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- PDB-5hyt: Structure of human C4b-binidng protein alpha chain CCP domains 1 ... -

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Basic information

Entry
Database: PDB / ID: 5hyt
TitleStructure of human C4b-binidng protein alpha chain CCP domains 1 and 2 in complex with the hypervariable region of group A Streptococcus M22 protein
Components
  • C4b-binding protein alpha chain
  • Precursor to Protein Sir22
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 / cell wall / 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 / cell wall / 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-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 ...C4b-binding protein alpha, oligomerization domain / Oligomerization domain of C4b-binding protein alpha / : / 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/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / 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 / Precursor to Protein Sir22
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsBuffalo, C.Z. / Bahn-Suh, A.J. / Ghosh, P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007240 United States
American Heart Association14PRE18320032 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI096837 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI077780 United States
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 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Precursor to Protein Sir22
B: C4b-binding protein alpha chain
C: Precursor to Protein Sir22
D: C4b-binding protein alpha chain
F: C4b-binding protein alpha chain
G: Precursor to Protein Sir22
H: C4b-binding protein alpha chain
E: Precursor to Protein Sir22


Theoretical massNumber of molelcules
Total (without water)96,1198
Polymers96,1198
Non-polymers00
Water1,26170
1
A: Precursor to Protein Sir22
B: C4b-binding protein alpha chain
C: Precursor to Protein Sir22
D: C4b-binding protein alpha chain


Theoretical massNumber of molelcules
Total (without water)48,0594
Polymers48,0594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: C4b-binding protein alpha chain
G: Precursor to Protein Sir22
H: C4b-binding protein alpha chain
E: Precursor to Protein Sir22


Theoretical massNumber of molelcules
Total (without water)48,0594
Polymers48,0594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.079, 80.348, 152.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Precursor to Protein Sir22


Mass: 9865.811 Da / Num. of mol.: 4 / Fragment: UNP residues 48-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: sir22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q54901
#2: Protein
C4b-binding protein alpha chain / C4bp / Proline-rich protein / PRP


Mass: 14163.894 Da / Num. of mol.: 4 / 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.: 70 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 2 M Ammonium Sulfate, 2% PEG 400, HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.54→76.47 Å / Num. obs: 28415 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.7
Reflection shellResolution: 2.54→2.68 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HYP

