6IOM

Crystal structure of human C4.4A

• PDB DOI: https://doi.org/10.2210/pdb6IOM/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2018-10-30 Released: 2020-01-15 
• Deposition Author(s): Huang, M.D., Jiang, Y.B., Yuan, C., Lin, L.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.256 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Crystal Structures of Human C4.4A Reveal the Unique Association of Ly6/uPAR/alpha-neurotoxin Domain

Jiang, Y.B., Lin, L., Chen, S., Jiang, L.G., Kriegbaum, M.C., Gardsvoll, H., Hansen, L.V., Li, J., Ploug, M., Yuan, C., Huang, M.D.

(2020) Int J Biol Sci 16: 981-993

• DOI: https://doi.org/10.7150/ijbs.39919

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.24 kDa 
• Atom Count: 2,928 
• Modelled Residue Count: 386 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ly6/PLAUR domain-containing protein 3	A, B	201	Homo sapiens	Mutation(s): 0  Gene Names: C4.4A
UniProt & NIH Common Fund Data Resources
Find proteins for O95274 (Homo sapiens) Explore O95274  Go to UniProtKB:  O95274
PHAROS:  O95274 GTEx:  ENSG00000124466
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: O95274-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.256 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.055	α = 90
b = 120.156	β = 90
c = 169.431	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Huang, M.D., Jiang, Y.B., Yuan, C., Lin, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31670739
National Natural Science Foundation of China	China	31570745
National Natural Science Foundation of China	China	31370737

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2020-01-22
  Changes: Derived calculations
• Version 1.2: 2020-03-04
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary