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- PDB-4jpp: Bacteriophage phiX174 H protein residues 143-282 -

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Basic information

Entry
Database: PDB / ID: 4jpp
TitleBacteriophage phiX174 H protein residues 143-282
ComponentsMinor spike protein H
KeywordsVIRAL PROTEIN / helical barrel / tail tube / pilot DNA during phage infection
Function / homologyMinor spike protein / Microvirus H protein (pilot protein) / lipopolysaccharide-mediated virion attachment to host cell / viral capsid / symbiont entry into host cell / identical protein binding / Minor spike protein H
Function and homology information
Biological speciesEnterobacteria phage phiX174 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSun, L. / Young, L.N. / Boudko, S.B. / Fokine, A. / Zhang, X. / Rossmann, M.G. / Fane, B.A.
CitationJournal: Nature / Year: 2014
Title: Icosahedral bacteriophage ΦX174 forms a tail for DNA transport during infection.
Authors: Lei Sun / Lindsey N Young / Xinzheng Zhang / Sergei P Boudko / Andrei Fokine / Erica Zbornik / Aaron P Roznowski / Ian J Molineux / Michael G Rossmann / Bentley A Fane /
Abstract: Prokaryotic viruses have evolved various mechanisms to transport their genomes across bacterial cell walls. Many bacteriophages use a tail to perform this function, whereas tail-less phages rely on ...Prokaryotic viruses have evolved various mechanisms to transport their genomes across bacterial cell walls. Many bacteriophages use a tail to perform this function, whereas tail-less phages rely on host organelles. However, the tail-less, icosahedral, single-stranded DNA ΦX174-like coliphages do not fall into these well-defined infection processes. For these phages, DNA delivery requires a DNA pilot protein. Here we show that the ΦX174 pilot protein H oligomerizes to form a tube whose function is most probably to deliver the DNA genome across the host's periplasmic space to the cytoplasm. The 2.4 Å resolution crystal structure of the in vitro assembled H protein's central domain consists of a 170 Å-long α-helical barrel. The tube is constructed of ten α-helices with their amino termini arrayed in a right-handed super-helical coiled-coil and their carboxy termini arrayed in a left-handed super-helical coiled-coil. Genetic and biochemical studies demonstrate that the tube is essential for infectivity but does not affect in vivo virus assembly. Cryo-electron tomograms show that tubes span the periplasmic space and are present while the genome is being delivered into the host cell's cytoplasm. Both ends of the H protein contain transmembrane domains, which anchor the assembled tubes into the inner and outer cell membranes. The central channel of the H-protein tube is lined with amide and guanidinium side chains. This may be a general property of viral DNA conduits and is likely to be critical for efficient genome translocation into the host.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Minor spike protein H
B: Minor spike protein H
C: Minor spike protein H
D: Minor spike protein H
E: Minor spike protein H


Theoretical massNumber of molelcules
Total (without water)79,7685
Polymers79,7685
Non-polymers00
Water9,332518
1
A: Minor spike protein H
B: Minor spike protein H
C: Minor spike protein H
D: Minor spike protein H
E: Minor spike protein H

A: Minor spike protein H
B: Minor spike protein H
C: Minor spike protein H
D: Minor spike protein H
E: Minor spike protein H


Theoretical massNumber of molelcules
Total (without water)159,53610
Polymers159,53610
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area55770 Å2
ΔGint-385 kcal/mol
Surface area62860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.699, 68.699, 372.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein
Minor spike protein H / H protein / Pilot protein


Mass: 15953.647 Da / Num. of mol.: 5 / Fragment: coiled coil domain (UNP residues 143-282)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage phiX174 (virus) / Gene: H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03646
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10-15% w/v PEG8000, 0.1 M Tris-HCl, pH 7.5, 20% w/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.00718 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2005
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00718 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 36540 / Num. obs: 35261 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Net I/σ(I): 4.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.495.60.327199.5
2.49-2.596.30.296199.7
2.59-2.77.10.228199.2
2.7-2.857.10.184199
2.85-3.027.10.128198.6
3.02-3.2670.099197.8
3.26-3.5970.087197.9
3.59-4.16.70.065194.9
4.1-5.166.60.062187.9
5.16-306.40.049191.7

