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

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Basic information

Entry
Database: PDB / ID: 8p6j
TitleStructure 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)
KeywordsPROTEIN BINDING / M protein / Streptococcus pyogenes / hypervariable region / collagen-binding domain
Function / homology
Function and homology information


extracellular region / membrane
Similarity search - Function
: / Streptococcal M proteins D repeats region profile. / : / Streptococcal M proteins C repeat profile. / 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
Similarity search - Domain/homology
Antiphagocytic M protein, type 3
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M3 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.324 Å
AuthorsWojnowska, M. / Schwarz-Linek, U.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N009681/1 United Kingdom
CitationJournal: Biorxiv / Year: 2024
Title: Structural basis for collagen recognition by the Streptococcus pyogenes M3 protein and its involvement in biofilm
Authors: Wojnowska, M. / Wajima, T. / Yelland, T. / Ludewig, H. / Hagan, R.M. / Watt, G. / Hamaia, S.W. / Bihan, D. / Malcor, J.D. / Bonna, A. / Bergsten, H. / Svensson, M. / Oppegaard, O. / Skrede, ...Authors: Wojnowska, M. / Wajima, T. / Yelland, T. / Ludewig, H. / Hagan, R.M. / Watt, G. / Hamaia, S.W. / Bihan, D. / Malcor, J.D. / Bonna, A. / Bergsten, H. / Svensson, M. / Oppegaard, O. / Skrede, S. / Arnell, P. / Hyldegaard, O. / Farndale, R.W. / Norrby-Teglund, A. / Schwarz-Linek, U.
History
DepositionMay 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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
Revision 1.2Jan 15, 2025Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
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.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
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)


Theoretical massNumber of molelcules
Total (without water)65,99710
Polymers65,99710
Non-polymers00
Water45025
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)


Theoretical massNumber of molelcules
Total (without water)32,9995
Polymers32,9995
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-73 kcal/mol
Surface area15110 Å2
MethodPISA
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


Theoretical massNumber of molelcules
Total (without water)32,9995
Polymers32,9995
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area10170 Å2
ΔGint-72 kcal/mol
Surface area14910 Å2
MethodPISA
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 number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d11Chains BBB CCC
d22Chains BBB FFF
d33Chains BBB GGG
d44Chains CCC FFF
d55Chains CCC GGG
d66Chains AAA DDD
d77Chains AAA EEE
d88Chains AAA HHH
d99Chains AAA JJJ
d1010Chains AAA III
d1111Chains DDD EEE
d1212Chains DDD HHH
d1313Chains DDD JJJ
d1414Chains DDD III
d1515Chains EEE HHH
d1616Chains EEE JJJ
d1717Chains EEE III
d1818Chains FFF GGG
d1919Chains HHH JJJ
d2020Chains HHH III
d2121Chains JJJ III

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d111ASPASPLYSLYSBBBA4 - 1064 - 106
d121ASPASPLYSLYSCCCB4 - 1064 - 106
d232ASPASPLYSLYSBBBA4 - 1064 - 106
d242ASPASPLYSLYSFFFF4 - 1064 - 106
d353ALAALALYSLYSBBBA5 - 1065 - 106
d363ALAALALYSLYSGGGG5 - 1065 - 106
d474METMETLYSLYSCCCB3 - 1063 - 106
d484METMETLYSLYSFFFF3 - 1063 - 106
d595ALAALALYSLYSCCCB5 - 1065 - 106
d5105ALAALALYSLYSGGGG5 - 1065 - 106
d6116GLYGLYHYPHYPAAAC6 - 291 - 24
d6126GLYGLYHYPHYPDDDD36 - 591 - 24
d7137GLYGLYHYPHYPAAAC6 - 291 - 24
d7147GLYGLYHYPHYPEEEE66 - 891 - 24
d8158GLYGLYHYPHYPAAAC6 - 291 - 24
d8168GLYGLYHYPHYPHHHH6 - 291 - 24
d9179GLYGLYHYPHYPAAAC6 - 291 - 24
d9189GLYGLYHYPHYPJJJI66 - 891 - 24
d101910PROPROPROPROAAAC7 - 282 - 23
d102010PROPROPROPROIIIJ37 - 582 - 23
d112111GLYGLYHYPHYPDDDD36 - 591 - 24
d112211GLYGLYHYPHYPEEEE66 - 891 - 24
d122212GLYGLYHYPHYPDDDD36 - 591 - 24
d122312GLYGLYHYPHYPHHHH6 - 291 - 24
d132413GLYGLYHYPHYPDDDD36 - 591 - 24
d132513GLYGLYHYPHYPJJJI66 - 891 - 24
d142614PROPROPROPRODDDD37 - 582 - 23
d142714PROPROPROPROIIIJ37 - 582 - 23
d152815GLYGLYHYPHYPEEEE66 - 891 - 24
d152915GLYGLYHYPHYPHHHH6 - 291 - 24
d163016GLYGLYHYPHYPEEEE66 - 891 - 24
d163116GLYGLYHYPHYPJJJI66 - 891 - 24
d173217PROPROPROPROEEEE67 - 882 - 23
d173317PROPROPROPROIIIJ37 - 582 - 23
d183318ALAALALYSLYSFFFF5 - 1065 - 106
d183418ALAALALYSLYSGGGG5 - 1065 - 106
d193519GLYGLYHYPHYPHHHH6 - 291 - 24
d193619GLYGLYHYPHYPJJJI66 - 891 - 24
d203720PROPROPROPROHHHH7 - 282 - 23
d203820PROPROPROPROIIIJ37 - 582 - 23
d213921PROPROPROPROJJJI67 - 882 - 23
d214021PROPROPROPROIIIJ37 - 582 - 23

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

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Components

#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 interestY
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.32→79.77 Å / Num. obs: 35250 / % possible obs: 90.2 % / Redundancy: 1.8 % / CC1/2: 1 / Net I/σ(I): 2.1
Reflection shellResolution: 2.32→2.34 Å / Num. unique obs: 997 / CC1/2: 0.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.324→79.769 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.314 / WRfactor Rwork: 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
RfactorNum. reflection% reflection
Rfree0.2853 947 4.849 %
Rwork0.2412 18583 -
all0.243 --
obs-19530 89.595 %
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: 40.861 Å2
Baniso -1Baniso -2Baniso -3
1--0.565 Å20.43 Å2-0.858 Å2
2--0.796 Å20.149 Å2
3----0.358 Å2
Refinement stepCycle: LAST / Resolution: 2.324→79.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 0 25 4036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134134
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173518
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.6665700
X-RAY DIFFRACTIONr_angle_other_deg1.171.588255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1115556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18725.689167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85715516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.104159
X-RAY DIFFRACTIONr_chiral_restr0.0490.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02663
X-RAY DIFFRACTIONr_nbd_refined0.1930.21087
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.22832
X-RAY DIFFRACTIONr_nbtor_refined0.150.22148
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21662
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.253
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3020.225
X-RAY DIFFRACTIONr_nbd_other0.2620.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.24
X-RAY DIFFRACTIONr_mcbond_it2.8984.6022245
X-RAY DIFFRACTIONr_mcbond_other2.8984.6022245
X-RAY DIFFRACTIONr_mcangle_it4.46.8932791
X-RAY DIFFRACTIONr_mcangle_other4.46.8932792
X-RAY DIFFRACTIONr_scbond_it3.4914.7631889
X-RAY DIFFRACTIONr_scbond_other3.494.7641890
X-RAY DIFFRACTIONr_scangle_it5.4577.0442908
X-RAY DIFFRACTIONr_scangle_other5.4567.0442909
X-RAY DIFFRACTIONr_lrange_it7.0158.1524658
X-RAY DIFFRACTIONr_lrange_other7.00958.1574659
X-RAY DIFFRACTIONr_ncsr_local_group_10.1150.052925
X-RAY DIFFRACTIONr_ncsr_local_group_20.0940.052964
X-RAY DIFFRACTIONr_ncsr_local_group_30.1090.052815
X-RAY DIFFRACTIONr_ncsr_local_group_40.1110.052946
X-RAY DIFFRACTIONr_ncsr_local_group_50.0970.052860
X-RAY DIFFRACTIONr_ncsr_local_group_60.0730.05410
X-RAY DIFFRACTIONr_ncsr_local_group_70.0640.05411
X-RAY DIFFRACTIONr_ncsr_local_group_80.1050.05410
X-RAY DIFFRACTIONr_ncsr_local_group_90.0660.05412
X-RAY DIFFRACTIONr_ncsr_local_group_100.0530.05375
X-RAY DIFFRACTIONr_ncsr_local_group_110.0440.05409
X-RAY DIFFRACTIONr_ncsr_local_group_120.1040.05410
X-RAY DIFFRACTIONr_ncsr_local_group_130.0420.05410
X-RAY DIFFRACTIONr_ncsr_local_group_140.0110.05375
X-RAY DIFFRACTIONr_ncsr_local_group_150.0950.05408
X-RAY DIFFRACTIONr_ncsr_local_group_160.0630.05415
X-RAY DIFFRACTIONr_ncsr_local_group_170.0440.05378
X-RAY DIFFRACTIONr_ncsr_local_group_180.0940.052824
X-RAY DIFFRACTIONr_ncsr_local_group_190.1060.05408
X-RAY DIFFRACTIONr_ncsr_local_group_200.0980.05373
X-RAY DIFFRACTIONr_ncsr_local_group_210.0430.05377
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
2.324-2.3840.346670.32513300.32615700.5270.53788.98090.33
2.384-2.450.339700.32614110.32716390.5140.52290.360.327
2.45-2.5210.384620.32813000.3314780.540.52892.15160.327
2.521-2.5980.342730.32212840.32314860.6170.62591.3190.328
2.598-2.6830.336670.27912430.28214490.7290.74790.40720.283
2.683-2.7770.322580.26112200.26413810.760.7992.54160.268
2.777-2.8820.352580.24912100.25413840.7720.81291.61850.255
2.882-30.251660.24610870.24612460.8170.81292.53610.255
3-3.1330.267600.23411160.23612580.7970.81893.48170.245
3.133-3.2850.27420.24310130.24411710.8030.82690.09390.255
3.285-3.4630.276580.2189590.22111440.8620.88788.89860.23
3.463-3.6720.255350.1958820.19710480.8790.91487.50.213
3.672-3.9250.246470.1967870.19810130.8950.9282.32970.218
3.925-4.2390.258320.2027600.2049220.9070.92285.90020.229
4.239-4.6420.233290.1846930.1868900.9140.92781.12360.209
4.642-5.1880.316320.2355940.247670.830.87981.61670.284
5.188-5.9860.289290.3065760.3056700.8770.86690.29850.346
5.986-7.3210.339250.2635030.2665800.8240.89191.03450.312
7.321-10.3110.236190.2074050.2084580.9250.92292.57640.264
10.311-79.7690.25180.2762100.2732440.9090.89293.44260.363

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