5hyp


Resolution: 2.54→76.47 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.01
RfactorNum. reflection% reflection
Rfree0.2744 2000 7.06 %
Rwork0.2134 --
obs0.2178 28328 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.54→76.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4844 0 0 70 4914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094964
X-RAY DIFFRACTIONf_angle_d1.4856704
X-RAY DIFFRACTIONf_dihedral_angle_d14.7481828
X-RAY DIFFRACTIONf_chiral_restr0.062744
X-RAY DIFFRACTIONf_plane_restr0.007868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.60350.41921390.34011836X-RAY DIFFRACTION99
2.6035-2.67390.37611410.30881849X-RAY DIFFRACTION100
2.6739-2.75260.28251390.28551839X-RAY DIFFRACTION99
2.7526-2.84150.32321410.281850X-RAY DIFFRACTION99
2.8415-2.9430.33851410.2831851X-RAY DIFFRACTION100
2.943-3.06090.40131410.27581855X-RAY DIFFRACTION100
3.0609-3.20020.33761420.27741871X-RAY DIFFRACTION100
3.2002-3.36890.32041420.2441879X-RAY DIFFRACTION100
3.3689-3.580.30381430.22161867X-RAY DIFFRACTION100
3.58-3.85640.29381430.21896X-RAY DIFFRACTION100
3.8564-4.24440.24021440.17511888X-RAY DIFFRACTION100
4.2444-4.85850.20781440.16231895X-RAY DIFFRACTION100
4.8585-6.12080.2471460.18221930X-RAY DIFFRACTION100
6.1208-76.50460.21011540.18842022X-RAY DIFFRACTION99
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)
17.8584-0.87924.92784.0229-2.59896.5381-0.1769-0.62710.5664-0.03280.30020.0785-0.2825-0.7084-0.12840.54530.05160.03670.4879-0.17450.4261-3.46842.896222.0044
25.74251.8739-1.37547.1863.57173.3793-0.39180.5711-0.1381-0.01450.09880.17260.42040.06890.09060.45820.00470.02190.5343-0.05830.192912.7688-12.65264.1792
39.8356-6.6516-1.3185.01691.3552.45210.51520.63110.4746-1.8323-0.7674-0.4888-0.02411.1157-0.16780.6410.11510.0330.97070.09620.51822.1722-13.8634.9297
46.7573-5.25570.69274.3769-1.28424.4749-0.185-0.5013-0.50310.3342-0.05280.58380.31990.09240.09240.3225-0.0580.02280.5387-0.12610.398110.6619-12.332511.4042
52.19110.66891.62941.9969-1.19614.7596-0.4091-0.37380.54690.44640.23580.4779-0.5875-0.7638-0.12820.57990.12010.01570.688-0.07770.4963-10.32666.877610.8608
61.4784-2.8677-0.45259.2382-2.52153.2390.72331.2527-1.0817-1.11760.141.2789-0.2016-2.136-0.40560.67540.1274-0.0221.2895-0.15580.496-13.09582.20516.5402
75.62592.52781.70232.3333-0.68088.07640.3912.16470.5392-0.9172-0.27362.2962-0.49840.2132-0.31920.86330.389-0.29521.31540.10861.1226-20.299411.9257-0.9179
80.1651-0.20730.50551.8103-0.16441.72970.26961.5243-0.10750.463-0.15360.47610.31580.4506-0.07140.67560.0838-0.0070.7442-0.0870.4564-4.61596.66123.0028
98.061-8.45396.42659.1459-6.8055.2488-0.40461.69771.64690.4615-0.9162-1.1799-0.90041.90140.78970.73510.0202-0.13640.876-0.03230.51070.26149.08148.7861
103.0201-4.09853.19326.5933-3.11874.7339-0.83712.36880.77881.2294-0.21210.649-2.19830.12340.44691.09610.3689-0.17750.92510.16480.8652-16.346916.68561.1426
117.6758-1.66395.05562.5243-3.88537.50870.52230.5519-0.6765-0.381-0.25240.25670.5248-0.4632-0.18650.42190.0929-0.01340.5005-0.18980.4794-6.93-4.951323.5587
122.899-1.5927-0.6278.2099-2.03275.8825-0.1736-0.7324-0.42050.15970.2579-0.04490.3347-0.2144-0.10240.42110.00390.07270.5464-0.01930.5182-1.8076-11.282146.7043
135.19261.33862.9411.41451.07684.4702-0.22-0.23960.3869-0.2393-0.140.7159-0.0629-1.55480.26710.53420.0206-0.0381.1966-0.28160.8123-27.4621-2.149825.5624
147.35044.191-1.54927.6549-0.81063.77740.0078-0.0852-0.81320.20940.066-0.85470.03640.1479-0.06780.41220.07650.05460.70750.14350.5610.8518-29.682418.9958
157.9469-1.66334.56553.3897-0.93247.9046-0.12220.0546-0.051-0.1739-0.02950.3930.0032-0.94610.05470.3043-0.03940.02980.5086-0.07240.3196-22.1663-29.46789.381
168.4352-1.54557.3643.3357-2.94239.09070.0516-0.5679-0.9044-0.05940.23480.29290.4393-0.1886-0.33850.40450.03860.08110.44840.09430.4013-13.5566-39.148330.5108
172.31122.8748-1.30553.5293-1.36191.09360.6567-0.13730.4590.6514-0.70820.61860.0195-1.3630.09810.59110.13670.13570.66160.04290.5174-15.7885-23.49655.8775
183.08622.5376-0.24966.01745.83429.12550.3661-0.52160.17731.42320.1581-0.18650.7949-0.5115-0.1120.79390.23250.05630.78710.20380.539-11.3025-27.266160.5144
194.1671.70391.33315.2633.76452.8532-0.06270.64450.416-0.0230.34250.0586-0.5675-0.7431-0.40960.45190.02260.0650.54620.20540.4281-11.8313-30.570446.141
207.02772.42751.65038.01564.73655.9570.27540.04161.04660.28250.2854-0.079-0.186-0.029-0.25250.6770.1170.15740.58070.0830.5164-10.2962-18.787852.6852
216.4881.2543.18359.33233.14963.53220.5199-0.9846-0.8094-0.3077-0.80621.58480.598-1.24110.18320.5565-0.0113-0.05550.80980.15690.8366-27.569-39.287730.6004
223.7471-0.71730.88938.43741.66997.957-0.5528-0.28490.51460.27270.21651.3346-0.754-1.93540.33640.46220.1820.0590.87940.17560.6425-30.8694-33.283531.1563
230.2340.4126-0.57323.1042-1.30731.38890.5862-1.0744-0.4493-0.27710.30691.38490.7877-1.7883-0.90910.5902-0.1688-0.05711.28650.42881.2343-39.3319-39.886831.7895
244.14062.2241-1.7415.33172.96234.22940.8867-0.5425-1.8191-0.6281-0.0531.17680.8622-1.4997-0.41330.6019-0.2164-0.21131.13870.39841.3496-34.2751-45.142934.4215
253.7784-1.3095.44443.8397-2.32417.78910.12130.6810.19180.2575-0.2345-0.0588-0.11360.50840.10690.4383-0.0195-0.01880.31240.01560.3293-12.0612-31.346227.4323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 80 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 13 )
3X-RAY DIFFRACTION3chain 'B' and (resid 14 through 27 )
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 59 )
5X-RAY DIFFRACTION5chain 'B' and (resid 60 through 73 )
6X-RAY DIFFRACTION6chain 'B' and (resid 74 through 86 )
7X-RAY DIFFRACTION7chain 'B' and (resid 87 through 102 )
8X-RAY DIFFRACTION8chain 'B' and (resid 103 through 109 )
9X-RAY DIFFRACTION9chain 'B' and (resid 110 through 115 )
10X-RAY DIFFRACTION10chain 'B' and (resid 116 through 124 )
11X-RAY DIFFRACTION11chain 'C' and (resid 52 through 79 )
12X-RAY DIFFRACTION12chain 'D' and (resid 0 through 59 )
13X-RAY DIFFRACTION13chain 'D' and (resid 60 through 124 )
14X-RAY DIFFRACTION14chain 'F' and (resid 1 through 59 )
15X-RAY DIFFRACTION15chain 'F' and (resid 60 through 124 )
16X-RAY DIFFRACTION16chain 'G' and (resid 52 through 80 )
17X-RAY DIFFRACTION17chain 'H' and (resid 0 through 13 )
18X-RAY DIFFRACTION18chain 'H' and (resid 14 through 33 )
19X-RAY DIFFRACTION19chain 'H' and (resid 34 through 47 )
20X-RAY DIFFRACTION20chain 'H' and (resid 48 through 59 )
21X-RAY DIFFRACTION21chain 'H' and (resid 60 through 74 )
22X-RAY DIFFRACTION22chain 'H' and (resid 75 through 86 )
23X-RAY DIFFRACTION23chain 'H' and (resid 87 through 109 )
24X-RAY DIFFRACTION24chain 'H' and (resid 110 through 124 )
25X-RAY DIFFRACTION25chain 'E' and (resid 52 through 79 )

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