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

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Basic information

Entry
Database: PDB / ID: 5hzp
TitleStructure of human C4b-binding protein alpha chain CCP domains 1 and 2 in complex with the hypervariable region of group A Streptococcus M49 protein.
Components
  • C4b-binding protein alpha chain
  • M protein, serotype 49
KeywordsIMMUNE SYSTEM / M protein / Compliment / 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 / : / phagocytosis / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of protein catabolic process ...regulation of opsonization / response to symbiotic bacterium / negative regulation of complement activation, classical pathway / T cell mediated immunity / cell wall / : / 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) ...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
PHOSPHATE ION / C4b-binding protein alpha chain / M protein, serotype 49
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M49 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.74 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 2, 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 1.3Oct 4, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: M protein, serotype 49
A: M protein, serotype 49
B: C4b-binding protein alpha chain
D: C4b-binding protein alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2159
Polymers49,7404
Non-polymers4755
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.068, 78.068, 345.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein M protein, serotype 49


Mass: 10529.470 Da / Num. of mol.: 2 / Fragment: UNP residues 42-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M49 (bacteria)
Gene: emm49 / Production host: Escherichia coli (E. coli) / References: UniProt: P16947
#2: Protein C4b-binding protein alpha chain / C4bp / Proline-rich protein / PRP


