RLA-A1 binding "ALMPGQFFV" at 2.29Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
RLA-A1
ALMPGQFFV
Species
Locus / Allele group
Strict assembly restriction of peptides from rabbit hemorrhagic disease virus presented by rabbit MHC class I molecule RLA-A1.
Andes virus (ANDV) nonlytically infects pulmonary microvascular endothelial cells (PMECs), causing acute pulmonary edema termed hantavirus pulmonary syndrome (HPS). In HPS patients, virtually every PMEC is infected; however, the mechanism by which ANDV induces vascular permeability and edema remains to be resolved. The ANDV nucleocapsid (N) protein activates the GTPase RhoA in primary human PMECs, causing VE-cadherin internalization from adherens junctions and PMEC permeability. We found that ANDV N protein failed to bind RhoA but coprecipitates RhoGDI (Rho GDP dissociation inhibitor), the primary RhoA repressor that normally sequesters RhoA in an inactive state. ANDV N protein selectively binds the RhoGDI C terminus (residues 69 to 204) but fails to form ternary complexes with RhoA or inhibit RhoA binding to the RhoGDI N terminus (residues 1 to 69). However, we found that ANDV N protein uniquely inhibits RhoA binding to an S34D phosphomimetic RhoGDI mutant. Hypoxia and vascular endothelial growth factor (VEGF) increase RhoA-induced PMEC permeability by directing protein kinase Cα (PKCα) phosphorylation of S34 on RhoGDI. Collectively, ANDV N protein alone activates RhoA by sequestering and reducing RhoGDI available to suppress RhoA. In response to hypoxia and VEGF-activated PKCα, ANDV N protein additionally directs the release of RhoA from S34-phosphorylated RhoGDI, synergistically activating RhoA and PMEC permeability. These findings reveal a fundamental edemagenic mechanism that permits ANDV to amplify PMEC permeability in hypoxic HPS patients. Our results rationalize therapeutically targeting PKCα and opposing protein kinase A (PKA) pathways that control RhoGDI phosphorylation as a means of resolving ANDV-induced capillary permeability, edema, and HPS. IMPORTANCE HPS-causing hantaviruses infect pulmonary endothelial cells (ECs), causing vascular leakage, pulmonary edema, and a 35% fatal acute respiratory distress syndrome (ARDS). Hantaviruses do not lyse or disrupt the endothelium but dysregulate normal EC barrier functions and increase hypoxia-directed permeability. Our findings reveal a novel underlying mechanism of EC permeability resulting from ANDV N protein binding to RhoGDI, a regulatory protein that normally maintains edemagenic RhoA in an inactive state and inhibits EC permeability. ANDV N sequesters RhoGDI and enhances the release of RhoA from S34-phosphorylated RhoGDI. These findings indicate that ANDV N induces the release of RhoA from PKC-phosphorylated RhoGDI, synergistically enhancing hypoxia-directed RhoA activation and PMEC permeability. Our data suggest inhibiting PKC and activating PKA phosphorylation of RhoGDI as mechanisms of inhibiting ANDV-directed EC permeability and therapeutically restricting edema in HPS patients. These findings may be broadly applicable to other causes of ARDS.
Structure deposition and release
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
![](https://images.histo.fyi/cleft/side/combined/6m24_1_combined_medium.png)
![](https://images.histo.fyi/cleft/yrb/6m24_1_yrb_medium.png)
![](https://images.histo.fyi/cleft/top/combined/6m24_1_combined_medium.png)
Data provenance
MHC:peptide complexes are visualised using PyMol. The peptide is superimposed on a consistent cutaway slice of the MHC binding cleft (displayed as a grey mesh) which best indicates the binding pockets for the P1/P5/PC positions (side view - pockets A, E, F) and for the P2/P3/PC-2 positions (top view - pockets B, C, D). In some cases peptides will use a different pocket for a specific peptide position (atypical anchoring). On some structures the peptide may appear to sterically clash with a pocket. This is an artefact of picking a standardised slice of the cleft and overlaying the peptide.
