Cutting Edge: Structural Basis for the Recognition of {beta}-Linked Glycolipid Antigens by Invariant NKT Cells.

Yu, E.D; Girardi, E; Wang, J; Zajonc, D.M.

3RZC

Structure of the self-antigen iGb3 bound to mouse CD1d and in complex with the iNKT TCR

Structural Similarities for the Entities in PDB 3RZC

The following structural similarities have been found using the jFATCAT-rigid algorithm [1,2].

To reduce the number of hits, a 40% sequence identity clustering has been applied and a representative chain taken from each cluster. If the representative chain consists of multiple domains, each domain is included in the search. If available, the SCOP 1.75 domain assignment [3] is used. Otherwise algorithmic domain assignments are computed using the ProteinDomainParser [4].

Currently viewing only significant results (P-value < 0.001). Show all available results.

Cluster data are up-to-date as of: Sep-27-2017

Info & Help Documentation

A detailed description of the procedure for the all vs. all alignments is available.

You can also use the structure comparison tool to compare any 2 given structures

Entity #1 | Chains A

Description: Antigen-presenting glycoprotein CD1d1 protein | Length: 285

No structure alignment results are available for 3RZC.A explicitly.

It is represented by chain XXXX.null which has more than 50% sequence identity.

Show structure comparison results for representative XXXX.null

Entity #2 | Chains B

Description: Beta-2-microglobulin protein | Length: 99

No structure alignment results are available for 3RZC.B explicitly.

It is represented by chain 1K5N.b which has more than 70% sequence identity.

Show structure comparison results for representative 1K5N.b

Entity #3 | Chains C

Description: Valpha14 protein | Length: 209

No structure alignment results are available for 3RZC.C explicitly.

It is represented by chain XXXX.null which has more than 50% sequence identity.

Show structure comparison results for representative XXXX.null

Entity #4 | Chains D

Description: Vbeta8.2 protein | Length: 241

No structure alignment results are available for 3RZC.D explicitly.

It is represented by chain XXXX.null which has more than 70% sequence identity.

Show structure comparison results for representative XXXX.null

References

[1] Andreas Prlić; Spencer Bliven; Peter W. Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne (2010)
Pre-calculated protein structure alignments at the RCSB PDB website
Bioinformatics 26: 2983-2985
[2] The all vs. all comparisons are based on jFATCAT (a Java port of the original FATCAT algorithm Yuzhen Ye & Adam Godzik (2003))
Flexible structure alignment by chaining aligned fragment pairs allowing twists.
Bioinformatics vol.19 suppl. 2. ii246-ii255.

[3] Andreeva A., Howorth D., Chandonia J.-M., Brenner S.E., Hubbard T.J.P., Chothia C., Murzin A.G. (2008).
Data growth and its impact on the SCOP database: new developments.
Nucl. Acids Res. 2008 36: D419-D425
[4] Alexandrov N., Shindyalov I. (2003)
PDP: protein domain parser.
Bioinformatics 2003 Feb;19(3);429-30.

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158367 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

3RZC

Structure of the self-antigen iGb3 bound to mouse CD1d and in complex with the iNKT TCR

Structural Similarities for the Entities in PDB 3RZC

Info & Help Documentation

No structure alignment results are available for 3RZC.A explicitly.

No structure alignment results are available for 3RZC.B explicitly.

No structure alignment results are available for 3RZC.C explicitly.

No structure alignment results are available for 3RZC.D explicitly.

References