PDB-31he: Xray crystal structure of PtsM receptor binding protein

Basic information

• Entry: Database: PDB / ID: 31he
• Title: Xray crystal structure of PtsM receptor binding protein
• Components: Tail fiber protein
• Keywords: VIRAL PROTEIN / Receptor binding protein / Phage / RBP / Virus
• Function / homology: :
• Biological species: Clostridioides difficile R20291 (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.42 Å
• Authors: Wilson, J.S. / Bullough, P.A. / Fagan, R.P.

Funding support

United Kingdom, 1items

Organization	Grant number	Country
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/P02002X/1	United Kingdom

• Citation: Journal: IUCrJ / Year: 2026; Title: How cryoEM has advanced our understanding of bacteriophages and bacteriocins targeting Clostridioides difficile.; Authors: Per A Bullough / Jason S Wilson / Hannah L Berry / Robert P Fagan / ; Abstract: We review the structural and functional characteristics of bacteriophages and bacteriocins (diffocins) that specifically target Clostridioides difficile, a significant healthcare concern due to its role in nosocomial infections. The advent of modern cryogenic electron microscopy (cryoEM) has revolutionized our understanding of these contractile injection systems, providing high-resolution insights into their mechanisms. We compare the structures of C. difficile phages and diffocins, highlighting their adaptations for penetrating the Gram-positive bacterial cell envelope - including the cell membrane, cell wall and proteinaceous surface layer. Diffocins, simpler in structure, utilize a combination of mechanical and enzymatic strategies, while some phages like ΦCD508 may rely on mechanical force alone. This review delves into the assembly and function of key components such as the contractile sheath, baseplate and receptor-binding proteins, offering a framework for engineering precision antimicrobials. We also present new experimental results, including refined cryoEM structures of the ΦCD508 pre- and post-contracted tail, a novel spontaneously contracted conformation and an X-ray crystal structure of a phage receptor-binding protein domain. This work underscores the potential of cryoEM in advancing our understanding of phage biology and its applications in developing targeted therapies against C. difficile.

History

Deposition	Jun 4, 2026	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 8, 2026	Provider: repository / Type: Initial release

Assembly

Deposited unit

AAA: Tail fiber protein

BBB: Tail fiber protein

hetero molecules

Summary:

• 116 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	115,834	4
Polymers	115,749	2
Non-polymers	85	2
Water	4,306	239

1

Summary:

• Idetical with deposited unit
• defined by author
• Evidence: gel filtration

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	4870 Å2
ΔGint	-47 kcal/mol
Surface area	14280 Å2

Unit cell

Length a, b, c (Å)	161.590, 67.370, 51.890
Angle α, β, γ (deg.)	90.000, 99.770, 90.000
Int Tables number	5
Space group name H-M	C121

Components

#1: Protein

AAA BBB Tail fiber protein

Details:

Mass: 57874.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile R20291 (bacteria)
Gene: SAMEA1402366_02093 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0AB74R428

#2: Chemical

AAA-601 ChemComp-NA / SODIUM ION

Details:

Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

#3: Chemical

BBB-701 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Details:

Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H₂O

• Has ligand of interest: N
• Has protein modification: N

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal grow: Temperature: 290 K / Method: vapor diffusion, sitting drop; Details: 0.1 M MgCl2, 0.1 M Na HEPES pH 7.5, 10% w/v PEG 4000

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
• Detector: Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 29, 2019
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9762 Å / Relative weight: 1
• Reflection: Resolution: 1.42→46.81 Å / Num. obs: 103206 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC_1/2: 1 / Net I/σ(I): 9.4
• Reflection shell: Resolution: 1.42→1.44 Å / Num. unique obs: 5146 / CC_1/2: 0.3

Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
FAST_DP		data reduction
FAST_DP		data scaling
PHASER		phasing
SHELXDE		phasing
BUCCANEER		model building

Refinement

Method to determine structure: SAD / Resolution: 1.42→46.789 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.965 / SU B: 1.198 / SU ML: 0.043 / Cross valid method: FREE R-VALUE / ESU R: 0.049 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions

	Rfactor	Num. reflection	% reflection
Rfree	0.2017	5081	4.923 %
Rwork	0.1852	98125	-
all	0.186	-	-
obs	-	103206	99.788 %

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 20.608 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.183 Å2	0 Å2	-0.91 Å2
2-	-	-0.264 Å2	0 Å2
3-	-	-	0.372 Å2

Refinement step

Cycle: LAST / Resolution: 1.42→46.789 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2579	0	5	239	2823

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	2704
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2321
X-RAY DIFFRACTION	r_angle_refined_deg	1.881	1.642	3687
X-RAY DIFFRACTION	r_angle_other_deg	1.565	1.575	5405
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.393	5	334
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.15	24.437	142
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.546	15	415
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	6.674	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	355
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	3078
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	618
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	409
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	2015
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	1331
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1297
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.162	0.2	136
X-RAY DIFFRACTION	r_metal_ion_refined	0.111	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.166	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.173	0.2	27
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.091	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	2.023	1.985	1294
X-RAY DIFFRACTION	r_mcbond_other	2.021	1.983	1293
X-RAY DIFFRACTION	r_mcangle_it	2.793	2.966	1618
X-RAY DIFFRACTION	r_mcangle_other	2.793	2.968	1619
X-RAY DIFFRACTION	r_scbond_it	3.839	2.316	1409
X-RAY DIFFRACTION	r_scbond_other	3.842	2.318	1410
X-RAY DIFFRACTION	r_scangle_it	5.59	3.344	2061
X-RAY DIFFRACTION	r_scangle_other	5.589	3.345	2062
X-RAY DIFFRACTION	r_lrange_it	7.145	23.64	2993
X-RAY DIFFRACTION	r_lrange_other	7.127	23.398	2964

LS refinement shell

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

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Rfactor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WRfactor Rwork
1.42-1.457	0.329	382	0.333	7225	0.332	7608	0.436	0.432	99.9869	0.329
1.457-1.497	0.339	374	0.332	7051	0.332	7425	0.652	0.648	100	0.322
1.497-1.54	0.298	354	0.305	6873	0.305	7231	0.766	0.775	99.9447	0.287
1.54-1.587	0.305	333	0.284	6649	0.285	6985	0.814	0.822	99.957	0.259
1.587-1.639	0.289	321	0.265	6485	0.266	6811	0.848	0.855	99.9266	0.234
1.639-1.697	0.263	335	0.24	6261	0.241	6599	0.889	0.891	99.9545	0.209
1.697-1.761	0.242	320	0.219	5991	0.22	6317	0.902	0.912	99.905	0.189
1.761-1.833	0.224	292	0.189	5802	0.191	6094	0.928	0.935	100	0.169
1.833-1.914	0.191	299	0.172	5601	0.173	5902	0.948	0.955	99.9661	0.157
1.914-2.007	0.184	270	0.168	5334	0.169	5604	0.959	0.962	100	0.157
2.007-2.116	0.182	280	0.166	5038	0.167	5322	0.959	0.965	99.9248	0.159
2.116-2.244	0.189	227	0.167	4857	0.168	5099	0.954	0.961	99.7058	0.164
2.244-2.398	0.193	264	0.166	4459	0.167	4727	0.955	0.96	99.9154	0.168
2.398-2.59	0.188	215	0.167	4228	0.168	4453	0.96	0.962	99.7754	0.172
2.59-2.836	0.177	176	0.17	3871	0.17	4070	0.955	0.958	99.4349	0.182
2.836-3.169	0.195	190	0.176	3468	0.177	3691	0.946	0.954	99.1059	0.197
3.169-3.657	0.181	145	0.166	3115	0.166	3288	0.959	0.964	99.1484	0.19
3.657-4.472	0.155	136	0.152	2613	0.152	2780	0.973	0.973	98.8849	0.188
4.472-6.296	0.193	110	0.165	2049	0.166	2169	0.973	0.975	99.539	0.211
6.296-46.789	0.233	58	0.242	1154	0.242	1246	0.952	0.94	97.2713	0.301