8YBC | pdb_00008ybc

Crystal structure of coiled coil domain of Golm1 (Golgi membrane protein 1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.321 (Depositor), 0.321 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 
    0.250 (Depositor) 

Starting Model: experimental
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Literature

The first structure of human Golm1 coiled coil domain reveals an unexpected tetramer and highlights its structural diversity.

Bai, W.Li, B.Wu, P.Li, X.Huang, X.Shi, N.Yang, C.Hu, F.Xie, X.

(2024) Int J Biol Macromol 275: 133624-133624

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.133624
  • Primary Citation of Related Structures:  
    8YBC

  • PubMed Abstract: 

    Golgi membrane protein 1 (Golm1), a transmembrane protein with diverse subcellular localizations, has garnered significant attention in recent years due to its strong association with the development and progression of liver diseases and numerous cancers. Interestingly, although Golm1 is a membrane protein, the C-terminal of Golm1, which contains a coiled coil domain and a flexible acid region, can also be detected in the plasma of patients with various liver diseases. Notably, the coiled coil domain of serum Golm1 is postulated to play a pivotal role in physiological and pathological functions. However, little is currently known about the structure of this coiled coil domain and the full-length protein, which may limit our understanding of Golm1. Therefore, this study aims to address this gap in knowledge and reports the first crystal structure of the coiled coil domain of Golm1 at a resolution of 2.28 Å. Meanwhile, we have also confirmed that the Golm1 coiled coil domain in solution can form tetramer. Our results reveal that Golm1 can form a novel tetrameric structure that differs from the previous reported dimeric structure Golm1 could assemble, which may provide novel insights into the diversity of physiological functions and pathological roles.


  • Organizational Affiliation
    • State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Golgi membrane protein 1
A, B, C, D
67Homo sapiensMutation(s): 0 
Gene Names: GOLM1C9orf155GOLPH2PSEC0242UNQ686/PRO1326
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBJ4 (Homo sapiens)
Explore Q8NBJ4 
Go to UniProtKB:  Q8NBJ4
PHAROS:  Q8NBJ4
GTEx:  ENSG00000135052 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NBJ4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.321 (Depositor), 0.321 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 0.250 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.81α = 90
b = 44.02β = 112.92
c = 63.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
Arcimboldophasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release