4ZET

Blood dendritic cell antigen 2 (BDCA-2) complexed with GalGlcNAcMan

• PDB DOI: https://doi.org/10.2210/pdb4ZET/pdb

• Classification: Carbohydrate-binding protein
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-04-20 Released: 2015-05-27 
• Deposition Author(s): Jegouzo, S.A.F., Feinberg, H., Dungarwalla, T., Drickamer, K., Weis, W.I., Taylor, M.E.
• Funding Organization(s): Wellcome Trust, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR), Department of Energy (DOE, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.263 
• R-Value Work: 0.178 
• R-Value Observed: 0.182 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 35.48 kDa 
• Atom Count: 2,480 
• Modelled Residue Count: 294 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type lectin domain family 4 member C	A, B	147	Homo sapiens	Mutation(s): 1  Gene Names: CLEC4C, BDCA2, CLECSF11, CLECSF7, DLEC, HECL, UNQ9361/PRO34150
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTT0 (Homo sapiens) Explore Q8WTT0  Go to UniProtKB:  Q8WTT0
PHAROS:  Q8WTT0 GTEx:  ENSG00000198178

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan:  G28052FT GlyCosmos:  G28052FT GlyGen:  G28052FT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.263 
• R-Value Work: 0.178 
• R-Value Observed: 0.182 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.559	α = 90
b = 67.645	β = 90
c = 118.142	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-05-27 
Deposition Author(s): Jegouzo, S.A.F., Feinberg, H., Dungarwalla, T., Drickamer, K., Weis, W.I., Taylor, M.E.

---

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	093599
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM103393
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	P41RR001209
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

• Version 1.0: 2015-05-27
  Type: Initial release
  
• Version 1.1: 2015-06-03
  Changes: Database references
• Version 1.2: 2015-07-15
  Changes: Database references
• Version 1.3: 2017-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
• Version 1.4: 2017-09-06
  Changes: Author supporting evidence
• Version 1.5: 2019-12-04
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary