[English] 日本語
Yorodumi
- PDB-4v96: The structure of a 1.8 MDa viral genome injection device suggests... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v96
TitleThe structure of a 1.8 MDa viral genome injection device suggests alternative infection mechanisms
Components
  • BPP
  • ORF46
  • ORF48
KeywordsVIRAL PROTEIN / Distal tail protein / Receptor-binding protein / Phage baseplate / host adsorption apparatus / genome injection device
Function / homology
Function and homology information


virus tail, baseplate / cell adhesion / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Distal tail protein, N-terminal / Baseplate upper protein, immunoglobulin like domain / Baseplate upper protein immunoglobulin like domain / BppU, N-terminal / Phage tail protein RIFT-related domain / BppU N-terminal domain / Lower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
Biological speciesLactococcus phage TP901-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.8 Å
AuthorsVeesler, D. / Spinelli, S. / Mahony, J. / Lichiere, J. / Blangy, S. / Bricogne, G. / Legrand, P. / Ortiz-Lombardia, M. / Campanacci, V. / van Sinderen, D. / Cambillau, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the phage TP901-1 1.8 MDa baseplate suggests an alternative host adhesion mechanism.
Authors: Veesler, D. / Spinelli, S. / Mahony, J. / Lichiere, J. / Blangy, S. / Bricogne, G. / Legrand, P. / Ortiz-Lombardia, M. / Campanacci, V. / van Sinderen, D. / Cambillau, C.
History
DepositionFeb 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4DIV, 4DIW
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: ORF48
AB: ORF48
AC: ORF48
AD: ORF48
AE: ORF48
AF: ORF48
AG: ORF48
AH: ORF48
AI: ORF48
AJ: ORF48
AK: ORF48
AL: ORF48
AM: ORF48
AN: ORF48
AO: ORF48
AP: ORF48
AQ: ORF48
AR: ORF48
AS: ORF46
AT: ORF46
AU: ORF46
AV: ORF46
AW: ORF46
AX: ORF46
BA: BPP
BB: BPP
BC: BPP
BD: BPP
BE: BPP
BF: BPP
BG: BPP
BH: BPP
BI: BPP
BJ: BPP
BK: BPP
BL: BPP
BM: BPP
BN: BPP
BO: BPP
BP: BPP
BQ: BPP
BR: BPP
BS: BPP
BT: BPP
BU: BPP
BV: BPP
BW: BPP
BX: BPP
BY: BPP
BZ: BPP
Ba: BPP
Bb: BPP
Bc: BPP
Bd: BPP
Be: BPP
Bf: BPP
Bg: BPP
Bh: BPP
Bi: BPP
Bj: BPP
Bk: BPP
Bl: BPP
Bm: BPP
Bn: BPP
Bo: BPP
Bp: BPP
Bq: BPP
Br: BPP
Bs: BPP
Bt: BPP
Bu: BPP
Bv: BPP
Bw: BPP
Bx: BPP
By: BPP
Bz: BPP
B1: BPP
B2: BPP


Theoretical massNumber of molelcules
Total (without water)1,776,02578
Polymers1,776,02578
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area153710 Å2
ΔGint-772 kcal/mol
Surface area318790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.530, 287.360, 323.140
Angle α, β, γ (deg.)90.00, 101.73, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
ORF48


Mass: 33876.148 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: BppU (ORF48) / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9AZ56
#2: Protein
ORF46


Mass: 29085.857 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: Dit (ORF46) / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9AZ58
#3: Protein ...
BPP / Baseplate protein


Mass: 18365.545 Da / Num. of mol.: 54
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: bpp, BppL (ORF49) / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9G096

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.08M Trizma pH8.0, 0.1M KCl, 15% PEG2000MME, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8856 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 3.8→45 Å / Num. all: 286540 / Num. obs: 284699 / % possible obs: 99.2 % / Observed criterion σ(I): 1.2 / Redundancy: 3.4 % / Biso Wilson estimate: 106.87 Å2 / Rsym value: 0.108 / Net I/σ(I): 8.72
Reflection shellResolution: 3.8→4 Å / Redundancy: 3.15 % / Mean I/σ(I) obs: 1.28 / Num. unique all: 40328 / Rsym value: 0.999 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.8→35.97 Å / Cor.coef. Fo:Fc: 0.9148 / Cor.coef. Fo:Fc free: 0.8671 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 1424 0.5 %RANDOM
Rwork0.2369 ---
obs0.237 284699 99.5 %-
all-286540 --
Displacement parametersBiso mean: 171.32 Å2
Baniso -1Baniso -2Baniso -3
1--18.8028 Å20 Å2-22.2413 Å2
2--7.4977 Å20 Å2
3---11.305 Å2
Refine analyzeLuzzati coordinate error obs: 1.291 Å
Refinement stepCycle: LAST / Resolution: 3.8→35.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms54199 0 0 0 54199
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.008121125HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.93164061HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d41307SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes2984HARMONIC2
X-RAY DIFFRACTIONt_gen_planes17636HARMONIC5
X-RAY DIFFRACTIONt_it121125HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.02
X-RAY DIFFRACTIONt_other_torsion16.76
X-RAY DIFFRACTIONt_chiral_improper_torsion16141SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact126359SEMIHARMONIC4
LS refinement shellResolution: 3.8→3.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3102 105 0.5 %
Rwork0.2719 20789 -
all0.2721 20894 -
obs--99.5 %

+
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