Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from Vibrio Vulnificus


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B-Cell Epitope
Epitope  
   
Complex PDB ID 3CFI
Accession Number 3DIEP0243
IEDB ID 98658
Epitope Sequence T81; N82; G83; E84; Y96; L98; D99; S100; D101; K126; R130; K132; D133; R135; E137; V139; W141; D145; T146; P147; A148; G149; Q150; E151; G152; V154
Starting Position81-84,96,98-101,126,130,132-133,135,137,139,141,145
Ending Position154
Epitope Type Discontinuous Epitope

Assay Information  
Assay Antigen SIAIFATLSVAAYQV VNQVQRSNELSQERT ARLNELQRALVMMDS DFRQI… Type II secretory pathway; component EpsJ (25-233) Vibrio vulnificus
PDB CategoryPROTEIN TRANSPORT/Immune system
Keyword General Secretory Pathway; Pseudopilins; Single Chain Antibody; Methylation; PROTEIN TRANSPORT/Immune system COMPLEX
Antibody Residues Interacting with Antigen Open in new window      Download dimplot pdb file
Antibody Chain 1 PDB Chain C
Antigen PDB ChainB
Contact Area for Antigen 716.2
Contact Area for Antibody710.3
CommentsIn comparison with the free antigen [PDB: 2RET]; the structure of the nanobody bound antigen; EspI:EpsJ; are different in the two loops: the ß2-ß3 and ß4-ß5 (residues W125-V137). The first loop is in an extended conformation in the free antigen; whereas it is bent by almost 90 degrees in the bound antigen at the Ca atom of Gln100 residue; the loop deviates by more than 16Å. The second loop has the largest difference of 4.8Å at the position of Pro128 and in contrast with the bound antigen; residues Ala132-Gly133 are highly flexible in the free antigen. Also; the Ca atom of Asn57 is shifted by 3.8Å.

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
2.58
R-Value
0.23186
Space Group
P 1
Unit Cell
Length(Å) Angle(°)
a = 46.72 α = 96.54
b = 67.243 β = 91.62
c = 128.255 γ = 90.2


Source Information  
Structure Determination Method X-RAY DIFFRACTION


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Ligand
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