Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.69 kDa 
• Atom Count: 2350 
• Modelled Residue Count: 265 
• Deposited Residue Count: 333 
• Unique protein chains: 1

6RX7

Structure of the KIV type 2 (KIV-2) domain of lipoprotein (a)

• PDB DOI: 10.2210/pdb6RX7/pdb

• Classification: LIPID TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-06-07 Released: 2020-07-08 
• Deposition Author(s): Santonastaso, A., Maggi, M., Scotti, C.
• Funding Organization(s): Fondazione CARIPLO

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.269 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Literature

High resolution structure of human apolipoprotein (a) kringle IV type 2: beyond the lysine binding site.

Santonastaso, A., Maggi, M., De Jonge, H., Scotti, C.

(2020) J Lipid Res 61: 1687-1696

• PubMed: 32907988 
• DOI: 10.1194/jlr.RA120001023
• Primary Citation of Related Structures:  
  6RX7


• PubMed Abstract: 
  

Lipoprotein (a) [Lp(a)] is characterized by an LDL-like composition in terms of lipids and apoB100, and by one copy of a unique glycoprotein, apo(a). The apo(a) structure is mainly based on the repetition of tandem kringle domains with high homology to plasminogen kringles 4 and 5. Among them, kringle IV type 2 (KIV-2) is present in a highly variable number of genetically encoded repeats, whose length is inversely related to Lp(a) plasma concentration and cardiovascular risk. Despite it being the major component of apo(a), the actual function of KIV-2 is still unclear. Here, we describe the first high-resolution crystallographic structure of this domain. It shows a general fold very similar to other KIV domains with high and intermediate affinity for the lysine analog, ε-aminocaproic acid. Interestingly, KIV-2 presents a lysine binding site (LBS) with a unique shape and charge distribution. KIV-2 affinity for predicted small molecule binders was found to be negligible in surface plasmon resonance experiments; and with the LBS being nonfunctional, we propose to rename it "pseudo-LBS". Further investigation of the protein by computational small-molecule docking allowed us to identify a possible heparin-binding site away from the LBS, which was confirmed by specific reverse charge mutations abolishing heparin binding. This study opens new possibilities to define the pathogenesis of Lp(a)-related diseases and to facilitate the design of specific therapeutic drugs.

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Organizational Affiliation: 

Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apolipoprotein(a)	A, B, C	111	Homo sapiens	Mutation(s): 0  Gene Names: LPA EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08519 (Homo sapiens) Explore P08519  Go to UniProtKB:  P08519
PHAROS:  P08519

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.269 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.246	α = 90
b = 42.839	β = 110.23
c = 61.175	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-06-07 
• Released Date: 2020-07-08 
Deposition Author(s): Santonastaso, A., Maggi, M., Scotti, C.

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Funding Organization	Location	Grant Number
Fondazione CARIPLO	Italy	42657763 (2013-0380)

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2020-11-11
  Changes: Derived calculations
• Version 1.2: 2021-01-20
  Changes: Database references