5B4Y | pdb_00005b4y

Crystal structure of the LA12 fragment of ApoER2

• PDB DOI: https://doi.org/10.2210/pdb5B4Y/pdb

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


• Deposited: 2016-04-20 Released: 2017-04-26 
• Deposition Author(s): Nogi, T., Tabata, S., Hirai, H., Yasui, N., Takagi, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.247 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the ectodomain from a LDLR close homologue in complex with its physiological ligand.

Hirai, H., Yasui, N., Yamashita, K., Tabata, S., Yamamoto, M., Takagi, J., Nogi, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.7 kDa 
• Atom Count: 668 
• Modeled Residue Count: 79 
• Deposited Residue Count: 85 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low-density lipoprotein receptor-related protein 8	A [auth B]	85	Homo sapiens	Mutation(s): 0  Gene Names: LRP8, APOER2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14114 (Homo sapiens) Explore Q14114  Go to UniProtKB:  Q14114
PHAROS:  Q14114 GTEx:  ENSG00000157193

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.247 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.162	α = 90
b = 41.78	β = 90
c = 55.063	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Nogi, T., Tabata, S., Hirai, H., Yasui, N., Takagi, J.

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary