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 7D73 | pdb_00007d73

Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (State I)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7D73

This is version 1.3 of the entry. See complete history. 

Literature

Cryo-EM structures of human GMPPA-GMPPB complex reveal how cells maintain GDP-mannose homeostasis.

Zheng, L., Liu, Z., Wang, Y., Yang, F., Wang, J., Huang, W., Qin, J., Tian, M., Cai, X., Liu, X., Mo, X., Gao, N., Jia, D.

(2021) Nat Struct Mol Biol 28: 1-12

  • DOI: https://doi.org/10.1038/s41594-021-00591-9
  • Primary Citation Related Structures: 
    7D72, 7D73, 7D74

  • PubMed Abstract: 

    GDP-mannose (GDP-Man) is a key metabolite essential for protein glycosylation and glycophosphatidylinositol anchor synthesis, and aberrant cellular GDP-Man levels have been associated with multiple human diseases. How cells maintain homeostasis of GDP-Man is unknown. Here, we report the cryo-EM structures of human GMPPA-GMPPB complex, the protein machinery responsible for GDP-Man synthesis, in complex with GDP-Man or GTP. Unexpectedly, we find that the catalytically inactive subunit GMPPA displays a much higher affinity to GDP-Man than the active subunit GMPPB and, subsequently, inhibits the catalytic activity of GMPPB through a unique C-terminal loop of GMPPA. Importantly, disruption of the interactions between GMPPA and GMPPB or the binding of GDP-Man to GMPPA in zebrafish leads to abnormal brain development and muscle abnormality, analogous to phenotypes observed in individuals carrying GMPPA or GMPPB mutations. We conclude that GMPPA acts as a cellular sensor to maintain mannose homeostasis through allosterically regulating GMPPB.


  • Organizational Affiliation: 
    • State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 510.84 kDa 
  • Atom Count: 35,292 
  • Modeled Residue Count: 4,495 
  • Deposited Residue Count: 4,560 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mannose-1-phosphate guanyltransferase alphaA,
B,
D [auth C],
E [auth D]
420Homo sapiensMutation(s): 0 
Gene Names: GMPPA
UniProt & NIH Common Fund Data Resources
Find proteins for Q96IJ6 (Homo sapiens)
Explore Q96IJ6 
Go to UniProtKB:  Q96IJ6
PHAROS:  Q96IJ6
GTEx:  ENSG00000144591 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96IJ6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Mannose-1-phosphate guanyltransferase beta360Homo sapiensMutation(s): 0 
Gene Names: GMPPB
EC: 2.7.7.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5P6 (Homo sapiens)
Explore Q9Y5P6 
Go to UniProtKB:  Q9Y5P6
PHAROS:  Q9Y5P6
GTEx:  ENSG00000173540 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5P6
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDD
(Subject of Investigation/LOI)

Query on GDD



Download:Ideal Coordinates CCD File
M [auth A],
P [auth C]
GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
C16 H25 N5 O16 P2
MVMSCBBUIHUTGJ-GDJBGNAASA-N
GTP
(Subject of Investigation/LOI)

Query on GTP



Download:Ideal Coordinates CCD File
N [auth B]
O [auth E]
Q [auth D]
R [auth F]
S [auth G]
N [auth B],
O [auth E],
Q [auth D],
R [auth F],
S [auth G],
T [auth I],
U [auth J],
V [auth K],
W [auth L],
X [auth H]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)--

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references, Structure summary
  • Version 1.2: 2021-12-01
    Changes: Database references
  • Version 1.3: 2025-09-17
    Changes: Advisory, Data collection, Derived calculations, Structure summary