1A6A

THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP BOUND TO HLA-DR3

• PDB DOI: https://doi.org/10.2210/pdb1A6A/pdb

• Classification: COMPLEX (TRANSMEMBRANE/GLYCOPROTEIN)
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1998-02-22 Released: 1998-05-27 
• Deposition Author(s): Ghosh, P., Amaya, M., Mellins, E., Wiley, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.325 
• R-Value Work: 0.246 
• R-Value Observed: 0.246 

Starting Model: experimental

Literature

The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3.

Ghosh, P., Amaya, M., Mellins, E., Wiley, D.C.

(1995) Nature 378: 457-462

• PubMed: 7477400 
• DOI: https://doi.org/10.1038/378457a0
• Primary Citation of Related Structures:  
  1A6A


• PubMed Abstract: 
  

  A complex between HLA-DR3 and a fragment of invariant chain called CLIP was isolated from a human cell line defective in antigen presentation and its X-ray crystal structure determined. Previous data indicate that this complex is an intermediate in class II histocompatibility maturation, occurring between invariant chain-DR3 and antigenic peptide-DR3 complexes. The structure shows that the CLIP fragment binds to DR3 in a way almost identical to that in which antigenic peptides bind class II histocompatibility glycoproteins. The structure is the substrate for the loading of antigenic peptides by an exchange process catalysed by DM.

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Organizational Affiliation: 

Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B1C1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.52 kDa 
• Atom Count: 3,158 
• Modelled Residue Count: 378 
• Deposited Residue Count: 378 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A	176	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
PHAROS:  P01903 GTEx:  ENSG00000204287
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P01903-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR-1 beta chain	B	187	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911
PHAROS:  P01911 GTEx:  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, gamma chain	C	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P04233 (Homo sapiens) Explore P04233  Go to UniProtKB:  P04233
PHAROS:  P04233 GTEx:  ENSG00000019582

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [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: 2.75 Å
• R-Value Free: 0.325 
• R-Value Work: 0.246 
• R-Value Observed: 0.246 
• Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.45	α = 90
b = 78.45	β = 90
c = 159.1	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
ROTAVATA/AGROVATA	data reduction
AMoRE	phasing
X-PLOR	refinement
CCP4	data scaling
ROTAVATA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-05-27 
Deposition Author(s): Ghosh, P., Amaya, M., Mellins, E., Wiley, D.C.

Revision History  

• Version 1.0: 1998-05-27
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Refinement description, Structure summary
• Version 1.4: 2023-08-02
  Changes: Advisory, Database references, Refinement description, Structure summary
• Version 1.5: 2024-10-23
  Changes: Data collection, Structure summary