Peptide neighbours
P1
ALA
TYR7
TYR171
TYR159
TYR59
GLN63
TRP167
MET5
|
P2
LEU
TYR9
MET45
GLN63
PHE99
ILE24
TYR7
TYR159
ILE66
|
P3
MET
TYR159
GLU163
TRP167
ILE66
|
P4
PRO
ILE66
|
P6
GLN
ASP69
THR73
ILE66
GLU152
THR70
|
P7
PHE
GLU152
ARG155
HIS156
TRP147
TYR116
THR73
ASN77
ARG114
|
P8
PHE
LYS146
THR143
VAL76
TRP147
THR73
ASN77
|
P9
VAL
ASN142
LYS146
THR143
ALA81
TRP147
TYR116
PHE95
THR80
TYR84
ASN77
TYR123
|
Colour key
Data provenance
Neighbours are calculated by finding residues with atoms within 5Å of each other using BioPython Neighboursearch module. The list of neighbours is then sorted and filtered to inlcude only neighbours where between the peptide and the MHC Class I alpha chain.
Colours selected to match the YRB scheme. [https://www.frontiersin.org/articles/10.3389/fmolb.2015.00056/full]
![](https://images.histo.fyi/cleft/pockets/labelled/6m24_1_labelled_medium.png)
![](https://images.histo.fyi/cleft/terminii/labelled/6m24_1_labelled_medium.png)
A Pocket
TYR159
GLU163
TRP167
TYR171
MET5
TYR59
GLN63
ILE66
TYR7
|
B Pocket
ILE24
VAL34
MET45
GLN63
ILE66
ALA67
TYR7
THR70
TYR9
PHE99
|
C Pocket
THR70
THR73
PHE74
TYR9
THR97
|
D Pocket
ARG114
ARG155
HIS156
TYR159
LEU160
PHE99
|
E Pocket
ARG114
TRP147
GLU152
HIS156
THR97
|
F Pocket
TYR116
TYR123
THR143
LYS146
TRP147
ASN77
THR80
ALA81
TYR84
PHE95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD 70 80 90 WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM |
2. Class I alpha
RLA-A1
|
10 20 30 40 50 60
GSHSMRYFYTSVSRPGLGEPRFIIVGYVDDTQFVRFDSDAASPRMEQRAPWMGQVEPEYW 70 80 90 100 110 120 DQQTQIAKDTAQTFRVNLNTALRYYNQSAAGSHTFQTMFGCEVWADGRFFHGYRQYAYDG 130 140 150 160 170 180 ADYIALNEDLRSWTAADTAAQNTQRKWEAAGEAERHRAYLERECVEWLRRYLEMGKETLQ 190 200 210 220 230 240 RADPPKAHVTHHPASDREATLRCWALGFYPAEISLTWQRDGEDQTQDTELVETRPGGDGT 250 260 270 FQKWAAVVVPSGEEQRYTCRVQHEGLPEPLTLTW |
3. Peptide
|
ALMPGQFFV
|
Data provenance
Sequences are retrieved via the Uniprot method of the RSCB REST API. Sequences are then compared to those derived from the PDB file and matched against sequences retrieved from the IPD-IMGT/HLA database for human sequences, or the IPD-MHC database for other species. Mouse sequences are matched against FASTA files from Uniprot. Sequences for the mature extracellular protein (signal petide and cytoplasmic tail removed) are compared to identical length sequences from the datasources mentioned before using either exact matching or Levenshtein distance based matching.
Downloadable data
Components
Data license
Footnotes
- Protein Data Bank Europe - Coordinate Server
- 1HHK - HLA-A*02:01 binding LLFGYPVYV at 2.5Å resolution - PDB entry for 1HHK
- Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. - PyMol CEALIGN Method - Publication
- PyMol - PyMol.org/pymol
- Levenshtein distance - Wikipedia entry
- Protein Data Bank Europe REST API - Molecules endpoint
- 3Dmol.js: molecular visualization with WebGL - 3DMol.js - Publication
- Protein Data Bank Europe REST API - Publication endpoint
- PubMed Central Europe REST API - Articles endpoint
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This work is licensed under a Creative Commons Attribution 4.0 International License.