5U66 | pdb_00005u66

Modified single helix from the B-domain of protein A bound to IgG1 Fc

• PDB DOI: https://doi.org/10.2210/pdb5U66/pdb

• Classification: immune system/inhibitor
• Organism(s): Staphylococcus aureus, Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2016-12-07 Released: 2017-05-24 
• Deposition Author(s): Ultsch, M.H., Eigenbrot, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.227 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

3-2-1: Structural insights from stepwise shrinkage of a three-helix Fc-binding domain to a single helix.

Ultsch, M., Braisted, A., Maun, H.R., Eigenbrot, C.

(2017) Protein Eng Des Sel 30: 619-625

• PubMed: 28475752 
• DOI: https://doi.org/10.1093/protein/gzx029
• Primary Citation Related Structures: 
  5U4Y, 5U52, 5U66


• PubMed Abstract: 
  

  The well-studied B-domain from Staphylococcal protein A is a 59 amino acid three-helix bundle that binds the Fc portion of IgG with a dissociation constant of ~35 nM. The B-domain variant bearing a Gly to Ala mutation (=Z-domain) has been the subject of efforts to minimize a domain's size while retaining its function. We report X-ray crystallographic characterization of three steps in such a process using complexes with Fc: the full three-helix Z-domain, a 34 amino acid two-helix version called Z34C and a 13 amino acid single helix stabilized with an exo-helix tether, called LH1.

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Organizational Affiliation: 
• Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080,USA.
Department of Protein Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080,USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 26.9 kDa 
• Atom Count: 2,112 
• Modeled Residue Count: 222 
• Deposited Residue Count: 222 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STAPLED PEPTIDE FROM DOMAIN B OF PROTEIN A	A [auth B]	15	Staphylococcus aureus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG1 fc derived from CD4-fc fusion	B [auth A]	207	Homo sapiens	Mutation(s): 0  Gene Names: DKFZp686C11235
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857 GTEx:  ENSG00000211896
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P01857-2

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G28663KH GlyCosmos: G28663KH GlyGen: G28663KH

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002261	A [auth B]	STAPLED PEPTIDE FROM DOMAIN B OF PROTEIN A	Oligopeptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.227 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.165	α = 90
b = 126.812	β = 90
c = 91.927	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Ultsch, M.H., Eigenbrot, C.

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.0: 2020-12-16
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 3.2: 2023-11-15
  Changes: Data collection, Derived calculations