7CTP | pdb_00007ctp

Crystal Structure of Human FAM129B/MINERVA/NIBAN2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.235 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.211 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7CTP

This is version 1.1 of the entry. See complete history

Literature

Structural Insight on Functional Regulation of Human MINERVA Protein.

Hahn, H.Lee, D.E.Jang, D.M.Kim, J.Lee, Y.Cheong, H.Han, B.W.Kim, H.S.

(2020) Int J Mol Sci 21

  • DOI: https://doi.org/10.3390/ijms21218186
  • Primary Citation Related Structures: 
    7CTP

  • PubMed Abstract: 

    MINERVA (melanoma invasion by ERK), also known as FAM129B, is a member of the FAM129 protein family, which is only present in vertebrates. MINERVA is involved in key signaling pathways regulating cell survival, proliferation and apoptosis and found upregulated in many types of cancer promoting invasion. However, the exact function of the protein remains elusive. X-ray crystallographic methods were implemented to determine the crystal structure of MINERVA ΔC , lacking C-terminal flexible region. Trypsin digestion was required before crystallization to obtain diffraction-quality crystals. While the N-terminal pleckstrin homology (PH) domain exhibits the typical fold of PH domains, lipid binding assay indicates specific affinity towards phosphatidic acid and inositol 3-phosphate. A helix-rich domain that constitutes the rest of the molecule demonstrates a novel L-shaped fold that encompasses the PH domain. The overall structure of MINERVA ΔC with binding assays and cell-based experiments suggest plasma membrane association of MINERVA and its function seem to be tightly regulated by various motifs within the C-terminal flexible region. Elucidation of MINERVA ΔC structure presents a novel fold for an α-helix bundle domain that would provide a binding platform for interacting partners.


  • Organizational Affiliation
    • Research Institute, National Cancer Center, Goyang, Gyeonggi 10408, Korea.

Macromolecule Content 

  • Total Structure Weight: 65.14 kDa 
  • Atom Count: 4,806 
  • Modeled Residue Count: 553 
  • Deposited Residue Count: 559 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein Niban 2559Homo sapiensMutation(s): 0 
Gene Names: NIBAN2C9orf88FAM129B
UniProt & NIH Common Fund Data Resources
Find proteins for Q96TA1 (Homo sapiens)
Explore Q96TA1 
Go to UniProtKB:  Q96TA1
PHAROS:  Q96TA1
GTEx:  ENSG00000136830 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96TA1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.235 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.211 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.559α = 90
b = 56.283β = 90
c = 201.007γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2019R1A2C1090251
National Research Foundation (NRF, Korea)Korea, Republic OfNRF_2011_0030001
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2020R1C1C1009512
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2017R1C1B2012225

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references, Derived calculations