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Processing

Software
NameVersionClassification
Locallymodified Blu-Ice GUI interface to EPICS controldata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→8 Å / SU ML: 0.29 / σ(F): 2 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2901 1627 4.97 %RANDOM
Rwork0.2454 ---
obs0.2477 32710 92.83 %-
all-35261 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5027 0 0 518 5545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125054
X-RAY DIFFRACTIONf_angle_d1.3226773
X-RAY DIFFRACTIONf_dihedral_angle_d18.4811999
X-RAY DIFFRACTIONf_chiral_restr0.09758
X-RAY DIFFRACTIONf_plane_restr0.006917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.46860.30171360.25022532X-RAY DIFFRACTION93
2.4686-2.54580.28791490.24162568X-RAY DIFFRACTION94
2.5458-2.63370.3121290.23942599X-RAY DIFFRACTION95
2.6337-2.73510.33641250.24762615X-RAY DIFFRACTION95
2.7351-2.85410.27861450.25452620X-RAY DIFFRACTION94
2.8541-2.99710.30581190.25032598X-RAY DIFFRACTION95
2.9971-3.17380.31021430.24752581X-RAY DIFFRACTION94
3.1738-3.40120.2861360.2482632X-RAY DIFFRACTION94
3.4012-3.71210.25261560.23232566X-RAY DIFFRACTION93
3.7121-4.18080.29161270.21972575X-RAY DIFFRACTION91
4.1808-5.03840.27171270.23512413X-RAY DIFFRACTION84
5.0384-7.99990.3061350.29852784X-RAY DIFFRACTION93
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)
10.33480.29741.11740.2840.78454.74690.16760.41310.0091-0.1348-0.0430.05860.4705-0.2611-0.1170.61850.09430.01440.8893-0.14970.2945-3.6056-50.7317-11.4726
20.1860.25630.59231.30930.42962.06140.06710.29870.0389-0.36290.03410.16230.1807-0.548-0.08560.55330.0383-0.02051.0121-0.12720.2575-12.3075-45.2744-12.2197
30.51380.40730.50140.57830.43480.7947-0.04280.15540.05520.09640.0684-0.0415-0.1096-0.00150.09240.6710.00850.0214-0.0569-0.05350.272-4.0973-2676.5504
40.05930.28270.12111.3707-0.26757.49680.08470.42640.1452-0.44650.03010.16760.0413-0.4512-0.10460.45490.0965-0.02461.0812-0.07180.25-16.4324-36.0253-10.7901
50.37350.07830.21790.58790.15610.2313-0.06610.23830.13380.1414-0.0161-0.0539-0.0322-0.04440.13960.73940.01890.0131-0.1563-0.02220.21840.3796-24.308274.2981
60.04630.12280.31860.6028-0.63758.48060.1120.49170.2098-0.1726-0.06760.0361-0.0245-0.3944-0.06160.45240.182-0.00511.07720.10970.301-14.2816-25.6294-11.6064
70.2214-0.0954-0.02740.6383-0.07640.1281-0.09930.14990.03130.10560.0233-0.067-0.011-0.06260.06460.71790.03580.0172-0.09740.03850.24666.5109-27.896877.0001
80.05580.1951-0.27530.6582-1.04734.02950.10550.44390.0945-0.1407-0.0088-0.0566-0.50040.036-0.08580.58250.17840.01470.9770.13620.2972-6.8994-18.9994-9.1166
90.2410.25230.06261.0460.50320.58430.020.02490.01450.05420.0483-0.11450.0635-0.0101-0.04470.65250.01730.0485-0.06-0.05690.2707-8.6561-30.388875.7923
100.1897-0.00820.0810.5331-0.00390.42290.05540.033-0.02710.05250.10650.0827-0.0136-0.0555-0.09040.7225-0.0309-0.0145-0.03510.05960.26269.4899-31.609674.373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 148 through 192 )
2X-RAY DIFFRACTION2chain 'B' and (resid 148 through 191 )
3X-RAY DIFFRACTION3chain 'B' and (resid 196 through 271 )
4X-RAY DIFFRACTION4chain 'C' and (resid 149 through 192 )
5X-RAY DIFFRACTION5chain 'C' and (resid 196 through 268 )
6X-RAY DIFFRACTION6chain 'D' and (resid 148 through 192 )
7X-RAY DIFFRACTION7chain 'D' and (resid 196 through 272 )
8X-RAY DIFFRACTION8chain 'E' and (resid 151 through 192 )
9X-RAY DIFFRACTION9chain 'A' and (resid 196 through 270 )
10X-RAY DIFFRACTION10chain 'E' and (resid 196 through 268 )

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