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- PDB-3ejc: Full length Receptor Binding Protein from Lactococcal phage TP901-1 -

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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 / symbiont entry into host cell / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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