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- PDB-8qgr: Stopper protein of phage 812 in closed conformation -

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Basic information

Entry
Database: PDB / ID: 8qgr
TitleStopper protein of phage 812 in closed conformation
ComponentsCapsid protein
KeywordsVIRUS / phage / neck / connector
Function / homologymetal ion binding / Capsid protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCienikova, Z. / Popelarova, B. / Plevka, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech Republic Czech Republic
CitationJournal: Commun Biol / Year: 2026
Title: Genome anchoring, retention, and release by neck proteins of Staphylococcus phage 812.
Authors: Zuzana Cieniková / Jiří Nováček / Marta Šiborová / Barbora Popelářová / Tibor Füzik / Tibor Botka / Martin Benešík / Pavol Bárdy / Roman Pantůček / Pavel Plevka /
Abstract: The virion of Staphylococcus phage 812 is formed by a capsid and a contractile tail joined together by neck proteins. The neck proteins are crucial for virion assembly, DNA packaging, and the ...The virion of Staphylococcus phage 812 is formed by a capsid and a contractile tail joined together by neck proteins. The neck proteins are crucial for virion assembly, DNA packaging, and the regulation of genome release, but their functions are not completely understood. Here, we show that the neck of phage 812 consists of portal, adaptor, stopper, tail terminator, and two types of decoration proteins. A dodecameric DNA-binding site at the surface of the portal complex anchors the phage genome inside the capsid. The adaptor complex induces a local B-to-A form transition of the DNA in the neck channel that could slow or pause genome translocation during ejection. The central channel of a stopper complex that is not attached to the tail terminator complex is closed by gating loops. In contrast, in the phage 812 virion, the gating loops are in an open conformation, and the DNA extends into the tail. The structure of neck proteins is not affected by tail sheath contraction. Therefore, the expulsion of tail tape measure proteins triggers the genome release.
History
DepositionSep 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8232
Polymers33,7571
Non-polymers651
Water2,630146
1
B: Capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)202,93612
Polymers202,5446
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
Unit cell
Length a, b, c (Å)93.366, 93.366, 122.531
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Capsid protein / Stopper protein


Mass: 33757.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage 812 (virus) / Strain: K1-420
Gene: 812_097, 812_099, 812a_099, 812F1_099, K1/420_099, K1_099
Plasmid: pET22T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1YTN7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6 M NaCl, 8% PEG 6000, 20% glycerol, 3% dextran sulphate sodium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2017
RadiationMonochromator: Si(111) single-crystal channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.2→37.2 Å / Num. obs: 16664 / % possible obs: 99.9 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 23.26
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 4.21 / Num. unique obs: 1627 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDS2016-11-01data reduction
Aimlessdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.159 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.172 / SU B: 5.096 / SU ML: 0.127 / Average fsc free: 0.9603 / Average fsc work: 0.9703 / Cross valid method: FREE R-VALUE / ESU R: 0.226 / ESU R Free: 0.18
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2192 1632 9.802 %
Rwork0.19 15017 -
all0.193 --
obs-16649 99.844 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.435 Å2
Baniso -1Baniso -2Baniso -3
1--1.375 Å2-0.687 Å2-0 Å2
2---1.375 Å20 Å2
3---4.46 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 1 146 1962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121852
X-RAY DIFFRACTIONr_bond_other_d00.0161788
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.6652504
X-RAY DIFFRACTIONr_angle_other_deg0.3931.5764127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.017512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6810347
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg2.014104
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.9711092
X-RAY DIFFRACTIONr_chiral_restr0.0560.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022113
X-RAY DIFFRACTIONr_gen_planes_other00.02399
X-RAY DIFFRACTIONr_nbd_refined0.2130.2332
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.21729
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2922
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2948
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1530.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.218
X-RAY DIFFRACTIONr_nbd_other0.1780.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.221
X-RAY DIFFRACTIONr_mcbond_it2.1293.105881
X-RAY DIFFRACTIONr_mcbond_other2.1283.105881
X-RAY DIFFRACTIONr_mcangle_it3.4315.5351096
X-RAY DIFFRACTIONr_mcangle_other3.435.5371097
X-RAY DIFFRACTIONr_scbond_it2.7983.572971
X-RAY DIFFRACTIONr_scbond_other2.7963.573972
X-RAY DIFFRACTIONr_scangle_it4.7216.3721408
X-RAY DIFFRACTIONr_scangle_other4.7196.3721409
X-RAY DIFFRACTIONr_lrange_it6.62133.2042091
X-RAY DIFFRACTIONr_lrange_other6.54632.7362065
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.2-2.2570.2691190.22610750.2311970.950.9599.74940.181
2.257-2.3190.2331270.20310270.20711550.9580.96199.91340.168
2.319-2.3860.241160.20610340.20911500.9470.9651000.173
2.386-2.4590.2481140.1949930.211070.9560.9681000.156
2.459-2.5390.228970.29720.20210690.9630.9721000.167
2.539-2.6280.271060.1969230.20310290.9530.9681000.163
2.628-2.7260.2831050.2089060.21510110.950.9671000.17
2.726-2.8370.272940.2168780.2219720.950.9651000.181
2.837-2.9620.315760.2298530.2359290.9340.961000.188
2.962-3.1060.236770.228270.2229040.9440.961000.182
3.106-3.2730.207850.217650.2098510.9670.97199.88250.187
3.273-3.4690.209720.1897390.1918110.9780.981000.176
3.469-3.7070.238760.1866980.1917740.9670.9821000.181
3.707-40.196790.1796470.1817260.9730.9811000.17
4-4.3770.203640.146150.1466800.9780.98899.85290.14
4.377-4.8850.159560.1475520.1486100.9850.98799.67210.146
4.885-5.6250.195610.1734870.1765510.980.98599.45550.17
5.625-6.850.185480.24320.1984830.980.98299.37890.194
6.85-9.5270.153340.1753590.1733930.9850.9831000.177
9.527-37.1590.188260.2082350.2062630.9790.97599.23950.22

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