Bioisis

"Complement fragment C3b complex with extracellular fibrinogenbinding protein (Efb) from S. aureus"

Experimental SAS Curve

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Low_res_thumbnail

Experimental Mass

206,000 Da

Experimental Details for BID:  C3bE2P
Experiment ID: 103
Collected at: ALS BL 12.3.1
Contributors: Weinkam, P ,  Hammel, M ,  Schneidman-duhovny, D ,  Webb, B ,  Sali, A ,  Tainer, J
The complement system is a major target of immune evasion by Staphylococcus aureus. Although many evasion proteins have been described, little is known about their molecular mechanisms of action. Here we demonstrate that the extracellular fibrinogenbinding protein (Efb) from S. aureus acts as an allosteric inhibitor by inducing conformational changes in complement fragment C3b that propagate across several domains and influence functional regions far distant from the Efb binding site. Most notably, the inhibitor impaired the interaction of C3b with complement factor B and, consequently, formation of the active C3 convertase. As this enzyme complex is critical for both activation and amplification of the complement response, its allosteric inhibition likely represents a fundamental contribution to the overall immune evasion strategy of S. aureus.
Solution state of complement fragment C3b in the complex with extracellular fibrinogen binding protein (Efb) from S. aureus. An equimolar C3b/Efb-C complex (0.5–1.2 mg per mL) measured by SAXS for both short (0.5 s) and long time exposure (5 s). An equimolar C3b/Efb-C complex (0.5–1.2 mg per mL) measured by SAXS for both short (0.5 s) and long time exposure (5 s).

Electron Pair Distribution

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       Dmax → 180 Å


Guinier Plot

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     Guinier Rg → 48.23 Å

Real Space Rg → 50.04 Å

The Guinier plot is used to estimate the radius of gyration, Rg, which is taken from the slope of a line observed at low scattering angles (typically in the range where q* Rg < 1.3). This should be in reasonable agreement with the real space Rg.


Kratky Plot

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The Kratky plot can be used to visually assess the degree of "unfoldedness" of a protein or RNA sample. The plot of a well-behaved folded protein approaches the baseline at high q values creating a parabolic shape.


Ensemble Model

A ENSEMBLE model was determined using the following:

Simulation MethodAllosMod-FoXS 
Simulation AlgorithmMD 
Ensemble Size10000 
Selection MethodMES 
Member Size
Scoring Functionchi 
Score0.2 

Ensemble Fit

Med_res_ensemble_fit

The red line is the calculated SAXS profile from the ENSEMBLE model scaled to the experimental SAXS curve (cyan).


Additional Experimental Details
Title

Complement fragment C3b complex with extracellular fibrinogenbinding protein (Efb) from S. aureus

Description

The complement system is a major target of immune evasion by Staphylococcus aureus. Although many evasion proteins have been described, little is known about their molecular mechanisms of action. Here we demonstrate that the extracellular fibrinogenbinding protein (Efb) from S. aureus acts as an allosteric inhibitor by inducing conformational changes in complement fragment C3b that propagate across several domains and influence functional regions far distant from the Efb binding site. Most notably, the inhibitor impaired the interaction of C3b with complement factor B and, consequently, formation of the active C3 convertase. As this enzyme complex is critical for both activation and amplification of the complement response, its allosteric inhibition likely represents a fundamental contribution to the overall immune evasion strategy of S. aureus.

Publication

Proceedings of the National Academy of Sciences of the United States of America, Vol. 107(41), 17621-17626

Contributors

Weinkam, P ,  Hammel, M ,  Schneidman-duhovny, D ,  Webb, B ,  Sali, A ,  Tainer, J

