7UCX | pdb_00007ucx

LRP8 11H1 Fab complexed to a cyclized CR1 peptide

• PDB DOI: https://doi.org/10.2210/pdb7UCX/pdb

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


• Deposited: 2022-03-17 Released: 2023-01-18 
• Deposition Author(s): Argiriadi, M.A., Deng, K., Egan, D., Gao, L., Gizatullin, F., Harlan, J., Karaoglu, D., Qiu, W., Goodearl, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.240 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

The use of cyclic peptide antigens to generate LRP8 specific antibodies

Argiriadi, M.A., Deng, K., Egan, D., Gao, L., Gizatullin, F., Harlan, J., Karaoglu Hanzatian, D., Qiu, W., Villanueva, R., Goodearl, A.

(2023) Front Drug Discov (Lausanne) 2

• DOI: https://doi.org/10.3389/fddsv.2022.1093153

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.85 kDa 
• Atom Count: 3,581 
• Modeled Residue Count: 438 
• Deposited Residue Count: 462 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclized CR1 peptide	A [auth B]	19	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q14114 (Homo sapiens) Explore Q14114  Go to UniProtKB:  Q14114
PHAROS:  Q14114 GTEx:  ENSG00000157193

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
11H1 Fab Heavy chain	B [auth H]	224	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
11H1 Fab Light chain	C [auth L]	219	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth B], E [auth H], F [auth L]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.240 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.265	α = 90
b = 79.827	β = 95.47
c = 67.066	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Argiriadi, M.A., Deng, K., Egan, D., Gao, L., Gizatullin, F., Harlan, J., Karaoglu, D., Qiu, W., Goodearl, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-08-09
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-20
  Changes: Database references, Structure summary