3WNX

Crystal structure of ERGIC-53/MCFD2, Calcium/Man3-bound form

• PDB DOI: https://doi.org/10.2210/pdb3WNX/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-18 Released: 2014-01-15 
• Deposition Author(s): Satoh, T., Suzuki, K., Yamaguchi, T., Kato, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.287 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 39.71 kDa 
• Atom Count: 2,265 
• Modelled Residue Count: 283 
• Deposited Residue Count: 350 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein ERGIC-53	A	246	Homo sapiens	Mutation(s): 0  Gene Names: ERGIC53
UniProt & NIH Common Fund Data Resources
Find proteins for P49257 (Homo sapiens) Explore P49257  Go to UniProtKB:  P49257
PHAROS:  P49257 GTEx:  ENSG00000074695

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Multiple coagulation factor deficiency protein 2	B	104	Homo sapiens	Mutation(s): 0  Gene Names: MCFD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NI22 (Homo sapiens) Explore Q8NI22  Go to UniProtKB:  Q8NI22
PHAROS:  Q8NI22 GTEx:  ENSG00000180398

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G53402KW GlyCosmos:  G53402KW GlyGen:  G53402KW

Small Molecules

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900111	C	2alpha-alpha-mannobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.287 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.257	α = 90
b = 58.212	β = 109.32
c = 55.435	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Satoh, T., Suzuki, K., Yamaguchi, T., Kato, K.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2014-02-19
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary