1NEZ

The Crystal Structure of a TL/CD8aa Complex at 2.1A resolution:Implications for Memory T cell Generation, Co-receptor Preference and Affinity

• PDB DOI: https://doi.org/10.2210/pdb1NEZ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2002-12-12 Released: 2003-04-08 
• Deposition Author(s): Liu, Y., Xiong, Y., Naidenko, O.V., Liu, J.H., Zhang, R., Joachimiak, A., Kronenberg, M., Cheroutre, H., Reinherz, E.L., Wang, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.279 
• R-Value Work: 0.217 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 73.04 kDa 
• Atom Count: 5,194 
• Modelled Residue Count: 615 
• Deposited Residue Count: 629 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, TLA(C) alpha chain	A	274	N/A	Mutation(s): 0
UniProt
Find proteins for P14432 (Mus musculus) Explore P14432  Go to UniProtKB:  P14432

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
IMPC:  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD8 alpha chain	C [auth G], D [auth H]	128	N/A	Mutation(s): 0
UniProt
Find proteins for P01731 (Mus musculus) Explore P01731  Go to UniProtKB:  P01731

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
TL	PDBBind:  1NEZ	Kd: 1.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.279 
• R-Value Work: 0.217 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.018	α = 90
b = 77.018	β = 90
c = 176.045	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-08 
Deposition Author(s): Liu, Y., Xiong, Y., Naidenko, O.V., Liu, J.H., Zhang, R., Joachimiak, A., Kronenberg, M., Cheroutre, H., Reinherz, E.L., Wang, J.H.

Revision History  

• Version 1.0: 2003-04-08
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2013-09-18
  Changes: Derived calculations
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary