4V00

Structural and functional characterization of a novel monotreme- specific protein from the milk of the platypus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structural characterization of a novel monotreme-specific protein with antimicrobial activity from the milk of the platypus.

Newman, J.Sharp, J.A.Enjapoori, A.K.Bentley, J.Nicholas, K.R.Adams, T.E.Peat, T.S.

(2018) Acta Crystallogr F Struct Biol Commun 74: 39-45

  • DOI: 10.1107/S2053230X17017708
  • Primary Citation of Related Structures:  
    4V00, 4V3J, 6B4M

  • PubMed Abstract: 
  • Monotreme lactation protein (MLP) is a recently identified protein with antimicrobial activity. It is present in the milk of monotremes and is unique to this lineage. To characterize MLP and to gain insight into the potential role of this protein in the evolution of lactation, the crystal structure of duck-billed platypus (Ornithorhynchus anatinus) MLP was determined at 1 ...

    Monotreme lactation protein (MLP) is a recently identified protein with antimicrobial activity. It is present in the milk of monotremes and is unique to this lineage. To characterize MLP and to gain insight into the potential role of this protein in the evolution of lactation, the crystal structure of duck-billed platypus (Ornithorhynchus anatinus) MLP was determined at 1.82 Å resolution. This is the first structure to be reported for this novel, mammalian antibacterial protein. MLP was expressed as a FLAG epitope-tagged protein in mammalian cells and crystallized readily, with at least three space groups being observed (P1, C2 and P2 1 ). A 1.82 Å resolution native data set was collected from a crystal in space group P1, with unit-cell parameters a = 51.2, b = 59.7, c = 63.1 Å, α = 80.15, β = 82.98, γ = 89.27°. The structure was solved by SAD phasing using a protein crystal derivatized with mercury in space group C2, with unit-cell parameters a = 92.7, b = 73.2, c = 56.5 Å, β = 90.28°. MLP comprises a monomer of 12 helices and two short β-strands, with much of the N-terminus composed of loop regions. The crystal structure of MLP reveals no three-dimensional similarity to any known structures and reveals a heretofore unseen fold, supporting the idea that monotremes may be a rich source for the identification of novel proteins. It is hypothesized that MLP in monotreme milk has evolved to specifically support the unusual lactation strategy of this lineage and may have played a central role in the evolution of these mammals.


    Organizational Affiliation

    Biomedical Manufacturing, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MONOTREME LACTATING PROTEINA, B366Ornithorhynchus anatinusMutation(s): 0 
Gene Names: LOC103165089MLP
UniProt
Find proteins for F6UME2 (Ornithorhynchus anatinus)
Explore F6UME2 
Go to UniProtKB:  F6UME2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF6UME2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.152α = 80.15
b = 59.721β = 82.98
c = 63.074γ = 89.27
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
PHASERphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2018-01-03
    Changes: Database references
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.3: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2019-05-15
    Changes: Data collection, Derived calculations, Experimental preparation, Structure summary
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary