Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 179.3 kDa 
• Atom Count: 10,935 
• Modelled Residue Count: 1,129 
• Deposited Residue Count: 1,375 
• Unique protein chains: 2

 1LSH

LIPID-PROTEIN INTERACTIONS IN LIPOVITELLIN

• PDB DOI:  https://doi.org/10.2210/pdb1LSH/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Ichthyomyzon unicuspis
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2002-05-17 Released: 2002-07-31 
• Deposition Author(s): Thompson, J.R., Banaszak, L.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.255 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

Literature

Lipid-protein interactions in lipovitellin.

Thompson, J.R., Banaszak, L.J.

(2002) Biochemistry 41: 9398-9409

• PubMed: 12135361 
• DOI: https://doi.org/10.1021/bi025674w
• Primary Citation of Related Structures:  
  1LSH


• PubMed Abstract: 
  

The refined molecular structure of lipovitellin is described using synchrotron cryocrystallographic data to 1.9 A resolution. Lipovitellin is the predominant lipoprotein found in the yolk of egg-laying animals and is involved in lipid and metal storage. It is thought to be related in amino acid sequence to segments of apolipoprotein B and the microsomal transfer protein responsible for the assembly of low-density lipoproteins. Lipovitellin contains a heterogeneous mixture of about 16% (w/w) noncovalently bound lipid, mostly phospholipid. Previous X-ray structural studies at ambient temperature described several different protein domains including a large cavity in each subunit of the dimeric protein. The cavity was free of any visible electron density for lipid molecules at room temperature, suggesting that only dynamic interactions exist with the protein. An important result from this crystallographic study at 100 K is the appearance of some bound ordered lipid along the walls of the binding cavity. The precise identification of the lipid type is difficult because of discontinuities in the electron density. Nonetheless, the conformations of 7 phospholipids and 43 segments of hydrocarbon chains greater than 5 atoms in length have been discovered. The conformations of the bound lipid and the interactions between protein and lipid provide insights into the factors governing lipoprotein formation.

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Related Citations: 

• The Structural Basis of Lipid Interactions in Lipovitellin, a Souble Lipoprotein
  Anderson, T.A., Levitt, D.G., Banaszak, L.J.
  (1998) Structure 6: 895

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Organizational Affiliation: 

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIPOVITELLIN (LV-1N, LV-1C)	A	1,056	Ichthyomyzon unicuspis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q91062 (Ichthyomyzon unicuspis) Explore Q91062  Go to UniProtKB:  Q91062

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LIPOVITELLIN (LV-2)	B	319	Ichthyomyzon unicuspis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q91062 (Ichthyomyzon unicuspis) Explore Q91062  Go to UniProtKB:  Q91062

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLD	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], MA [auth B]	di-heneicosanoyl phosphatidyl choline C50 H101 N O8 P QFFSGJSMHPWZOB-QSCHNALKSA-O
UPL	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], KA [auth A], L [auth A], LA [auth A], M [auth A], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID C34 H70 QPCSNFPFMCVVAI-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.255 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.17	α = 90
b = 84.52	β = 100.39
c = 89.53	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-07-31 
Deposition Author(s): Thompson, J.R., Banaszak, L.J.

Revision History  

• Version 1.0: 2002-07-31
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2019-12-25
  Changes: Advisory, Database references, Derived calculations, Polymer sequence, Refinement description
• Version 2.1: 2021-08-18
  Changes: Advisory, Database references, Derived calculations, Structure summary