6VFU

Crystal structure of human protocadherin 19 EC1-EC4

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

  • Deposited: 2020-01-06 Released: 2020-03-11 
  • Deposition Author(s): Harrison, O.J., Brasch, J., Shapiro, L.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.266 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Literature

Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered delta-Protocadherins.

Harrison, O.J.Brasch, J.Katsamba, P.S.Ahlsen, G.Noble, A.J.Dan, H.Sampogna, R.V.Potter, C.S.Carragher, B.Honig, B.Shapiro, L.

(2020) Cell Rep 30: 2655-2671.e7

  • DOI: https://doi.org/10.1016/j.celrep.2020.02.003
  • Primary Citation of Related Structures:  
    6VFP, 6VFQ, 6VFR, 6VFT, 6VFU, 6VFV, 6VFW, 6VG1, 6VG4

  • PubMed Abstract: 

    Non-clustered δ1- and δ2-protocadherins, close relatives of clustered protocadherins, function in cell adhesion and motility and play essential roles in neural patterning. To understand the molecular interactions underlying these functions, we used solution biophysics to characterize binding of δ1- and δ2-protocadherins, determined crystal structures of ectodomain complexes from each family, and assessed ectodomain assembly in reconstituted intermembrane junctions by cryoelectron tomography (cryo-ET). Homophilic trans (cell-cell) interactions were preferred for all δ-protocadherins, with additional weaker heterophilic interactions observed exclusively within each subfamily. As expected, δ1- and δ2-protocadherin trans dimers formed through antiparallel EC1-EC4 interfaces, like clustered protocadherins. However, no ectodomain-mediated cis (same-cell) interactions were detectable in solution; consistent with this, cryo-ET of reconstituted junctions revealed dense assemblies lacking the characteristic order observed for clustered protocadherins. Our results define non-clustered protocadherin binding properties and their structural basis, providing a foundation for interpreting their functional roles in neural patterning.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protocadherin-19A [auth C],
B [auth A],
C [auth B]
430Homo sapiensMutation(s): 0 
Gene Names: PCDH19KIAA1313
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAB3 (Homo sapiens)
Explore Q8TAB3 
Go to UniProtKB:  Q8TAB3
PHAROS:  Q8TAB3
GTEx:  ENSG00000165194 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TAB3
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q8TAB3-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
D
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
CA [auth A],
P [auth C],
PA [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
DA [auth A],
Q [auth C]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
G [auth C]
GA [auth B]
H [auth C]
AA [auth A],
BA [auth A],
G [auth C],
GA [auth B],
H [auth C],
HA [auth B],
I [auth C],
IA [auth B],
J [auth C],
JA [auth B],
K [auth C],
KA [auth B],
L [auth C],
LA [auth B],
M [auth C],
MA [auth B],
N [auth C],
NA [auth B],
O [auth C],
OA [auth B],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
EA [auth A],
FA [auth A],
R [auth C],
S [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.266 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.971α = 90
b = 108.971β = 90
c = 309.663γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01MH114817
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM118584
National Science Foundation (NSF, United States)United StatesMCB-1412472

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Structure summary