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GeezerVison is showing www.rcsb.org — RCSB PDB - 4K71: Crystal structure of a high affinity Human Serum Albumin variant bound to the Neonatal Fc Receptor

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  • Validation fo-fc coefficients (CIF - gz)
  • Biological Assembly 1 (CIF - gz) 
  • Biological Assembly 2 (CIF - gz) 
  • Biological Assembly 3 (CIF - gz) 
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  • Biological Assembly 2 (PDB - gz)
  • Biological Assembly 3 (PDB - gz)
 Data API 

 4K71 | pdb_00004k71

Crystal structure of a high affinity Human Serum Albumin variant bound to the Neonatal Fc Receptor

  • PDB DOI: https://doi.org/10.2210/pdb4K71/pdb
  • Classification: LIPID TRANSPORT
  • Organism(s): Homo sapiens
  • Expression System: Saccharomyces cerevisiae, Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2013-04-16 Released: 2013-10-23 
  • Deposition Author(s): Schmidt, M.M., Townson, S.A., Andreucci, A., Dombrowski, C., Erbe, D.V., King, B., Kovalchin, J.T., Masci, A., Murillo, A., Schirmer, E.B., Furfine, E.S., Barnes, T.M.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.255 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4K71

This is version 1.2 of the entry. See complete history. 

Literature

  • Download Mendeley

Crystal structure of an HSA/FcRn complex reveals recycling by competitive mimicry of HSA ligands at a pH-dependent hydrophobic interface.

Schmidt, M.M., Townson, S.A., Andreucci, A.J., King, B.M., Schirmer, E.B., Murillo, A.J., Dombrowski, C., Tisdale, A.W., Lowden, P.A., Masci, A.L., Kovalchin, J.T., Erbe, D.V., Wittrup, K.D., Furfine, E.S., Barnes, T.M.

(2013) Structure 21: 1966-1978

  • PubMed: 24120761 Search on PubMed
  • DOI: https://doi.org/10.1016/j.str.2013.08.022
  • Primary Citation Related Structures: 
    4K71

  • PubMed Abstract: 

    The long circulating half-life of serum albumin, the most abundant protein in mammalian plasma, derives from pH-dependent endosomal salvage from degradation, mediated by the neonatal Fc receptor (FcRn). Using yeast display, we identified human serum albumin (HSA) variants with increased affinity for human FcRn at endosomal pH, enabling us to solve the crystal structure of a variant HSA/FcRn complex. We find an extensive, primarily hydrophobic interface stabilized by hydrogen-bonding networks involving protonated histidines internal to each protein. The interface features two key FcRn tryptophan side chains inserting into deep hydrophobic pockets on HSA that overlap albumin ligand binding sites. We find that fatty acids (FAs) compete with FcRn, revealing a clash between ligand binding and recycling, and that our high-affinity HSA variants have significantly increased circulating half-lives in mice and monkeys. These observations open the way for the creation of biotherapeutics with significantly improved pharmacokinetics.


  • Organizational Affiliation: 
    • Eleven Biotherapeutics, Inc., Cambridge, MA 02142, USA.
Asymmetric Unit

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (SO4)

Biological Assembly 1  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (SO4)


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


Find Similar Assemblies

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

Biological Assembly 2  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (SO4)


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


Find Similar Assemblies

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

Biological Assembly 3  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (SO4)


Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A4B4C4 


Find Similar Assemblies

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

  • Total Structure Weight: 219.08 kDa 
  • Atom Count: 15,259 
  • Modeled Residue Count: 1,888 
  • Deposited Residue Count: 1,916 
  • Unique protein chains: 3

