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6M2J

RLA-A1 binding "TLIDLTELI" at 2.20Å resolution

Data provenance

Structure downloaded from PDB Europe using the Coordinate Server. Aligned to residues 1-180 of 1HHK2 using the CEALIGN3 function of PyMol4. Chain assigment using a Levenshtein distance5 method using data from the PDBe REST API6. Organism data from PDBe REST API. Data for both of these operations from the Molecules endpoint. Structure visualised with 3DMol7.

Information sections


Complex type

Class i with peptide

1. Beta 2 microglobulin
['B']
2. Class I alpha
RLA-A1
['A']
3. Peptide
TLIDLTELI
['C']

Species


Locus / Allele group


Publication

Strict assembly restriction of peptides from rabbit hemorrhagic disease virus presented by rabbit MHC class I molecule RLA-A1.

Zhang Q, Liu K, Yue C, Zhang D, Lu D, Xiao W, Liu P, Zhao Y, Gao G, Ding C, Lyu J, Liu WJ
J. Virol. (2020) [doi:10.1128/jvi.00396-20]  [pubmed:32522857

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

Deposited: 2020-02-27
Released: 2020-07-08
Revised: 2020-09-02

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Nonamer (9 amino acids)

Sequence: TLIDLTELI

Interactive view
Cutaway side view (static)
Surface top view (static - coloured by atom property)
Cutaway top view (static)

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 THR

TYR171
TYR159
TYR7
TRP167
MET5
GLN63
TYR59
P2 LEU

TYR9
TYR159
TYR7
GLN63
MET45
PHE99
ILE24
ILE66
P3 ILE

TYR9
TYR159
THR70
ILE66
GLU163
P4 ASP

ILE66
THR73
ARG155
ASP69
THR70
P5 LEU

GLU152
ARG155
HIS156
TYR159
ARG114
P6 THR

THR73
ARG155
P7 GLU

TYR9
HIS156
THR97
TYR116
TRP147
ARG114
THR70
ASN77
THR73
PHE74
P8 LEU

ASN77
TRP147
THR73
LYS146
VAL76
P9 ILE

THR143
TYR123
THR80
TRP147
ALA81
ASN77
LYS146
TYR84
PHE95

Colour key

Aromatic Hydrophobic Acidic Basic Neutral/polar

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]


Binding cleft pockets


Peptide sidechain binding pockets (static)
Peptide terminii and backbone binding residues (static)
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

Binds N-terminus Binds P1 backbone Binds P2 backbone Binds PC-1 backbone Binds C-terminus

Data provenance

N-/C-terminus and peptide backbone binding residues are assigned according to previously published information and pockets are assigned according to an adaptation of a previously published set of residues. All numbering is currently that of the 'canonical' structures of human and mouse MHC Class I molecules.

Chain sequences

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
TLIDLTELI


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

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Complete structures

Aligned structures [cif]
  1. 6M2J assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 6M2J assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6M2J assembly 1  
Peptide only [cif]
  1. 6M2J assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6m2j

Data license

The data above is made available under a Creative Commons CC-BY 4.0 license. This means you can copy, remix, transform, build upon and redistribute the material, but you must give appropriate credit, provide a link to the license, and indicate if changes were made.
If you use any data downloaded from this site in a publication, please cite 'https://www.histo.fyi/'. A preprint is in preparation.

Footnotes