PDB-8p6j: Structure of the hypervariable region of Streptococcus pyogenes M...

ID or keywords:

Entry

Database: PDB / ID: 8p6j

Title

Structure of the hypervariable region of Streptococcus pyogenes M3 protein in complex with a collagen peptide

Components

Antiphagocytic M protein, type 3
collagen II-27 Toolkit peptide (JDM238)

Keywords

PROTEIN BINDING / M protein / Streptococcus pyogenes / hypervariable region / collagen-binding domain

Function / homology

M protein-type anchor domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / membrane / Antiphagocytic M protein, type 3

Function and homology information

Biological species

Streptococcus pyogenes serotype M3 (bacteria)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.324 Å

Authors

Wojnowska, M. / Schwarz-Linek, U.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Structural basis for collagen recognition by the Streptococcus pyogenes M3 protein
Authors: Wojnowska, M. / Yelland, T. / Ludewig, H. / Hagan, R.M. / Watt, G. / Hamaia, S. / Bihan, D. / Farndale, R.W. / Schwarz-Linek, U.

History

Deposition	May 26, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 21, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _struct.title / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8p6j.cif.gz	120.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8p6j.ent.gz		Display	PDB format
PDBx/mmJSON format	8p6j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8p6j_validation.pdf.gz	488 KB	Display	wwPDB validaton report
Full document	8p6j_full_validation.pdf.gz	490.2 KB	Display
Data in XML	8p6j_validation.xml.gz	19.3 KB	Display
Data in CIF	8p6j_validation.cif.gz	27.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p6/8p6j ftp://data.pdbj.org/pub/pdb/validation_reports/p6/8p6j	HTTPS FTP

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Related structure data

Related structure data	8p6kC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

BBB: Antiphagocytic M protein, type 3

CCC: Antiphagocytic M protein, type 3

AAA: collagen II-27 Toolkit peptide (JDM238)

DDD: collagen II-27 Toolkit peptide (JDM238)

EEE: collagen II-27 Toolkit peptide (JDM238)

FFF: Antiphagocytic M protein, type 3

GGG: Antiphagocytic M protein, type 3

HHH: collagen II-27 Toolkit peptide (JDM238)

JJJ: collagen II-27 Toolkit peptide (JDM238)

III: collagen II-27 Toolkit peptide (JDM238)

66 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

BBB: Antiphagocytic M protein, type 3

CCC: Antiphagocytic M protein, type 3

HHH: collagen II-27 Toolkit peptide (JDM238)

JJJ: collagen II-27 Toolkit peptide (JDM238)

III: collagen II-27 Toolkit peptide (JDM238)

defined by author&software
Evidence: assay for oligomerization, full-length M3 has been shown to form a homodimer using CD
33 kDa, 5 polymers

2

AAA: collagen II-27 Toolkit peptide (JDM238)

DDD: collagen II-27 Toolkit peptide (JDM238)

EEE: collagen II-27 Toolkit peptide (JDM238)

FFF: Antiphagocytic M protein, type 3

GGG: Antiphagocytic M protein, type 3

defined by author&software
33 kDa, 5 polymers

Unit cell

Length a, b, c (Å)	31.832, 51.503, 80.186
Angle α, β, γ (deg.)	87.326, 84.780, 89.394
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d1	1	Chains BBB CCC
d2	2	Chains BBB FFF
d3	3	Chains BBB GGG
d4	4	Chains CCC FFF
d5	5	Chains CCC GGG
d6	6	Chains AAA DDD
d7	7	Chains AAA EEE
d8	8	Chains AAA HHH
d9	9	Chains AAA JJJ
d10	10	Chains AAA III
d11	11	Chains DDD EEE
d12	12	Chains DDD HHH
d13	13	Chains DDD JJJ
d14	14	Chains DDD III
d15	15	Chains EEE HHH
d16	16	Chains EEE JJJ
d17	17	Chains EEE III
d18	18	Chains FFF GGG
d19	19	Chains HHH JJJ
d20	20	Chains HHH III
d21	21	Chains JJJ III

