[English] 日本語
Yorodumi
- PDB-6tjp: Crystal structure of T7 bacteriophage portal protein, 13mer, clos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tjp
TitleCrystal structure of T7 bacteriophage portal protein, 13mer, closed valve - P212121
ComponentsPortal protein
KeywordsVIRAL PROTEIN / DNA packaging
Function / homologyPortal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / Portal protein
Function and homology information
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.74 Å
AuthorsFabrega-Ferrer, M. / Cuervo, A. / Fernandez, F.J. / Machon, C. / Perez-Luque, R. / Pous, J. / Vega, M.C. / Carrascosa, J.L. / Coll, M.
Funding support Spain, 7items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU 2014-54181 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2014-53550-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-83720-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesMDM-2014-0435 Spain
Spanish Ministry of Science, Innovation, and UniversitiesSEV-2013-0347 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2011-09071 Spain
European Commission653706
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure.
Authors: Fabrega-Ferrer, M. / Cuervo, A. / Fernandez, F.J. / Machon, C. / Perez-Luque, R. / Pous, J. / Vega, M.C. / Carrascosa, J.L. / Coll, M.
#1: Journal: Nat Commun / Year: 2019
Title: Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism.
Authors: Ana Cuervo / Montserrat Fàbrega-Ferrer / Cristina Machón / José Javier Conesa / Francisco J Fernández / Rosa Pérez-Luque / Mar Pérez-Ruiz / Joan Pous / M Cristina Vega / José L Carrascosa / Miquel Coll /
Abstract: Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been ...Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been packaged, the tail components assemble on the portal to render the mature infective virion. The tail tightly seals the ejection conduit until infection, when its interaction with the host membrane triggers the opening of the channel and the viral genome is delivered to the host cell. Using high-resolution cryo-electron microscopy and X-ray crystallography, here we describe various structures of the T7 bacteriophage portal and fiber-less tail complex, which suggest a possible mechanism for DNA retention and ejection: a portal closed conformation temporarily retains the genome before the tail is assembled, whereas an open portal is found in the tail. Moreover, a fold including a seven-bladed β-propeller domain is described for the nozzle tail protein.
History
DepositionNov 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.citation_id / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein
M: Portal protein


Theoretical massNumber of molelcules
Total (without water)769,26213
Polymers769,26213
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area132260 Å2
ΔGint-702 kcal/mol
Surface area219730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.850, 238.570, 265.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A3 - 47
121chain 'A'A55 - 480
231chain 'B'B3 - 47
241chain 'B'B55 - 480
351chain 'C'C3 - 47
361chain 'C'C55 - 480
471chain 'D'D3 - 47
481chain 'D'D55 - 480
591chain 'E'E3 - 47
5101chain 'E'E55 - 480
6111chain 'F'F3 - 47
6121chain 'F'F55 - 480
7131chain 'G'G3 - 47
7141chain 'G'G55 - 480
8151chain 'H'H3 - 47
8161chain 'H'H55 - 480
9171chain 'I'I3 - 47
9181chain 'I'I55 - 480
10191chain 'J'J3 - 47
10201chain 'J'J55 - 480
11211chain 'K'K3 - 47
11221chain 'K'K55 - 480
12231chain 'L'L3 - 47
12241chain 'L'L55 - 480
13251chain 'M'M3 - 47
13261chain 'M'M55 - 480

-
Components

#1: Protein
Portal protein / Gene product 8 / Gp8 / Head-to-tail connector


Mass: 59173.984 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P03728

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M CaCl2, 0.1 M HEPES pH 7.5 and 18 % [w/v] PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 5, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.74→49.47 Å / Num. obs: 78414 / % possible obs: 88.61 % / Redundancy: 3.5 % / Biso Wilson estimate: 130.76 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.8
Reflection shellResolution: 3.74→3.87 Å / Num. unique obs: 7216 / CC1/2: 0.558

-
Processing

Software
NameVersionClassification
REFMAC5.5refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Partial cryo-EM model

Resolution: 3.74→49.47 Å / SU ML: 0.5614 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1603
RfactorNum. reflection% reflection
Rfree0.2857 3915 5 %
Rwork0.2439 --
obs0.246 78301 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 151.9 Å2
Refinement stepCycle: LAST / Resolution: 3.74→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48126 0 0 0 48126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003348880
X-RAY DIFFRACTIONf_angle_d0.685266157
X-RAY DIFFRACTIONf_chiral_restr0.04317501
X-RAY DIFFRACTIONf_plane_restr0.00438671
X-RAY DIFFRACTIONf_dihedral_angle_d9.60926773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.74-3.780.38461080.42162051X-RAY DIFFRACTION77.52
3.78-3.830.37941400.35162653X-RAY DIFFRACTION99.82
3.83-3.880.34581410.35512673X-RAY DIFFRACTION99.54
3.88-3.940.40291390.34512647X-RAY DIFFRACTION99.61
3.94-3.990.31351410.32962676X-RAY DIFFRACTION99.58
3.99-4.050.36271390.33332626X-RAY DIFFRACTION99.5
4.05-4.110.35651400.33352671X-RAY DIFFRACTION99.96
4.11-4.180.34561390.31042643X-RAY DIFFRACTION99.39
4.18-4.250.33211400.29942664X-RAY DIFFRACTION99.72
4.25-4.330.34441390.30822657X-RAY DIFFRACTION99.47
4.33-4.410.371410.29062658X-RAY DIFFRACTION99.68
4.41-4.50.3081390.26012652X-RAY DIFFRACTION99.39
4.5-4.60.2681420.25612693X-RAY DIFFRACTION99.61
4.6-4.710.27681390.25672645X-RAY DIFFRACTION99.5
4.71-4.830.26141410.24092679X-RAY DIFFRACTION99.23
4.83-4.960.29141410.23172680X-RAY DIFFRACTION99.75
4.96-5.10.29631390.23062636X-RAY DIFFRACTION99.14
5.1-5.270.32021410.24372677X-RAY DIFFRACTION99.3
5.27-5.460.25811420.2362696X-RAY DIFFRACTION99.27
5.46-5.670.32931410.26512689X-RAY DIFFRACTION99.75
5.67-5.930.28111410.24932665X-RAY DIFFRACTION99.22
5.93-6.240.29251410.26032679X-RAY DIFFRACTION99.16
6.24-6.630.27171420.24952707X-RAY DIFFRACTION98.99
6.63-7.140.28221410.2332682X-RAY DIFFRACTION98.91
7.15-7.860.26181440.2022725X-RAY DIFFRACTION99.2
7.86-8.990.22631420.17992710X-RAY DIFFRACTION98.72
8.99-11.310.2141450.15522737X-RAY DIFFRACTION98.33
11.31-49.470.27161470.21962815X-RAY DIFFRACTION96.39

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more