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- PDB-5i0q: Structure of human C4b-binding protein alpha chain CCP domains 1 ... -

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Basic information

Entry
Database: PDB / ID: 5i0q
TitleStructure of human C4b-binding protein alpha chain CCP domains 1 and 2 in complex with the hypervariable region of mutant group A Streptococcus M2 (K65A, N66A) protein
Components
  • C4b-binding protein alpha chain
  • M protein, serotype 2.1
KeywordsIMMUNE SYSTEM / M protein / Complement / Streptococcus pyogenes / hypervariable antigen
Function / homology
Function and homology information


regulation of opsonization / response to symbiotic bacterium / negative regulation of complement activation, classical pathway / T cell mediated immunity / phagocytosis / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of protein catabolic process / blood microparticle / innate immune response ...regulation of opsonization / response to symbiotic bacterium / negative regulation of complement activation, classical pathway / T cell mediated immunity / phagocytosis / 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 / M protein-type anchor domain / Complement Module, domain 1 / Complement Module; domain 1 / YSIRK type signal peptide / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) ...C4b-binding protein alpha, oligomerization domain / Oligomerization domain of C4b-binding protein alpha / M protein repeat / M protein repeat / M protein-type anchor domain / Complement Module, domain 1 / Complement Module; domain 1 / YSIRK type signal peptide / 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 / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
C4b-binding protein alpha chain / M protein, serotype 2.1
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.293 Å
AuthorsBuffalo, C.Z. / Bahn-Suh, A.J. / Ghosh, P.
CitationJournal: Nat Microbiol / Year: 2016
Title: Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein.
Authors: Buffalo, C.Z. / Bahn-Suh, A.J. / Hirakis, S.P. / Biswas, T. / Amaro, R.E. / Nizet, V. / Ghosh, P.
History
DepositionFeb 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M protein, serotype 2.1
B: C4b-binding protein alpha chain


Theoretical massNumber of molelcules
Total (without water)26,6652
Polymers26,6652
Non-polymers00
Water2,378132
1
A: M protein, serotype 2.1
B: C4b-binding protein alpha chain

A: M protein, serotype 2.1
B: C4b-binding protein alpha chain


Theoretical massNumber of molelcules
Total (without water)53,3294
Polymers53,3294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_455z-1/4,-y+3/4,x+1/41
Unit cell
Length a, b, c (Å)148.598, 148.598, 148.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11B-289-

HOH

21B-302-

HOH

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Components

#1: Protein M protein, serotype 2.1


Mass: 12500.826 Da / Num. of mol.: 1 / Fragment: UNP residues 42-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: emmL2.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P50468
#2: Protein C4b-binding protein alpha chain / C4bp / Proline-rich protein / PRP


Mass: 14163.894 Da / Num. of mol.: 1 / Fragment: UNP residues 49-172
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 5.13 Å3/Da / Density % sol: 76.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 1.5 M Ammonium Sulfate, 0.1 M Bis-Tris Propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.29→49.533 Å / Num. obs: 47421 / % possible obs: 100 % / Redundancy: 40.5 % / CC1/2: 0.99 / Net I/σ(I): 46.4
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 32.6 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 3.22 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementResolution: 2.293→49.533 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22
RfactorNum. reflection% reflection
Rfree0.2243 2568 10.06 %
Rwork0.2034 --
obs0.2055 47375 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.293→49.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 0 132 1384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091283
X-RAY DIFFRACTIONf_angle_d1.4161728
X-RAY DIFFRACTIONf_dihedral_angle_d16.459474
X-RAY DIFFRACTIONf_chiral_restr0.06190
X-RAY DIFFRACTIONf_plane_restr0.005224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2935-2.37540.28854700.25934185X-RAY DIFFRACTION98
2.3754-2.47050.27374850.25334274X-RAY DIFFRACTION100
2.4705-2.5830.2244750.21774241X-RAY DIFFRACTION100
2.583-2.71910.21794800.19844276X-RAY DIFFRACTION100
2.7191-2.88950.24134820.21734278X-RAY DIFFRACTION100
2.8895-3.11260.24494770.21254249X-RAY DIFFRACTION100
3.1126-3.42570.22134750.20594267X-RAY DIFFRACTION100
3.4257-3.92120.22174750.20054276X-RAY DIFFRACTION100
3.9212-4.93960.18344760.16964277X-RAY DIFFRACTION100
4.9396-49.54420.2274710.19974286X-RAY DIFFRACTION100
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)
17.73160.23391.3162.15550.43135.822-0.1585-0.8487-1.36680.2979-0.11990.32681.9439-0.84880.29380.88060.09860.23261.02160.43820.736944.371646.569285.9653
23.80890.59130.67534.2175-2.58765.3894-0.19070.88250.2016-0.96910.75160.84740.6852-0.9941-0.33340.5853-0.29910.05950.58880.21460.440933.242254.685563.9281
32.6047-3.06434.0225.3926-4.82726.21730.10080.42210.5575-0.18560.27070.52640.284-0.6441-0.37030.35020.00760.03690.66910.38270.659235.488771.355851.6476
48.3267-2.5233.22993.2517-1.19424.84280.1558-0.1137-0.01560.19770.0326-0.080.69460.3835-0.15210.3910.07490.14290.18480.03620.229858.374454.747972.2231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 53 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 86 )
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 59 )
4X-RAY DIFFRACTION4chain 'B' and (resid 60 through 124 )

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