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- EMDB-8064: In vitro assembled star-shaped hubless T4 baseplate -

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Basic information

Entry
Database: EMDB / ID: EMD-8064
TitleIn vitro assembled star-shaped hubless T4 baseplate
Map dataNone
Sample
  • Complex: In vitro assembled hubless T4 baseplate
    • Protein or peptide: Baseplate wedge protein gp7
    • Protein or peptide: Baseplate wedge protein gp8
    • Protein or peptide: Baseplate wedge protein gp6
    • Protein or peptide: Baseplate wedge protein gp53
    • Protein or peptide: Baseplate wedge protein gp10
KeywordsT4 / baseplate / complex / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / viral release from host cell / identical protein binding
Similarity search - Function
Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Baseplate wedge protein gp10 ...Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Baseplate wedge protein gp10 / Baseplate wedge protein gp6 / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Baseplate wedge protein gp10 / Baseplate wedge protein gp53 / Baseplate wedge protein gp6 / Baseplate wedge protein gp7 / Baseplate wedge protein gp8
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYap ML / Klose T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Role of bacteriophage T4 baseplate in regulating assembly and infection.
Authors: Moh Lan Yap / Thomas Klose / Fumio Arisaka / Jeffrey A Speir / David Veesler / Andrei Fokine / Michael G Rossmann /
Abstract: Bacteriophage T4 consists of a head for protecting its genome and a sheathed tail for inserting its genome into a host. The tail terminates with a multiprotein baseplate that changes its conformation ...Bacteriophage T4 consists of a head for protecting its genome and a sheathed tail for inserting its genome into a host. The tail terminates with a multiprotein baseplate that changes its conformation from a "high-energy" dome-shaped to a "low-energy" star-shaped structure during infection. Although these two structures represent different minima in the total energy landscape of the baseplate assembly, as the dome-shaped structure readily changes to the star-shaped structure when the virus infects a host bacterium, the dome-shaped structure must have more energy than the star-shaped structure. Here we describe the electron microscopy structure of a 3.3-MDa in vitro-assembled star-shaped baseplate with a resolution of 3.8 Å. This structure, together with other genetic and structural data, shows why the high-energy baseplate is formed in the presence of the central hub and how the baseplate changes to the low-energy structure, via two steps during infection. Thus, the presence of the central hub is required to initiate the assembly of metastable, high-energy structures. If the high-energy structure is formed and stabilized faster than the low-energy structure, there will be insufficient components to assemble the low-energy structure.
History
DepositionFeb 23, 2016-
Header (metadata) releaseMar 2, 2016-
Map releaseMar 2, 2016-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5hx2
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5hx2
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8064.png

Downloads & links

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Map

FileDownload / File: emd_8064.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 640 pix.
= 832. Å		1.3 Å/pix.
x 640 pix.
= 832. Å		1.3 Å/pix.
x 640 pix.
= 832. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.38871998 - 0.60327184
Average (Standard dev.)0.00004162967 (±0.0113522485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 832.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z832.000832.000832.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS640640640
D min/max/mean-0.3890.6030.000

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Supplemental data

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Sample components

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Entire : In vitro assembled hubless T4 baseplate

EntireName: In vitro assembled hubless T4 baseplate
Components
  • Complex: In vitro assembled hubless T4 baseplate
    • Protein or peptide: Baseplate wedge protein gp7
    • Protein or peptide: Baseplate wedge protein gp8
    • Protein or peptide: Baseplate wedge protein gp6
    • Protein or peptide: Baseplate wedge protein gp53
    • Protein or peptide: Baseplate wedge protein gp10

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Supramolecule #1: In vitro assembled hubless T4 baseplate

SupramoleculeName: In vitro assembled hubless T4 baseplate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 3.3 MDa

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Macromolecule #1: Baseplate wedge protein gp7

