vertices of the particle is occupied by a portal assembled from twelve copies of the portal protein. The φBB1 scaffolding protein is entirely α-helical and has an elongated shape with a small globular domain in the middle. Within the tubular section of the procapsid, the internal scaffold is built of stacked rings, each composed of 32 scaffolding protein molecules, which run in opposite directions from both caps with a heterogeneous part in the middle. Inside the portal-containing cap, the scaffold is organized asymmetrically with ten scaffolding protein molecules bound to the portal. The φBB1 procapsid structure provides better insight into the vast structural diversity of bacteriophages and presents clues of how elongated bacteriophage particles might be assembled.
History
DepositionSep 27, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18518.png

Downloads & links

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Map

FileDownload / File: emd_18518.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.6672 Å
Density
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.020578962 - 0.04726299
Average (Standard dev.)0.0003765729 (±0.002417489)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 1200.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18518_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18518_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_18518_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 : Procapsid of Borrelia bacteriophage BB1

EntireName: Procapsid of Borrelia bacteriophage BB1
Components
  • Complex: Procapsid of Borrelia bacteriophage BB1
    • Protein or peptide: Cytosolic proteinCytosol
    • Protein or peptide: Decoration protein P03
    • Protein or peptide: Decoration protein P04
    • Protein or peptide: DUF228 domain-containing protein
    • Protein or peptide: Scaffold protein
    • Protein or peptide: Putative phage portal protein

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Supramolecule #1: Procapsid of Borrelia bacteriophage BB1

SupramoleculeName: Procapsid of Borrelia bacteriophage BB1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)

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Macromolecule #1: Cytosolic protein

MacromoleculeName: Cytosolic protein / type: protein_or_peptide / ID: 1 / Number of copies: 415 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 36.255551 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MELFDENYYA KAVANIIGEV KDPIMYKWFS PDQIEDVDLQ MGYQKTVKWD AFLNANPTTI ANEVNTISTI GFSSEVVRLN YLKLQYKFR HLKQTSEKFY TSDSYIGDIN NNLLPFAQAY KLASSEIIKL INHFVLTGTV SIQKDGKNQK RLLPNMYGLL N MPEQIKEE ...String:
MELFDENYYA KAVANIIGEV KDPIMYKWFS PDQIEDVDLQ MGYQKTVKWD AFLNANPTTI ANEVNTISTI GFSSEVVRLN YLKLQYKFR HLKQTSEKFY TSDSYIGDIN NNLLPFAQAY KLASSEIIKL INHFVLTGTV SIQKDGKNQK RLLPNMYGLL N MPEQIKEE VASGDKDKMD KIFEKIEAGL SKLELGDEFS TPMMVIVDPA TSLKLVKPYA AAQGAASSCE KWEDVLIQTI KA INNREDV YIETSNLLKH KILIYPLNSE LIKFKPSKYM LPTPNEQVDK DSTDVAHSYI DFVLGGLLAT RKTILQVNIK QS

UniProtKB: Cytosolic protein

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Macromolecule #2: Decoration protein P03

MacromoleculeName: Decoration protein P03 / type: protein_or_peptide / ID: 2 / Number of copies: 280 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 20.026479 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSDITKIKQE FDKKVAEIQA LMKNPQQDSG LLSNSIDFRD QNLIFSNSGG VCTSSKDKIE NYPAKGYPYK RGVKLSFGDG TTELEVEAG GGDDLYGVCS DIDEFSGMAT VIPITNNFTG YLTLKKDGQN GVNPGDKLNF NQHGELEKVT GAQKSVNAIA L SKAHKLTE DLFIVLASVF GNRAIKG

UniProtKB: Uncharacterized protein

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Macromolecule #3: Decoration protein P04

MacromoleculeName: Decoration protein P04 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 28.067344 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MALKGNMQVE NLEAVEDPQV DLGAQVSAAP RAKRQARQAE DVQGEDPYLE SISELDDVLL KFKKYSKSMS SIENKVFSSS SGCFKSKNE RVDAYSFACS SYTDKIEEYL YDPANSFPYK RGVKLVPKEN SIYVEVGADT DMYGICVDVC EFSCTAYVLP I TNNFEGYL ...String:
MALKGNMQVE NLEAVEDPQV DLGAQVSAAP RAKRQARQAE DVQGEDPYLE SISELDDVLL KFKKYSKSMS SIENKVFSSS SGCFKSKNE RVDAYSFACS SYTDKIEEYL YDPANSFPYK RGVKLVPKEN SIYVEVGADT DMYGICVDVC EFSCTAYVLP I TNNFEGYL VTRNPSIKIG EILDINNNGV IIKAGGGPPT AINIYALSDS FTINFAPEDG NQDQNRYPRQ EYSINLIKVA IF GNRGLEK TVNPDGG

UniProtKB: Uncharacterized protein

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Macromolecule #4: DUF228 domain-containing protein

MacromoleculeName: DUF228 domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 130 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 21.274934 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MGDTTQLVKE YQEKRSKLEK FMKNPQHDAS LLSNSNEFRD KNVEFFASGG TRTSKFDKLE NHPFLGYPYK RGVKRVIQEA QDNQSHYEP HVEAGGGEDL YGICIDIDEF SKTATIVPIT NNFEGYLVAK DSTVKVKDKL IFNKDGALEK VTGAPNKATI N ATALTDAK QISNEVYLVK VAVFGNKAMS RN

UniProtKB: DUF228 domain-containing protein

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Macromolecule #5: Scaffold protein

MacromoleculeName: Scaffold protein / type: protein_or_peptide / ID: 5 / Number of copies: 826 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 26.710363 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MTEKEEKEDL QAQDKEEQQI KADTKVISVQ EFEEYMRFKE QANSKSKETS RDLSINERIT KELAEVEERE RIEKQLLLEA ERINEIDTL AKAHLSNHFN KEVLLAKGYT LKDIMQAQRR ELVRKFVPIE QIKAIAKVSD ISHIDGEILE QLVSLAKVNI K LRKNASSS ...String:
MTEKEEKEDL QAQDKEEQQI KADTKVISVQ EFEEYMRFKE QANSKSKETS RDLSINERIT KELAEVEERE RIEKQLLLEA ERINEIDTL AKAHLSNHFN KEVLLAKGYT LKDIMQAQRR ELVRKFVPIE QIKAIAKVSD ISHIDGEILE QLVSLAKVNI K LRKNASSS SSSVDSIKGN IAIKSEERAS LLDSNFVPIN FTEFVQAISN TYKQRRIQFY ENLKRHKRTS IA

UniProtKB: Uncharacterized protein

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Macromolecule #6: Putative phage portal protein

MacromoleculeName: Putative phage portal protein / type: protein_or_peptide / ID: 6 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 47.095508 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MCDLRKTKLI DKISSLELYK YSIFFRNYIE NVAEDCLKNG LILESAAHNV SEVELARLKV QLKNALLNCI ISYRFHGIGY VLVKTKDTL IDLEQPVNIE LPIGFEYLDY EYVRDLGVDF DHITYKVKSN NKNNSLDAVK IHKSRLIIYE NFDYILKRYV P CYTESFLL ...String:
MCDLRKTKLI DKISSLELYK YSIFFRNYIE NVAEDCLKNG LILESAAHNV SEVELARLKV QLKNALLNCI ISYRFHGIGY VLVKTKDTL IDLEQPVNIE LPIGFEYLDY EYVRDLGVDF DHITYKVKSN NKNNSLDAVK IHKSRLIIYE NFDYILKRYV P CYTESFLL DIYLFEKIYV EIERRIENHN FLFYKDESLV QLQDALSSAT TSLSALTQSN NDRGSGILSS FLRKQNSNNH SK DISNLRN LNDSLSQELA RLKSNLNNEG MFYTATPSAS LEVIKYDLSY LKEALALIKA KIGADTKEPL TRSFNEQAKG LGN DGKGDR SNYYDFLKGV QEQVENSCNL KLTKYFGLDM KFNSLIMLSE EQKVERDIKL IELYSKYNQL IQSSSFNNEE LAML KEKLF SF

UniProtKB: Phage portal 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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris-HClTris
100.0 mMsodium chlorideNaClSodium chloride
10.0 mMmagnesium sulfateMgSO4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: GIF Bioquantum
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 44.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: low-pass filtered previous reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1.3) / Details: Entry represents 3D class 2 (21.2 % of particles)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3)
Details: Half-maps for the 3D class were reconstructed with relion_reconstruct using the --class and --subset options. The actual particle distribution between the two subsets were 0.528 : 0.472.
Number images used: 5505
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: previous reconstruction
Output model

PDB-8qo0:
Asymmetric structure of the Borrelia bacteriophage BB1 procapsid, 3D class 2

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