6OAE | pdb_00006oae

Crystal Structure of Human Mucin-like Protocadherin EC1-2

• PDB DOI: https://doi.org/10.2210/pdb6OAE/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-03-15 Released: 2020-03-18 
• Deposition Author(s): Johnson, Z.R., Gray, M.E., Sotomayor, M.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Mucin-like Protocadherin EC1-2

Gray, M.E., Johnson, Z.R., Modak, D., Sotomayor, M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: assay for oligomerization, gel filtration

Macromolecule Content 

• Total Structure Weight: 24.64 kDa 
• Atom Count: 1,795 
• Modeled Residue Count: 204 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-like protocadherin	A	215	Homo sapiens	Mutation(s): 0  Gene Names: MUPCDH
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBB8 (Homo sapiens) Explore Q9HBB8  Go to UniProtKB:  Q9HBB8
PHAROS:  Q9HBB8 GTEx:  ENSG00000099834

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CA (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.427	α = 90
b = 78.379	β = 90
c = 121.39	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Johnson, Z.R., Gray, M.E., Sotomayor, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK095811

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary