5B4X

Crystal structure of the ApoER2 ectodomain in complex with the Reelin R56 fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ReelinA, C725Mus musculusMutation(s): 1 
Gene Names: RelnRl
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q60841 (Mus musculus)
Explore Q60841 
Go to UniProtKB:  Q60841
IMPC:  MGI:103022
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60841
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Low density lipoprotein receptor-related protein 8, apolipoprotein e receptor, isoform CRA_eB, D570Homo sapiensMutation(s): 0 
Gene Names: LRP8hCG_33395APOER2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14114 (Homo sapiens)
Explore Q14114 
Go to UniProtKB:  Q14114
PHAROS:  Q14114
GTEx:  ENSG00000157193 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14114
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
O [auth B],
T [auth C],
Y [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
U [auth D],
V [auth D],
W [auth D],
X [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, C L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 205.951α = 90
b = 205.951β = 90
c = 169.84γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan22247010
JSPSJapan20770084
JSPSJapan05J09821
MEXTJapan17082004

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary