2JKR

AP2 CLATHRIN ADAPTOR CORE with Dileucine peptide RM(phosphoS)QIKRLLSE

• PDB DOI:  https://doi.org/10.2210/pdb2JKR/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Mus musculus, Homo sapiens, Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-08-29 Released: 2008-10-28 
• Deposition Author(s): Owen, D.J., McCoy, A.J., Kelly, B.T., Evans, P.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.260 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Literature

A Structural Explanation for the Binding of Endocytic Dileucine Motifs by the Ap2 Complex.

Kelly, B.T., Mccoy, A.J., Spaete, K., Miller, S.E., Evans, P.R., Hoening, S., Owen, D.J.

(2008) Nature 456: 976

• PubMed: 19140243 
• DOI: https://doi.org/10.1038/nature07422
• Primary Citation of Related Structures:  
  2JKR, 2JKT

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 412.88 kDa 
• Atom Count: 28,120 
• Modelled Residue Count: 3,504 
• Deposited Residue Count: 3,604 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-2 COMPLEX SUBUNIT ALPHA-2	A, E [auth L]	623	Mus musculus	Mutation(s): 0  Gene Names: Ap2a2, Adtab
UniProt & NIH Common Fund Data Resources
Find proteins for P17427 (Mus musculus) Explore P17427  Go to UniProtKB:  P17427
IMPC:  MGI:101920

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-2 COMPLEX SUBUNIT BETA-1	B, C [auth E]	591	Homo sapiens	Mutation(s): 0  Gene Names: AP2B1, ADTB2, CLAPB1
UniProt & NIH Common Fund Data Resources
Find proteins for P63010 (Homo sapiens) Explore P63010  Go to UniProtKB:  P63010
PHAROS:  P63010

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-2 COMPLEX SUBUNIT SIGMA-1	D [auth I], I [auth S]	142	Mus musculus	Mutation(s): 0  Gene Names: Ap2s1, Ap17, Claps2
UniProt & NIH Common Fund Data Resources
Find proteins for P62743 (Mus musculus) Explore P62743  Go to UniProtKB:  P62743
IMPC:  MGI:2141861

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-2 COMPLEX SUBUNIT MU-1	F [auth M], J [auth U]	435	Rattus norvegicus	Mutation(s): 0  Gene Names: Ap2m1
UniProt
Find proteins for P84092 (Rattus norvegicus) Explore P84092  Go to UniProtKB:  P84092

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
CD4 PEPTIDE	G [auth P], H [auth Q]	11	Homo sapiens	Mutation(s): 0  Gene Names: CD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens) Explore P01730  Go to UniProtKB:  P01730
PHAROS:  P01730

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth L], BA [auth L], CA [auth L], DA [auth L], EA [auth L], FA [auth L], GA [auth L], HA [auth L], IA [auth M], JA [auth M], K [auth A], KA [auth M], L [auth A], LA [auth U], M [auth A], MA [auth U], N [auth A], NA [auth U], O [auth A], OA [auth U], P [auth A], Q [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth E], W [auth E], X [auth E], Y [auth E], Z [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	G [auth P], H [auth Q]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.260 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.9	α = 90
b = 169.9	β = 90
c = 321.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Owen, D.J., McCoy, A.J., Kelly, B.T., Evans, P.R.

Revision History  

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2012-06-20
  Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance