[English] 日本語
Yorodumi
- PDB-3ejc: Full length Receptor Binding Protein from Lactococcal phage TP901-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ejc
TitleFull length Receptor Binding Protein from Lactococcal phage TP901-1
ComponentsBaseplate protein (BPP)
KeywordsVIRAL PROTEIN / SUGAR BINDING PROTEIN / Lactococcus lactis / siphoviridae / receptor binding protein / phage TP901-1 / P335 species
Function / homology
Function and homology information


virus tail, baseplate / cell adhesion / virion attachment to host cell
Similarity search - Function
Helix Hairpins - #2190 / Lower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain / Phage tail base-plate Siphoviridae RBP, head domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain / Adenovirus pIV-like, attachment domain / Helix Hairpins / Helix non-globular / Special ...Helix Hairpins - #2190 / Lower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain / Phage tail base-plate Siphoviridae RBP, head domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain / Adenovirus pIV-like, attachment domain / Helix Hairpins / Helix non-globular / Special / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesLactococcus phage TP901-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSpinelli, S. / Lichiere, J. / Blangy, S. / Sciara, G. / Cambillau, C. / Campanacci, V.
CitationJournal: J Biol Chem / Year: 2010
Title: Structure and molecular assignment of lactococcal phage TP901-1 baseplate.
Authors: Cecilia Bebeacua / Patrick Bron / Livia Lai / Christina Skovgaard Vegge / Lone Brøndsted / Silvia Spinelli / Valérie Campanacci / David Veesler / Marin van Heel / Christian Cambillau /
Abstract: P335 lactococcal phages infect the gram(+) bacterium Lactococcus lactis using a large multiprotein complex located at the distal part of the tail and termed baseplate (BP). The BP harbors the ...P335 lactococcal phages infect the gram(+) bacterium Lactococcus lactis using a large multiprotein complex located at the distal part of the tail and termed baseplate (BP). The BP harbors the receptor-binding proteins (RBPs), which allow the specific recognition of saccharidic receptors localized on the host cell surface. We report here the electron microscopic structure of the phage TP901-1 wild-type BP as well as those of two mutants bppL (-) and bppU(-), lacking BppL (the RBPs) or both peripheral BP components (BppL and BppU), respectively. We also achieved an electron microscopic reconstruction of a partial BP complex, formed by BppU and BppL. This complex exhibits a tripod shape and is composed of nine BppLs and three BppUs. These structures, combined with light-scattering measurements, led us to propose that the TP901-1 BP harbors six tripods at its periphery, located around the central tube formed by ORF46 (Dit) hexamers, at its proximal end, and a ORF47 (Tal) trimer at its distal extremity. A total of 54 BppLs (18 RBPs) are thus available to mediate host anchoring with a large apparent avidity. TP901-1 BP exhibits an infection-ready conformation and differs strikingly from the lactococcal phage p2 BP, bearing only 6 RBPs, and which needs a conformational change to reach its activated state. The comparison of several Siphoviridae structures uncovers a close organization of their central BP core whereas striking differences occur at the periphery, leading to diverse mechanisms of host recognition.
History
DepositionSep 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
A: Baseplate protein (BPP)


Theoretical massNumber of molelcules
Total (without water)17,9941
Polymers17,9941
Non-polymers00
Water2,486138
1
A: Baseplate protein (BPP)

A: Baseplate protein (BPP)

A: Baseplate protein (BPP)


Theoretical massNumber of molelcules
Total (without water)53,9823
Polymers53,9823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area14170 Å2
ΔGint-66 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.710, 41.710, 465.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-192-

HOH

21A-199-

HOH

31A-221-

HOH

41A-222-

HOH

51A-243-

HOH

61A-249-

HOH

71A-273-

HOH

81A-295-

HOH

-
Components

#1: Protein Baseplate protein (BPP)


Mass: 17994.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: bpp / Plasmid: PDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) PLysS / References: UniProt: Q9G096
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 300 nL of protein at 5 mg/mL were mixed with 100 nL of 20% PEG 8000, 0.2 M Mg Acetate tetrahydrate, 0.1 M Na Cacodylate pH 6.5 using a Cartesian Pixsys Robot, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 14330 / Num. obs: 14190 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 5.6
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2025 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2f0c

2f0c


Resolution: 1.85→28.54 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.914 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.157 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23844 1427 10.1 %RANDOM
Rwork0.19224 ---
obs0.19673 12762 99.94 %-
all-12762 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 3.853 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---0.48 Å2
Refine analyzeLuzzati coordinate error free: 0.148 Å
Refinement stepCycle: LAST / Resolution: 1.85→28.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 0 138 1342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211227
X-RAY DIFFRACTIONr_bond_other_d0.0010.02822
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9461662
X-RAY DIFFRACTIONr_angle_other_deg0.83732015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0535162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.6324.46847
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46215201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.804156
X-RAY DIFFRACTIONr_chiral_restr0.0770.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021385
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02234
X-RAY DIFFRACTIONr_nbd_refined0.220.2229
X-RAY DIFFRACTIONr_nbd_other0.2090.2800
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2575
X-RAY DIFFRACTIONr_nbtor_other0.0890.2706
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.236
X-RAY DIFFRACTIONr_mcbond_it0.621.51023
X-RAY DIFFRACTIONr_mcbond_other0.091.5341
X-RAY DIFFRACTIONr_mcangle_it0.77721283
X-RAY DIFFRACTIONr_scbond_it1.7493494
X-RAY DIFFRACTIONr_scangle_it2.6754.5379
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 98 -
Rwork0.246 939 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.60462.7994-3.22451.01650.933814.35820.41-1.441-0.03320.331-0.47510.0124-2.06291.19240.06510.6484-0.1945-0.08520.59130.00390.01425.271-17.4949.998
20.78130.28980.83770.7232-2.538714.0843-0.0823-0.00490.02760.14740.02250.0123-1.0091-0.69990.05990.37070.01910.01010.3973-0.02040.0468-1.981-18.936-4.551
32.7742-1.3434-0.81463.62050.98397.91620.03940.1068-0.1159-0.2104-0.08180.0511-0.0821-0.33040.04240.3502-0.00090.01750.30430.0038-0.0407-0.806-23.009-26.929
41.62210.5112-0.09071.86640.33852.14790.0883-0.2110.07630.2147-0.1049-0.0527-0.2270.15360.01660.0819-0.0219-0.00490.0764-0.00650.0466.289-14.122-58.811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 17
2X-RAY DIFFRACTION2A18 - 36
3X-RAY DIFFRACTION3A37 - 63
4X-RAY DIFFRACTION4A64 - 164

+
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://pdbjlvh1.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