7RDV | pdb_00007rdv

TFH TCR bound to MHC Class II IAd presenting aggrecan epitope

• PDB DOI: https://doi.org/10.2210/pdb7RDV/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-11 Released: 2022-07-27 
• Deposition Author(s): Lim, J.J., Rossjohn, J., Reid, H.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

TFH TCR bound to MHC Class II IAd presenting aggrecan epitope

Lim, J.J., Rossjohn, J., Reid, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 94.08 kDa 
• Atom Count: 6,052 
• Modelled Residue Count: 787 
• Deposited Residue Count: 824 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class II histocompatibility antigen, A-D alpha chain	A	181	Mus musculus	Mutation(s): 0  Gene Names: H2-Aa
UniProt
Find proteins for P04228 (Mus musculus) Explore P04228  Go to UniProtKB:  P04228
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class II histocompatibility antigen, A-D beta chain	B	186	Mus musculus	Mutation(s): 0  Gene Names: H2-Ab1
UniProt
Find proteins for P01921 (Mus musculus) Explore P01921  Go to UniProtKB:  P01921

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TFH TCR alpha chain	C	205	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TFH TCR beta chain	D	240	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Aggrecan core peptide	E [auth H]	12	Homo sapiens	Mutation(s): 0  Gene Names: ACAN, AGC1, CSPG1, MSK16
UniProt & NIH Common Fund Data Resources
Find proteins for P16112 (Homo sapiens) Explore P16112  Go to UniProtKB:  P16112
PHAROS:  P16112 GTEx:  ENSG00000157766

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.562	α = 90
b = 102.562	β = 90
c = 195.695	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): Lim, J.J., Rossjohn, J., Reid, H.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1083192

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary