6T3O | pdb_00006t3o

Crystal structure of the human myomesin domain 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.244 (Depositor) 
  • R-Value Work: 
    0.198 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6T3O

This is version 1.2 of the entry. See complete history

Literature

Myomedin scaffold variants targeted to 10E8 HIV-1 broadly neutralizing antibody mimic gp41 epitope and elicit HIV-1 virus-neutralizing sera in mice.

Kuchar, M.Kosztyu, P.Daniel Liskova, V.Cerny, J.Petrokova, H.Vroblova, E.Maly, M.Vankova, L.Krupka, M.Raskova Kafkova, L.Turanek Knotigova, P.Duskova, J.Dohnalek, J.Masek, J.Turanek, J.Raska, M.Maly, P.

(2021) Virulence 12: 1271-1287

  • DOI: https://doi.org/10.1080/21505594.2021.1920251
  • Primary Citation Related Structures: 
    6T3O

  • PubMed Abstract: 

    One of the proposed strategies for the development of a more efficient HIV-1 vaccine is based on the identification of proteins binding to a paratope of chosen broadly neutralizing antibody (bNAb) that will mimic cognate HIV-1 Env (glyco)protein epitope and could be used as potent immunogens for induction of protective virus-neutralizing antibodies in the immunized individuals. To verify this "non-cognate ligand" concept, we developed a highly complex combinatorial library designed on a scaffold of human myomesin-1 protein domain and selected proteins called Myomedins specifically binding to variable regions of HIV-1 broadly neutralizing antibody 10E8. Immunization of mice with these Myomedin variants elicited the production of HIV-1 Env-specific antibodies. Hyperimmune sera bound to Env pseudotyped viruses and weakly/moderately neutralized 54% of tested clade A, B, C, and AE pseudotyped viruses variants in vitro . These results demonstrate that Myomedin variants have the potential to mimic Env epitopes and could be used as potential HIV-1 vaccine components.


  • Organizational Affiliation
    • Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Vestec, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 15.44 kDa 
  • Atom Count: 1,002 
  • Modeled Residue Count: 109 
  • Deposited Residue Count: 132 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Myomesin-1132Homo sapiensMutation(s): 0 
Gene Names: MYOM1
UniProt & NIH Common Fund Data Resources
Find proteins for P52179 (Homo sapiens)
Explore P52179 
Go to UniProtKB:  P52179
PHAROS:  P52179
GTEx:  ENSG00000101605 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52179
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AZI

Query on AZI



Download:Ideal Coordinates CCD File
B [auth A]AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ
A
L-PEPTIDE LINKINGC7 H16 N2 O2LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.244 (Depositor) 
  • R-Value Work:  0.198 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.599α = 90
b = 58.599β = 90
c = 62.821γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicCZ.02.1.01/0.0/0.0/16_025/0007397

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description