Genomics and Proteomics

The experiment is composed of 2 genes/ORFs

Abbreviated name: C3b

Annotation: complement C3b fragment

SPMYSIITPN ILRLESEETM VLEAHDAQGD VPVTVTVHDF PGKKLVLSSE KTVLTPATNH MGNVTFTIPA NREFKSEKGR NKFVTVQATF GTQVVEKVVL VSLQSGYLFI QTDKTIYTPG STVLYRIFTV NHKLLPVGRT VMVNIENPEG IPVKQDSLSS QNQLGVLPLS WDIPELVNMG QWKIRAYYEN SPQQVFSTEF EVKEYVLPSF EVIVEPTEKF YYIYNEKGLE VTITARFLYG KKVEGTAFVI FGIQDGEQRI SLPESLKRIP IEDGSGEVVL SRKVLLDGVR AEDLVGKSLY VSATVILHSG SDMVQAERSG IPIVTSPYQI HFTKTPKYFK PGMPFDLMVF VTNPDGSPAY RVPVAVQGED TVQSLTQGDG VAKLSINTHP SQKPLSITVR TKKQELSEAE QATRTMQALP YSTVGNSNNY LHLSVLRTEL RPGETLNVNF LLRMDRAHEA KIRYYTYLIM NKGRLLKAGR QVREPGQDLV VLPLSITTDF IPSFRLVAYY TLIGASGQRE VVADSVWVDV KDSCVGSLVV KSGQSEDRQP VPGQQMTLKI EGDHGARVVL VAVDKGVFVL NKKNKLTQSK IWDVVEKADI GCTPGSGKDY AGVFSDAGLT FTSSSGQQTA QRAELQCPQD EDIIAEENIV SRSEFPESWL WNVEDLKEPP KNGISTKLMN IFLKDSITTW EILAVSMSDK KGICVADPFE VTVMQDFFID LRLPYSVVRN EQVEIRAVLY NYRQNQELKV RVELLHNPAF CSLATTKRRH QQTVTIPPKS SLSVPYVIVP LKTGLQEVEV KAAVYHHFIS DGVRKSLKVV PEGIRMNKTV AVRTLDPERL GREGVQKEDI PPADLSDQVP DTESETRILL QGTPVAQMTE DAVDAERLKH LIVTPSGCGE ENMIGMTPTV IAVHYLDETE QWEKFGLEKR QGALELIKKG YTQQLAFRQP SSAFAAFVKR APSTWLTAYV VKVFSLAVNL IAIDSQVLCG AVKWLILEKQ KPDGVFQEDA PVIHQEMIGG LRNNNEKDMA LTAFVLISLQ EAKDICEEQV NSLPGSITKA GDFLEANYMN LQRSYTVAIA GYALAQMGRL KGPLLNKFLT TAKDKNRWED PGKQLYNVEA TSYALLALLQ LKDFDFVPPV VRWLNEQRYY GGGYGSTQAT FMVFQALAQY QKDAPDHQEL NLDVSLQLPS RSSKITHRIH WESASLLRSE ETKENEGFTV TAEGKGQGTL SVVTMYHAKA KDQLTCNKFD LKVTIKPAPE TEKRPQDAKN TMILEICTRY RGDQDATMSI LDISMMTGFA PDTDDLKQLA NGVDRYISKY ELDKAFSDRN TLIIYLDKVS HSEDDCLAFK VHQYFNVELI QPGAVKVYAY YNLEESCTRF YHPEKEDGKL NKLCRDELCR CAEENCFIQK DKVTLEERLD KACEPGVDYV YKTRLVKVQL SNDFDEYIMA IEQTIKSGSD EVQVGQQRTF ISPIKCREAL KLEEKKHYLM WGLSSDFWGE KPNLSYIIGK DTWVEHWPEE DECQDEENQK QCQDLGAFTE SMVVFGCPN
categoryamino acid composition(%)
HydrophobicI(5.2) V(9.2) L(9.2) M(2.1) A(5.8) G(5.9) P(4.9)
AromaticF(3.7) W(1.1) Y(3.6)
HydrophilicR(4.3) K(6.8) E(7.6) D(5.6) Q(5.5) N(3.7) H(1.7) S(6.5) T(6.5) C(1.4)

Abbreviated name: EFBC

Annotation: C-terminus of extracellular fibrinogen binding from S. aureus protein (Efb)

FNKPAATDAT IKKEQKLIQA QNLVREFEKT HTVSAHRKAQ KAVNLVSFEY KVKKMVLQER IDNVLKQGLV R
categoryamino acid composition(%)
HydrophobicI(4.2) V(11.3) L(8.5) M(1.4) A(9.9) G(1.4) P(1.4)
AromaticF(4.2) W(0.0) Y(1.4)
HydrophilicR(5.6) K(15.5) E(7.0) D(2.8) Q(8.5) N(5.6) H(2.8) S(2.8) T(5.6) C(0.0)