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serum albumin
A, D
585Homo sapiensMutation(s): 4 
Gene Names: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens)
Explore P02768 
Go to UniProtKB:  P02768
GTEx:  ENSG00000163631 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02768
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
IgG receptor FcRn large subunit p51
B, E
274Homo sapiensMutation(s): 0 
Gene Names: FCGRT, FCRN
UniProt & NIH Common Fund Data Resources
Find proteins for P55899 (Homo sapiens)
Explore P55899 
Go to UniProtKB:  P55899
GTEx:  ENSG00000104870 
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UniProt GroupP55899
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
C, F
99Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
GTEx:  ENSG00000166710 
Entity Groups
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UniProt GroupP61769
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
  • SDF format, chain G [auth A]
  • SDF format, chain H [auth A]
  • SDF format, chain I [auth A]
  • SDF format, chain J [auth A]
  • SDF format, chain K [auth A]
  • SDF format, chain L [auth A]
  • SDF format, chain M [auth A]
  • SDF format, chain N [auth B]
  • SDF format, chain O [auth B]
  • SDF format, chain P [auth C]
  • SDF format, chain Q [auth C]
  • SDF format, chain S [auth D]
  • SDF format, chain T [auth D]
  • SDF format, chain U [auth D]
  • SDF format, chain V [auth D]
  • SDF format, chain W [auth D]
  • SDF format, chain X [auth E]
  • SDF format, chain Y [auth F]
  • SDF format, chain R [auth D]
  • MOL2 format, chain G [auth A]
  • MOL2 format, chain H [auth A]
  • MOL2 format, chain I [auth A]
  • MOL2 format, chain J [auth A]
  • MOL2 format, chain K [auth A]
  • MOL2 format, chain L [auth A]
  • MOL2 format, chain M [auth A]
  • MOL2 format, chain N [auth B]
  • MOL2 format, chain O [auth B]
  • MOL2 format, chain P [auth C]
  • MOL2 format, chain Q [auth C]
  • MOL2 format, chain S [auth D]
  • MOL2 format, chain T [auth D]
  • MOL2 format, chain U [auth D]
  • MOL2 format, chain V [auth D]
  • MOL2 format, chain W [auth D]
  • MOL2 format, chain X [auth E]
  • MOL2 format, chain Y [auth F]
  • MOL2 format, chain R [auth D]
  • mmCIF format, chain G [auth A]
  • mmCIF format, chain H [auth A]
  • mmCIF format, chain I [auth A]
  • mmCIF format, chain J [auth A]
  • mmCIF format, chain K [auth A]
  • mmCIF format, chain L [auth A]
  • mmCIF format, chain M [auth A]
  • mmCIF format, chain N [auth B]
  • mmCIF format, chain O [auth B]
  • mmCIF format, chain P [auth C]
  • mmCIF format, chain Q [auth C]
  • mmCIF format, chain S [auth D]
  • mmCIF format, chain T [auth D]
  • mmCIF format, chain U [auth D]
  • mmCIF format, chain V [auth D]
  • mmCIF format, chain W [auth D]
  • mmCIF format, chain X [auth E]
  • mmCIF format, chain Y [auth F]
  • mmCIF format, chain R [auth D]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth B],
O [auth B],
P [auth C],
Q [auth C],
R [auth D],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
W [auth D],
X [auth E],
Y [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Interactions
  • Focus chain G [auth A]
  • Focus chain H [auth A]
  • Focus chain I [auth A]
  • Focus chain J [auth A]
  • Focus chain K [auth A]
  • Focus chain L [auth A]
  • Focus chain M [auth A]
  • Focus chain N [auth B]
  • Focus chain O [auth B]
  • Focus chain P [auth C]
  • Focus chain Q [auth C]
  • Focus chain R [auth D]
  • Focus chain S [auth D]
  • Focus chain T [auth D]
  • Focus chain U [auth D]
  • Focus chain V [auth D]
  • Focus chain W [auth D]
  • Focus chain X [auth E]
  • Focus chain Y [auth F]
Interactions & Density
  • Focus chain G [auth A]
  • Focus chain H [auth A]
  • Focus chain I [auth A]
  • Focus chain J [auth A]
  • Focus chain K [auth A]
  • Focus chain L [auth A]
  • Focus chain M [auth A]
  • Focus chain N [auth B]
  • Focus chain O [auth B]
  • Focus chain P [auth C]
  • Focus chain Q [auth C]
  • Focus chain R [auth D]
  • Focus chain S [auth D]
  • Focus chain T [auth D]
  • Focus chain U [auth D]
  • Focus chain V [auth D]
  • Focus chain W [auth D]
  • Focus chain X [auth E]
  • Focus chain Y [auth F]

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.255 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.893α = 90
b = 203.536β = 90
c = 100.561γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Released Date: 2013-10-23 
  • Deposition Author(s): Schmidt, M.M., Townson, S.A., Andreucci, A., Dombrowski, C., Erbe, D.V., King, B., Kovalchin, J.T., Masci, A., Murillo, A., Schirmer, E.B., Furfine, E.S., Barnes, T.M.

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references
  • Version 1.2: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary
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