MacromoleculeName: Baseplate wedge protein gp7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 119.336516 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTVKAPSVTS LRISKLSANQ VQVRWDDVGA NFYYFVEIAE TKTNSGENLP SNQYRWINLG YTANNSFFFD DADPLTTYII RVATAAQDF EQSDWIYTEE FETFATNAYT FQNMIEMQLA NKFIQEKFTL NNSDYVNFNN DTIMAALMNE SFQFSPSYVD V SSISNFII ...String:
MTVKAPSVTS LRISKLSANQ VQVRWDDVGA NFYYFVEIAE TKTNSGENLP SNQYRWINLG YTANNSFFFD DADPLTTYII RVATAAQDF EQSDWIYTEE FETFATNAYT FQNMIEMQLA NKFIQEKFTL NNSDYVNFNN DTIMAALMNE SFQFSPSYVD V SSISNFII GENEYHEIQG SIQQVCKDIN RVYLMESEGI LYLFERYQPV VKVSNDKGQT WKAVKLFNDR VGYPLSKTVY YQ SANTTYV LGYDKIFYGR KSTDVRWSAD DVRFSSQDIT FAKLGDQLHL GFDVEIFATY ATLPANVYRI AEAITCTDDY IYV VARDKV RYIKTSNALI DFDPLSPTYS ERLFEPDTMT ITGNPKAVCY KMDSICDKVF ALIIGEVETL NANPRTSKII DSAD KGIYV LNHDEKTWKR VFGNTEEERR RIQPGYANMS TDGKLVSLSS SNFKFLSDNV VNDPETAAKY QLIGAVKYEF PREWL ADKH YHMMAFIADE TSDWETFTPQ PMKYYAEPFF NWSKKSNTRC WINNSDRAVV VYADLKYTKV IENIPETSPD RLVHEY WDD GDCTIVMPNV KFTGFKKYAS GMLFYKASGE IISYYDFNYR VRDTVEIIWK PTEVFLKAFL QNQEHETPWS PEEERGL AD PDLRPLIGTM MPDSYLLQDS NFEAFCEAYI QYLSDGYGTQ YNNLRNLIRN QYPREEHAWE YLWSEIYKRN IYLNADKR D AVARFFESRS YDFYSTKGIE ASYKFLFKVL YNEEVEIEIE SGAGTEYDII VQSDSLTEDL VGQTIYTATG RCNVTYIER SYSNGKLQWT VTIHNLLGRL IAGQEVKAER LPSFEGEIIR GVKGKDLLQN NIDYINRSRS YYVMKIKSNL PSSRWKSDVI RFVHPVGFG FIAITLLTMF INVGLTLKHT ETIINKYKNY KWDSGLPTEY ADRIAKLTPT GEIEHDSVTG EAIYEPGPMA G VKYPLPDD YNAENNNSIF QGQLPSERRK LMSPLFDASG TTFAQFRDLV NKRLKDNIGN PRDPENPTQV KIDE

UniProtKB: Baseplate wedge protein gp7

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Macromolecule #2: Baseplate wedge protein gp8

MacromoleculeName: Baseplate wedge protein gp8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 38.041668 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNDSSVIYRA IVTSKFRTEK MLNFYNSIGS GPDKNTIFIT FGRSEPWSSN ENEVGFAPPY PTDSVLGVTD MWTHMMGTVK VLPSMLDAV IPRRDWGDTR YPDPYTFRIN DIVVCNSAPY NATESGAGWL VYRCLDVPDT GMCSIASLTD KDECLKLGGK W TPSARSMT ...String:
MNDSSVIYRA IVTSKFRTEK MLNFYNSIGS GPDKNTIFIT FGRSEPWSSN ENEVGFAPPY PTDSVLGVTD MWTHMMGTVK VLPSMLDAV IPRRDWGDTR YPDPYTFRIN DIVVCNSAPY NATESGAGWL VYRCLDVPDT GMCSIASLTD KDECLKLGGK W TPSARSMT PPEGRGDAEG TIEPGDGYVW EYLFEIPPDV SINRCTNEYI VVPWPEELKE DPTRWGYEDN LTWQQDDFGL IY RVKANTI RFKAYLDSVY FPEAALPGNK GFRQISIITN PLEAKAHPND PNVKAEKDYY DPEDLMRHSG EMIYMENRPP IIM AMDQTE EINILFTF

UniProtKB: Baseplate wedge protein gp8

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Macromolecule #3: Baseplate wedge protein gp6

MacromoleculeName: Baseplate wedge protein gp6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 74.492641 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MANTPVNYQL TRTANAIPEI FVGGTFAEIK QNLIEWLNGQ NEFLDYDFEG SRLNVLCDLL AYNTLYIQQF GNAAVYESFM RTANLRSSV VQAAQDNGYL PTSKSAAQTE IMLTCTDALN RNYITIPRGT RFLAYAKDTS VNPYNFVSRE DVIAIRDKNN Q YFPRLKLA ...String:
MANTPVNYQL TRTANAIPEI FVGGTFAEIK QNLIEWLNGQ NEFLDYDFEG SRLNVLCDLL AYNTLYIQQF GNAAVYESFM RTANLRSSV VQAAQDNGYL PTSKSAAQTE IMLTCTDALN RNYITIPRGT RFLAYAKDTS VNPYNFVSRE DVIAIRDKNN Q YFPRLKLA QGRIVRTEII YDKLTPIIIY DKNIDRNQVK LYVDGAEWIN WTRKSMVHAG STSTIYYMRE TIDGNTEFYF GE GEISVNA SEGALTANYI GGLKPTQNST IVIEYISTNG ADANGAVGFS YADTLTNITV ININENPNDD PDFVGADGGG DPE DIERIR ELGTIKRETQ QRCVTATDYD TFVSERFGSI IQAVQTFTDS TKPGYAFIAA KPKSGLYLTT VQREDIKNYL KDYN LAPIT PSIISPNYLF IKTNLKVTYA LNKLQESEQW LEGQIIDKID RYYTEDVEIF NSSFAKSKML TYVDDADHSV IGSSA TIQM VREVQNFYKT PEAGIKYNNQ IKDRSMESNT FSFNSGRKVV NPDTGLEEDV LYDVRIVSTD RDSKGIGKVI IGPFAS GDV TENENIQPYT GNDFNKLANS DGRDKYYVIG EINYPADVIY WNIAKINLTS EKFEVQTIEL YSDPTDDVIF TRDGSLI VF ENDLRPQYLT IDLEPISQ

UniProtKB: Baseplate wedge protein gp6

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Macromolecule #4: Baseplate wedge protein gp53

MacromoleculeName: Baseplate wedge protein gp53 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 22.990885 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLFTFFDPIE YAAKTVNKNA PTIPMTDIFR NYKDYFKRAL AGYRLRTYYI KGSPRPEELA NAIYGNPQLY WVLLMCNDNY DPYYGWITS QEAAYQASIQ KYKNVGGDQI VYHVNENGEK FYNLISYDDN PYVWYDKGDK ARKYPQYEGA LAAVDTYEAA V LENEKLRQ ...String:
MLFTFFDPIE YAAKTVNKNA PTIPMTDIFR NYKDYFKRAL AGYRLRTYYI KGSPRPEELA NAIYGNPQLY WVLLMCNDNY DPYYGWITS QEAAYQASIQ KYKNVGGDQI VYHVNENGEK FYNLISYDDN PYVWYDKGDK ARKYPQYEGA LAAVDTYEAA V LENEKLRQ IKIIAKSDIN SFMNDLIRIM EKSYGNDK

UniProtKB: Baseplate wedge protein gp53

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Macromolecule #5: Baseplate wedge protein gp10

MacromoleculeName: Baseplate wedge protein gp10 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 66.28168 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKQNINIGNV VDDGTGDYLR KGGIKINENF DELYYELGDG DVPYSAGAWK TYNASSGQTL TAEWGKSYAI NTSSGRVTIN LPKGTVNDY NKVIRARDVF ATWNVNPVTL VAASGDTIKG SAVPVEINVR FSDLELVYCA PGRWEYVKNK QIDKITSSDI S NVARKEFL ...String:
MKQNINIGNV VDDGTGDYLR KGGIKINENF DELYYELGDG DVPYSAGAWK TYNASSGQTL TAEWGKSYAI NTSSGRVTIN LPKGTVNDY NKVIRARDVF ATWNVNPVTL VAASGDTIKG SAVPVEINVR FSDLELVYCA PGRWEYVKNK QIDKITSSDI S NVARKEFL VEVQGQTDFL DVFRGTSYNV NNIRVKHRGN ELYYGDVFSE NSDFGSPGEN EGELVPLDGF NIRLRQPCNI GD TVQIETF MDGVSQWRSS YTRRQIRLLD SKLTSKTSLE GSIYVTDLST MKSIPFSAFG LIPGEPINPN SLEVRFNGIL QEL AGTVGM PLFHCVGADS DDEVECSVLG GTWEQSHTDY SVETDENGIP EILHFDSVFE HGDIINITWF NNDLGTLLTK DEII DETDN LYVSQGPGVD ISGDVNLTDF DKIGWPNVEA VQSYQRAFNA VSNIFDTIYP IGTIYENAVN PNNPVTYMGF GSWKL FGQG KVLVGWNEDI SDPNFALNNN DLDSGGNPSH TAGGTGGSTS VTLENANLPA TETDEEVLIV DENGSVIVGG CQYDPD ESG PIYTKYREAK ASTNSTHTPP TSITNIQPYI TVYRWIRIA

UniProtKB: Baseplate wedge protein gp10

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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

Concentration2 mg/mL
BufferpH: 8
GridModel: CF-1.2/1.3-4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Details: 400-mesh copper CF-1.2/1.3-4C
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: GATAN CRYOPLUNGE 3 / Details: Plunged into liquid ethane (GATAN CRYOPLUNGE 3)..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.74 µm / Calibrated defocus min: 0.4 µm / Calibrated magnification: 38168 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 3-38 / Number grids imaged: 2 / Number real images: 1725 / Average exposure time: 7.6 sec. / Average electron dose: 35.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 69920
Startup modelType of model: OTHER
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final 3D classificationSoftware - Name: RELION (ver. 1.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 45607
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3h2t

source_name: PDB, initial_model_type: experimental model

1n80

source_name: PDB, initial_model_type: experimental model

2fkk

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-5hx2:
In vitro assembled star-shaped hubless T4 baseplate

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