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d1	1	1	ASP	ASP	LYS	LYS	BBB	A	4 - 106	4 - 106
d1	2	1	ASP	ASP	LYS	LYS	CCC	B	4 - 106	4 - 106
d2	3	2	ASP	ASP	LYS	LYS	BBB	A	4 - 106	4 - 106
d2	4	2	ASP	ASP	LYS	LYS	FFF	F	4 - 106	4 - 106
d3	5	3	ALA	ALA	LYS	LYS	BBB	A	5 - 106	5 - 106
d3	6	3	ALA	ALA	LYS	LYS	GGG	G	5 - 106	5 - 106
d4	7	4	MET	MET	LYS	LYS	CCC	B	3 - 106	3 - 106
d4	8	4	MET	MET	LYS	LYS	FFF	F	3 - 106	3 - 106
d5	9	5	ALA	ALA	LYS	LYS	CCC	B	5 - 106	5 - 106
d5	10	5	ALA	ALA	LYS	LYS	GGG	G	5 - 106	5 - 106
d6	11	6	GLY	GLY	HYP	HYP	AAA	C	6 - 29	1 - 24
d6	12	6	GLY	GLY	HYP	HYP	DDD	D	36 - 59	1 - 24
d7	13	7	GLY	GLY	HYP	HYP	AAA	C	6 - 29	1 - 24
d7	14	7	GLY	GLY	HYP	HYP	EEE	E	66 - 89	1 - 24
d8	15	8	GLY	GLY	HYP	HYP	AAA	C	6 - 29	1 - 24
d8	16	8	GLY	GLY	HYP	HYP	HHH	H	6 - 29	1 - 24
d9	17	9	GLY	GLY	HYP	HYP	AAA	C	6 - 29	1 - 24
d9	18	9	GLY	GLY	HYP	HYP	JJJ	I	66 - 89	1 - 24
d10	19	10	PRO	PRO	PRO	PRO	AAA	C	7 - 28	2 - 23
d10	20	10	PRO	PRO	PRO	PRO	III	J	37 - 58	2 - 23
d11	21	11	GLY	GLY	HYP	HYP	DDD	D	36 - 59	1 - 24
d11	22	11	GLY	GLY	HYP	HYP	EEE	E	66 - 89	1 - 24
d12	22	12	GLY	GLY	HYP	HYP	DDD	D	36 - 59	1 - 24
d12	23	12	GLY	GLY	HYP	HYP	HHH	H	6 - 29	1 - 24
d13	24	13	GLY	GLY	HYP	HYP	DDD	D	36 - 59	1 - 24
d13	25	13	GLY	GLY	HYP	HYP	JJJ	I	66 - 89	1 - 24
d14	26	14	PRO	PRO	PRO	PRO	DDD	D	37 - 58	2 - 23
d14	27	14	PRO	PRO	PRO	PRO	III	J	37 - 58	2 - 23
d15	28	15	GLY	GLY	HYP	HYP	EEE	E	66 - 89	1 - 24
d15	29	15	GLY	GLY	HYP	HYP	HHH	H	6 - 29	1 - 24
d16	30	16	GLY	GLY	HYP	HYP	EEE	E	66 - 89	1 - 24
d16	31	16	GLY	GLY	HYP	HYP	JJJ	I	66 - 89	1 - 24
d17	32	17	PRO	PRO	PRO	PRO	EEE	E	67 - 88	2 - 23
d17	33	17	PRO	PRO	PRO	PRO	III	J	37 - 58	2 - 23
d18	33	18	ALA	ALA	LYS	LYS	FFF	F	5 - 106	5 - 106
d18	34	18	ALA	ALA	LYS	LYS	GGG	G	5 - 106	5 - 106
d19	35	19	GLY	GLY	HYP	HYP	HHH	H	6 - 29	1 - 24
d19	36	19	GLY	GLY	HYP	HYP	JJJ	I	66 - 89	1 - 24
d20	37	20	PRO	PRO	PRO	PRO	HHH	H	7 - 28	2 - 23
d20	38	20	PRO	PRO	PRO	PRO	III	J	37 - 58	2 - 23
d21	39	21	PRO	PRO	PRO	PRO	JJJ	I	67 - 88	2 - 23
d21	40	21	PRO	PRO	PRO	PRO	III	J	37 - 58	2 - 23

NCS ensembles :

#1: Protein	Antiphagocytic M protein, type 3 Mass: 13276.930 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M3 (bacteria) Gene: emm3, SpyM3_1727 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UWN1
#2: Protein/peptide	collagen II-27 Toolkit peptide (JDM238) Mass: 2148.244 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM Tris pH8.5, 8% PEG10k protein 1:1.5 peptide

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 3, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.32→79.77 Å / Num. obs: 35250 / % possible obs: 90.2 % / Redundancy: 1.8 % / CC_1/2: 1 / Net I/σ(I): 2.1
Reflection shell	Resolution: 2.32→2.34 Å / Num. unique obs: 997 / CC_1/2: 0.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.324→79.769 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.895 / WR_factor R_free: 0.314 / WR_factor R_work: 0.27 / SU B: 17.265 / SU ML: 0.384 / Average fsc free: 0.7474 / Average fsc work: 0.7642 / Cross valid method: FREE R-VALUE / ESU R: 0.768 / ESU R Free: 0.326
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2853	947	4.849 %
R_work	0.2412	18583	-
all	0.243	-	-
obs	-	19530	89.595 %