Mass: 14340.655 Da / Num. of mol.: 2 / Fragment: UNP residues 49-172 / Mutation: L29M,L46M
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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 5.29 Å3/Da / Density % sol: 76.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.9 / Details: 1.6 M Sodium Potassium Phosphate pH 6.9.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.74→71.135 Å / Num. obs: 29382 / % possible obs: 99.8 % / Redundancy: 9.4 % / CC1/2: 0.61 / Net I/σ(I): 11.3
Reflection shellResolution: 2.74→2.89 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIX1.9_1692phasing
RefinementResolution: 2.74→71.135 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.25
RfactorNum. reflection% reflection
Rfree0.3132 1989 6.93 %
Rwork0.2546 --
obs0.2586 28700 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.74→71.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 25 20 3191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093236
X-RAY DIFFRACTIONf_angle_d1.2194353
X-RAY DIFFRACTIONf_dihedral_angle_d19.7741219
X-RAY DIFFRACTIONf_chiral_restr0.044456
X-RAY DIFFRACTIONf_plane_restr0.004573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7405-2.83840.43091700.42112279X-RAY DIFFRACTION86
2.8384-2.95210.45781940.38712611X-RAY DIFFRACTION98
2.9521-3.08650.41821960.36242637X-RAY DIFFRACTION99
3.0865-3.24920.39082000.33852667X-RAY DIFFRACTION99
3.2492-3.45270.37171980.31052636X-RAY DIFFRACTION99
3.4527-3.71930.32542010.25022704X-RAY DIFFRACTION99
3.7193-4.09360.29662000.1992693X-RAY DIFFRACTION100
4.0936-4.68580.22572030.18532721X-RAY DIFFRACTION100
4.6858-5.90320.29052080.21842787X-RAY DIFFRACTION100
5.9032-71.15930.29062190.2492976X-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)
18.63866.4482-0.84944.9889-0.91730.5407-1.04081.195-2.1128-1.73940.0054-1.42920.6715-0.06941.03291.2597-0.610.32312.3958-0.10461.1473-17.619415.477111.5892
20.0328-0.00130.13840.1799-0.91535.7553-0.05710.42660.29360.22940.0870.0608-0.2884-0.5069-0.06530.8816-0.28280.04241.45860.11320.1503-17.259722.02464.6805
30.6182-0.0646-0.59120.253-0.23626.3948-0.04480.3876-0.08920.1685-0.05040.1469-0.1017-0.0218-0.01250.8162-0.1016-0.00791.44530.0240.1876-13.358116.109260.7673
41.38320.79360.23740.45320.13390.03940.12330.0119-0.98492.0525-0.7648-0.7191-1.49230.64750.61821.5447-0.2496-0.16911.98750.56331.1781-1.8491-4.054846.7022
54.29252.8331-1.54186.6799-4.345.8733-0.0339-1.1898-1.35681.2411-0.2149-0.2340.9947-0.15040.23681.5051-0.32070.06412.10350.39440.7511-3.38632.398248.541
67.5274.6395.20263.9563.07823.8769-0.4651-2.98542.39411.9385-0.55540.6937-1.6886-0.13031.04512.23840.347-0.10852.1064-0.48071.0514-26.952342.657350.9353
76.16895.5046.46694.96465.95837.4271-0.1484-3.91592.15392.7506-1.0821.5027-0.5819-1.07491.1892.81860.5532-0.02242.9533-0.60861.4739-29.965741.850459.2735
88.6391.486.64973.5321-1.09096.63430.1295-3.32630.84413.96370.3583-0.04080.6182-0.1583-0.46851.8831-0.01860.10132.4608-0.00860.6919-26.22134.610153.1158
94.5584-1.38095.77023.6354-0.39547.8766-0.1223-0.23570.03561.43390.2406-0.3716-0.25721.367-0.1721.21940.15270.04751.77180.00260.4162-22.748929.943644.7437
106.5601-3.59830.16373.8375-3.03825.4875-0.3379-2.31581.29712.97440.5429-1.2649-2.73431.4561-0.21662.87170.2049-0.60982.7759-0.53591.5185-18.964545.158655.5288
112.3347-0.3916-3.67061.14240.31115.85-0.5189-1.1671.17571.44770.5656-0.5644-1.61431.1592-0.09161.49290.452-0.25032.2395-0.49750.9356-20.773337.386745.6474
123.8986-0.43654.11842.7562-1.65954.88610.09380.6018-0.2323-0.04850.2676-0.1481.50820.7577-0.42760.7108-0.0951-0.07041.77230.15690.3539-25.723819.927322.5483
132.68-0.4462-1.64637.8293.23382.0002-0.03390.15240.0708-0.83080.1438-0.1933-1.11990.6761-0.10020.6114-0.1484-0.02221.76260.15270.4326-24.685929.020622.7374
141.0535-0.1707-0.59551.9547-0.40733.33940.1873-0.07230.2713-0.4335-0.10390.1120.0644-0.03970.05630.8839-0.21280.04191.502-0.0281-0.13131.201620.875319.5173
151.9079-2.7491-2.25693.98963.22642.71020.02980.6695-0.2369-1.5197-0.08170.1246-0.4643-0.9614-0.01591.237-0.2512-0.03022.12340.11770.561-32.332324.942811.5805
161.0178-0.9108-1.14963.77891.72994.24710.018-0.0026-0.08210.0585-0.02350.25960.5647-0.62770.14980.9238-0.14920.08721.81690.2580.0393-33.897622.955624.5674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 56 through 60 )
2X-RAY DIFFRACTION2chain 'C' and (resid 61 through 126 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 126 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 10 )
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 62)
6X-RAY DIFFRACTION6chain 'D' and (resid 0 through 13 )
7X-RAY DIFFRACTION7chain 'D' and (resid 14 through 27 )
8X-RAY DIFFRACTION8chain 'D' and (resid 28 through 33 )
9X-RAY DIFFRACTION9chain 'D' and (resid 34 through 44 )
10X-RAY DIFFRACTION10chain 'D' and (resid 45 through 53 )
11X-RAY DIFFRACTION11chain 'D' and (resid 54 through 62 )
12X-RAY DIFFRACTION12chain 'D' and (resid 63 through 73 )
13X-RAY DIFFRACTION13chain 'D' and (resid 74 through 86 )
14X-RAY DIFFRACTION14chain 'B' and (resid 63 through 124)
15X-RAY DIFFRACTION15chain 'D' and (resid 87 through 102 )
16X-RAY DIFFRACTION16chain 'D' and (resid 103 through 124 )

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