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- PDB-5hyp: Structure of human C4b-binding protein alpha cain CCP domains 1 a... -

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Basic information

Entry
Database: PDB / ID: 5hyp
TitleStructure of human C4b-binding protein alpha cain CCP domains 1 and 2 in complex with the hypervariable region of group A Streptococcus M28 protein
Components
  • C4b-binding protein alpha chain
  • M28 protein
KeywordsIMMUNE SYSTEM / M protein / Complement / Streptococcus pyogenes / Hypervariable antigen
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 D repeats region profile. / : / Streptococcal M proteins C repeat profile. / : / Complement Module, domain 1 ...C4b-binding protein alpha, oligomerization domain / Oligomerization domain of C4b-binding protein alpha / M protein repeat / M protein repeat / : / Streptococcal M proteins D repeats region profile. / : / Streptococcal M proteins C repeat profile. / : / Complement Module, domain 1 / M protein-type anchor domain / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.024 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C4b-binding protein alpha chain
B: M28 protein


Theoretical massNumber of molelcules
Total (without water)26,3572
Polymers26,3572
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.192, 133.192, 133.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: 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
#2: Protein M28 protein


Mass: 12193.425 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: emm28 / Production host: Escherichia coli (E. coli) / References: UniProt: W0T1Y4
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: 3.74 Å3/Da / Density % sol: 67.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 1.5 M Ammonium Sulfate, 0.1 M Bis-Tris Propane

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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: 3.02→44.397 Å / Num. obs: 8361 / % possible obs: 99.8 % / Redundancy: 9.5 % / CC1/2: 0.48 / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.2
Reflection shellResolution: 3.02→3.07 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.81 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HYU

5hyu


Resolution: 3.024→44.397 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2877 770 9.95 %
Rwork0.2512 --
obs0.2549 7741 92.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.024→44.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 0 0 1215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091247
X-RAY DIFFRACTIONf_angle_d1.3071686
X-RAY DIFFRACTIONf_dihedral_angle_d20.276453
X-RAY DIFFRACTIONf_chiral_restr0.052187
X-RAY DIFFRACTIONf_plane_restr0.005217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.024-3.21340.38611090.3333975X-RAY DIFFRACTION81
3.2134-3.46140.35951190.27941062X-RAY DIFFRACTION86
3.4614-3.80960.29751240.23331149X-RAY DIFFRACTION93
3.8096-4.36040.25241330.20921178X-RAY DIFFRACTION95
4.3604-5.4920.25641360.23331254X-RAY DIFFRACTION99
5.492-44.40210.29071490.27061353X-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)
14.88581.1018-0.98534.91115.12877.89820.2794-1.05481.660.33150.0831.2919-1.4889-1.1684-0.56271.36610.52920.18041.0792-0.05721.2961-34.8990.4991-12.8404
28.787-5.9937-3.46964.11833.90328.95730.57540.98920.6516-1.95180.0404-0.92250.4493-0.422-0.85291.31570.02820.17040.510.12760.7434-19.8976-14.7573-35.4819
37.1161-2.1415-5.412410.81583.32773.3232-0.04740.7724-0.75760.6127-0.4959-1.10014.0849-0.70190.72281.59560.20430.05440.7794-0.01130.6889-17.4871-24.0758-35.0855
47.37910.7599-3.79185.22113.06589.1043-0.0357-1.05910.20191.4939-0.0587-0.45350.18740.84740.06861.73120.0085-0.02360.62570.05990.6058-14.5282-0.795-29.051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 86 )
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 124 )
4X-RAY DIFFRACTION4chain 'B' and (resid 55 through 83 )

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