The Immunogenicity of a Proline-Substituted Altered Peptide Ligand toward the Cancer-Associated TEIPP Neoepitope Trh4 Is Unrelated to Complex Stability.

Hafstrand, I.; Doorduijn, E.M.; Sun, R.; Talyzina, A.; Sluijter, M.; Pellegrino, S.; Sandalova, T.; Duru, A.D.; van Hall, T.; Achour, A.

doi:10.2210/pdb5mzm/pdb

Macromolecule Content

Total Structure Weight: 89949.08
Atom Count: 6263
Residue Count: 768
Unique protein chains: 3

5MZM

Structure of H-2Db in complex with TEIPP APL Trh4 p3P

DOI: 10.2210/pdb5MZM/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli, synthetic construct

Deposited: 2017-02-01 Released: 2018-03-21
Deposition Author(s): Hafstrand, I., Achour, A., Sandalova, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.4 Å
R-Value Free: 0.268
R-Value Work: 0.226

wwPDB Validation3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The Immunogenicity of a Proline-Substituted Altered Peptide Ligand toward the Cancer-Associated TEIPP Neoepitope Trh4 Is Unrelated to Complex Stability.

Hafstrand, I., Doorduijn, E.M., Sun, R., Talyzina, A., Sluijter, M., Pellegrino, S., Sandalova, T., Duru, A.D., van Hall, T., Achour, A.

(2018) J. Immunol. 200: 2860-2868

PubMed: 29507106 Search on PubMed

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
H-2 class I histocompatibility antigen, D-B alpha chain	A, D	276	Mus musculus	Mutation(s): 0 Gene Names: H2-D1
Find proteins for P01899 (Mus musculus) Go to UniProtKB: P01899
Protein Feature View Full Protein Feature View for P01899

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B, E	99	Mus musculus	Mutation(s): 0 Gene Names: B2m
Find proteins for P01887 (Mus musculus) Go to UniProtKB: P01887
Protein Feature View Full Protein Feature View for P01887

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Ceramide synthase 5 derived peptide Trh4 p3P	C, F	9	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
SO4 Query on SO4 Download SDF File Download CCD File	B	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
GOL Query on GOL Download SDF File Download CCD File	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.4 Å
R-Value Free: 0.268
R-Value Work: 0.226
Space Group: I 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 91.350	α = 90.00
b = 125.010	β = 103.53
c = 98.053	γ = 90.00

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
iMOSFLM	data reduction
PHENIX	refinement
REFMAC	refinement

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

Deposited Date: 2017-02-01
Released Date: 2018-03-21
Deposition Author(s): Hafstrand, I., Achour, A., Sandalova, T.

Revision History

Version 1.0: 2018-03-21
Type: Initial release
Version 1.1: 2018-04-18
Type: Data collection, Database references

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

148969 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

5MZM

Structure of H-2Db in complex with TEIPP APL Trh4 p3P

The Immunogenicity of a Proline-Substituted Altered Peptide Ligand toward the Cancer-Associated TEIPP Neoepitope Trh4 Is Unrelated to Complex Stability.

Entity ID: 1

Entity ID: 2

Entity ID: 3

Experimental Data

Structure Validation

Deposition Data

Revision History