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- PDB-7yw0: Bacteroides fragilis Hcp5 -

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Basic information

Entry
Database: PDB / ID: 7yw0
TitleBacteroides fragilis Hcp5
ComponentsBacterodales T6SS protein TssD (Hcp)
KeywordsSTRUCTURAL PROTEIN / Hcp5 / Bacteroides fragilis / T6SS
Function / homologyHemolysin coregulated protein (Hcp) TssD / Hemolysin coregulated protein Hcp (TssD) / type VI protein secretion system complex / Bacterodales T6SS protein TssD (Hcp)
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsWen, Y. / He, W. / Bai, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870132 China
CitationJournal: Cell Rep / Year: 2023
Title: Structure and assembly of type VI secretion system cargo delivery vehicle.
Authors: Wenbo He / Ke Wu / Zhenlin Ouyang / Yixin Bai / Wen Luo / Di Wu / Hao An / Yucheng Guo / Min Jiao / Qian Qin / Jiaxin Zhang / Yi Wu / Junjun She / Peter M Hwang / Fang Zheng / Li Zhu / Yurong Wen /
Abstract: Type VI secretion system is widely used in Gram-negative bacteria for injecting toxic effectors into neighboring prokaryotic or eukaryotic cells. Various effectors can be loaded onto the T6SS ...Type VI secretion system is widely used in Gram-negative bacteria for injecting toxic effectors into neighboring prokaryotic or eukaryotic cells. Various effectors can be loaded onto the T6SS delivery tube via its core components: Hcp, VgrG, or PAAR. Here, we report 2.8-Å resolution cryo-EM structure of intact T6SS Hcp5-VgrG-PAAR cargo delivery system and crystal structure of unbound Hcp5 from B. fragilis NCTC 9343. Loading of Hcp5 hexameric ring onto VgrG causes expansion of its inner cavity and external surface, explaining how structural changes could be propagated to regulate co-polymerization and surrounding contractile sheath. High-affinity binding between Hcp and VgrG causes entropically unfavorable structuring of long loops. Furthermore, interactions between VgrG trimer and Hcp hexamer are asymmetric, with three of the six Hcp monomers exhibiting a major loop flip. Our study provides insights into the assembly, loading, and firing of T6SS nanomachine that contributes to bacterial inter-species competition and host interactions.
History
DepositionAug 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterodales T6SS protein TssD (Hcp)
B: Bacterodales T6SS protein TssD (Hcp)


Theoretical massNumber of molelcules
Total (without water)29,0112
Polymers29,0112
Non-polymers00
Water1,13563
1
A: Bacterodales T6SS protein TssD (Hcp)
B: Bacterodales T6SS protein TssD (Hcp)

A: Bacterodales T6SS protein TssD (Hcp)
B: Bacterodales T6SS protein TssD (Hcp)

A: Bacterodales T6SS protein TssD (Hcp)
B: Bacterodales T6SS protein TssD (Hcp)


Theoretical massNumber of molelcules
Total (without water)87,0326
Polymers87,0326
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area14610 Å2
ΔGint-83 kcal/mol
Surface area31890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.102, 77.102, 79.491
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 3 - 127 / Label seq-ID: 3 - 127

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Bacterodales T6SS protein TssD (Hcp) / Type VI secretion system needle protein Hcp / Hcp5


Mass: 14505.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria)
Gene: tssD_4, CQW34_01545, DW228_07065, DWW08_15770, EC81_0218805, F2Z25_09975, F2Z89_01225, F9000_04115, FSA06_12535, H3T27_02635, HMPREF0101_00911, HMPREF1018_02079, IB64_010900
Production host: Escherichia coli (E. coli) / References: UniProt: A0A081TQ32
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.98→34.79 Å / Num. obs: 18727 / % possible obs: 98.39 % / Redundancy: 20.3 % / CC1/2: 1 / Net I/σ(I): 21.47
Reflection shellResolution: 1.98→2.05 Å / Num. unique obs: 1848 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4w64

4w64


Resolution: 1.98→34.69 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.779 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2903 1857 10 %RANDOM
Rwork0.2326 ---
obs0.2383 16719 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.53 Å2 / Biso mean: 59.233 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å2-0 Å2-0 Å2
2---2.43 Å2-0 Å2
3---4.86 Å2
Refinement stepCycle: final / Resolution: 1.98→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 0 63 1929
Biso mean---59.15 -
Num. residues----239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121897
X-RAY DIFFRACTIONr_angle_refined_deg1.571.6322558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.295232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.65624.31695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.15415321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.196156
X-RAY DIFFRACTIONr_chiral_restr0.1080.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021418
Refine LS restraints NCS

Ens-ID: 1 / Number: 3365 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.98→2.031 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 134 -
Rwork0.433 1234 -
all-1368 -
obs--98.84 %

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