6FGO | pdb_00006fgo

Fc in complex with engineered calcium binding domain Z


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.232 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6FGO

This is version 2.2 of the entry. See complete history

Literature

Protein Engineering Allows for Mild Affinity-based Elution of Therapeutic Antibodies.

Kanje, S.Venskutonyte, R.Scheffel, J.Nilvebrant, J.Lindkvist-Petersson, K.Hober, S.

(2018) J Mol Biology 430: 3427-3438

  • DOI: https://doi.org/10.1016/j.jmb.2018.06.004
  • Primary Citation Related Structures: 
    6FGO

  • PubMed Abstract: 

    Presented here is an engineered protein domain, based on Protein A, that displays a calcium-dependent binding to antibodies. This protein, Z Ca , is shown to efficiently function as an affinity ligand for mild purification of antibodies through elution with ethylenediaminetetraacetic acid. Antibodies are commonly used tools in the area of biological sciences and as therapeutics, and the most commonly used approach for antibody purification is based on Protein A using acidic elution. Although this affinity-based method is robust and efficient, the requirement for low pH elution can be detrimental to the protein being purified. By introducing a calcium-binding loop in the Protein A-derived Z domain, it has been re-engineered to provide efficient antibody purification under mild conditions. Through comprehensive analyses of the domain as well as the Z Ca -Fc complex, the features of this domain are well understood. This novel protein domain provides a very valuable tool for effective and gentle antibody and Fc-fusion protein purification.


  • Organizational Affiliation
    • CBH, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 133.43 kDa 
  • Atom Count: 9,382 
  • Modeled Residue Count: 1,094 
  • Deposited Residue Count: 1,116 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin gamma-1 heavy chainA,
C [auth B],
E [auth C],
G [auth D]
210Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX5 (Homo sapiens)
Explore P0DOX5 
Go to UniProtKB:  P0DOX5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOX5
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Z-CaB [auth E],
D [auth F],
F [auth G],
H
69Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A0U3TLJ6 (Staphylococcus aureus)
Explore A0A0U3TLJ6 
Go to UniProtKB:  A0A0U3TLJ6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U3TLJ6
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
I, K
8N-Glycosylation
Glycosylation Resources
GlyTouCan: G80858MF
GlyCosmos: G80858MF
GlyGen: G80858MF
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
J
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G45889JQ
GlyCosmos: G45889JQ
GlyGen: G45889JQ
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
L
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
HA [auth C],
IA [auth C],
JA [auth C],
M [auth A],
N [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AA [auth F]
BA [auth F]
KA [auth C]
LA [auth C]
MA [auth C]
AA [auth F],
BA [auth F],
KA [auth C],
LA [auth C],
MA [auth C],
O [auth A],
P [auth A],
Q [auth A],
QA [auth D],
RA [auth D],
S [auth E],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
NA [auth G],
R [auth E],
SA [auth H],
Z [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
GA [auth C]
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
OA [auth D],
PA [auth D],
T [auth B],
U [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.232 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.229α = 90
b = 120.296β = 90
c = 126.33γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
VinnovaSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-23
    Changes: Structure summary