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- PDB-8tgt: Structure of human C4b-binding protein alpha chain CCP domains 1 ... -

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Basic information

Entry
Database: PDB / ID: 8tgt
TitleStructure of human C4b-binding protein alpha chain CCP domains 1 and 2 in complex with the hypervariable region of group A Streptococcus M68 protein
Components
  • C4b-binding protein alpha chain
  • M protein
KeywordsIMMUNE SYSTEM / immune evasion / human complement
Function / homology
Function and homology information


regulation of opsonization / negative regulation of complement activation, classical pathway / response to symbiotic bacterium / T cell mediated immunity / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of protein catabolic process / blood microparticle / innate immune response / extracellular space ...regulation of opsonization / negative regulation of complement activation, classical pathway / response to symbiotic bacterium / T cell mediated immunity / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of protein catabolic process / blood microparticle / innate immune response / extracellular space / RNA binding / extracellular region / plasma membrane
Similarity search - Function
C4b-binding protein alpha, oligomerization domain / Oligomerization domain of C4b-binding protein alpha / M protein repeat / M protein repeat / : / Streptococcal M proteins C repeat profile. / : / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain ...C4b-binding protein alpha, oligomerization domain / Oligomerization domain of C4b-binding protein alpha / M protein repeat / M protein repeat / : / Streptococcal M proteins C repeat profile. / : / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily
Similarity search - Domain/homology
C4b-binding protein alpha chain / M protein
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsKolesinski, P. / Ghosh, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH R01 AI154149 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Conservation of C4BP-binding sequence patterns in Streptococcus pyogenes M and Enn proteins.
Authors: Kolesinski, P. / McGowan, M. / Botteaux, A. / Smeesters, P.R. / Ghosh, P.
History
DepositionJul 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: 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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _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
A: M protein
B: M protein
C: C4b-binding protein alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9479
Polymers39,6853
Non-polymers2626
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-67 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.037, 49.664, 80.403
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-201-

CA

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Components

#1: Protein M protein


Mass: 12760.388 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: emm / Production host: Escherichia coli (E. coli) / References: UniProt: Q6V9M3
#2: Protein C4b-binding protein alpha chain / C4bp / Proline-rich protein / PRP


Mass: 14163.894 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C4BPA, C4BP / Production host: Escherichia coli (E. coli) / References: UniProt: P04003
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.0, 14% PEG 3350, 10% ethylene glycol, 0.2 M calcium chloride, 1 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9789, 0.918, 0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2022
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.9181
30.97931
ReflectionResolution: 2.5→39.3 Å / Num. obs: 15422 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.275 / Rrim(I) all: 0.286 / Net I/σ(I): 8.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 13.2 % / Rmerge(I) obs: 3.524 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1715 / CC1/2: 0.65 / Rrim(I) all: 3.666 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→37.63 Å / SU ML: 0.4044 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 40.3029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3441 1327 10.14 %
Rwork0.3126 11756 -
obs0.3158 13083 84.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.58 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 0 9 20 1632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00151626
X-RAY DIFFRACTIONf_angle_d0.34182208
X-RAY DIFFRACTIONf_chiral_restr0.027254
X-RAY DIFFRACTIONf_plane_restr0.0016295
X-RAY DIFFRACTIONf_dihedral_angle_d3.0582239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.461170.389995X-RAY DIFFRACTION66.11
2.6-2.720.42811190.36941068X-RAY DIFFRACTION71.33
2.72-2.860.39211300.35441106X-RAY DIFFRACTION72.41
2.86-3.040.38291380.33451216X-RAY DIFFRACTION80.12
3.04-3.270.45681490.30911337X-RAY DIFFRACTION87.62
3.27-3.60.34291600.31431401X-RAY DIFFRACTION92.04
3.6-4.120.32111660.27041492X-RAY DIFFRACTION95.78
4.12-5.190.27381680.27641519X-RAY DIFFRACTION97.07
5.19-37.630.33741800.3391622X-RAY DIFFRACTION97.41
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)
11.00653473777-0.6698500300052.54154335168-0.0576021268415-1.394849078564.1265993559-0.17222374762-0.1787300795170.0929070569778-0.0282863237858-0.174471495117-0.02212376658240.2148282227260.442872781950.4332042644610.6682001410310.291041306475-0.05919432672471.21057472665-0.03065034551310.40640376506957.296333870831.980078392870.947317099
2-0.04678239038240.08475924624060.1172283048830.267303671397-1.676343428738.91620623211-0.14803746759-0.2212139050730.05768151724820.01064359076110.0327298190408-0.07258487037240.0633678239261-0.2008296708920.1076125581350.4437661879380.1703544937370.01411395343250.9808679600420.01103789362660.30283554061261.530889036924.079086483171.4623416115
31.46981003974-1.297913895750.5856908146131.692340850010.1292741902880.9031900136750.3512073292350.4138686406430.587172188065-0.418835803098-0.385207765482-0.3211098027230.3179328703340.1115326052550.02515100844760.3000497986840.1648682021760.03869139579370.6410543756190.1730463243050.3751882685482.827165167718.3244613737105.835876822
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 52 through 127)AA52 - 1271 - 76
22(chain 'B' and resid 42 through 135)BB42 - 1351 - 90
33(chain 'C' and resid 29 through 123)CC29 - 1231 - 70

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