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: 40.861 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.565 Å²	0.43 Å²	-0.858 Å²
2-	-	0.796 Å²	0.149 Å²
3-	-	-	-0.358 Å²

Refinement step

Cycle: LAST / Resolution: 2.324→79.769 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4011	0	0	25	4036

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	4134
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	3518
X-RAY DIFFRACTION	r_angle_refined_deg	1.253	1.666	5700
X-RAY DIFFRACTION	r_angle_other_deg	1.17	1.58	8255
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.111	5	556
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.187	25.689	167
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.857	15	516
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.104	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.049	0.2	551
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4744
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	663
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	1087
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.171	0.2	2832
X-RAY DIFFRACTION	r_nbtor_refined	0.15	0.2	2148
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	1662
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	53
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.302	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.262	0.2	87
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.125	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	2.898	4.602	2245
X-RAY DIFFRACTION	r_mcbond_other	2.898	4.602	2245
X-RAY DIFFRACTION	r_mcangle_it	4.4	6.893	2791
X-RAY DIFFRACTION	r_mcangle_other	4.4	6.893	2792
X-RAY DIFFRACTION	r_scbond_it	3.491	4.763	1889
X-RAY DIFFRACTION	r_scbond_other	3.49	4.764	1890
X-RAY DIFFRACTION	r_scangle_it	5.457	7.044	2908
X-RAY DIFFRACTION	r_scangle_other	5.456	7.044	2909
X-RAY DIFFRACTION	r_lrange_it	7.01	58.152	4658
X-RAY DIFFRACTION	r_lrange_other	7.009	58.157	4659
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.115	0.05	2925
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.094	0.05	2964
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.109	0.05	2815
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.111	0.05	2946
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.097	0.05	2860
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.073	0.05	410
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.064	0.05	411
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.105	0.05	410
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.066	0.05	412
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.053	0.05	375
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.044	0.05	409
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.104	0.05	410
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.042	0.05	410
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.011	0.05	375
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.095	0.05	408
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.063	0.05	415
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.044	0.05	378
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.094	0.05	2824
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.106	0.05	408
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.098	0.05	373
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.043	0.05	377

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.324-2.384	0.346	67	0.325	1330	0.326	1570	0.527	0.537	88.9809	0.33
2.384-2.45	0.339	70	0.326	1411	0.327	1639	0.514	0.522	90.36	0.327
2.45-2.521	0.384	62	0.328	1300	0.33	1478	0.54	0.528	92.1516	0.327
2.521-2.598	0.342	73	0.322	1284	0.323	1486	0.617	0.625	91.319	0.328
2.598-2.683	0.336	67	0.279	1243	0.282	1449	0.729	0.747	90.4072	0.283
2.683-2.777	0.322	58	0.261	1220	0.264	1381	0.76	0.79	92.5416	0.268
2.777-2.882	0.352	58	0.249	1210	0.254	1384	0.772	0.812	91.6185	0.255
2.882-3	0.251	66	0.246	1087	0.246	1246	0.817	0.812	92.5361	0.255
3-3.133	0.267	60	0.234	1116	0.236	1258	0.797	0.818	93.4817	0.245
3.133-3.285	0.27	42	0.243	1013	0.244	1171	0.803	0.826	90.0939	0.255
3.285-3.463	0.276	58	0.218	959	0.221	1144	0.862	0.887	88.8986	0.23
3.463-3.672	0.255	35	0.195	882	0.197	1048	0.879	0.914	87.5	0.213
3.672-3.925	0.246	47	0.196	787	0.198	1013	0.895	0.92	82.3297	0.218
3.925-4.239	0.258	32	0.202	760	0.204	922	0.907	0.922	85.9002	0.229
4.239-4.642	0.233	29	0.184	693	0.186	890	0.914	0.927	81.1236	0.209
4.642-5.188	0.316	32	0.235	594	0.24	767	0.83	0.879	81.6167	0.284
5.188-5.986	0.289	29	0.306	576	0.305	670	0.877	0.866	90.2985	0.346
5.986-7.321	0.339	25	0.263	503	0.266	580	0.824	0.891	91.0345	0.312
7.321-10.311	0.236	19	0.207	405	0.208	458	0.925	0.922	92.5764	0.264
10.311-79.769	0.25	18	0.276	210	0.273	244	0.909	0.892	93.4426	0.363

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