8KCQ | pdb_00008kcq

Solution structures of the N-terminal divergent caplonin homology (NN-CH) domains of human intraflagellar transport protein 54

• PDB DOI: https://doi.org/10.2210/pdb8KCQ/pdb
• BMRB: 36589

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Cell-free gateway cloning vector N-term 8xHis mcherry pCellFree_G05
• Mutation(s): No 


• Deposited: 2023-08-08 Released: 2024-05-22 
• Deposition Author(s): Dang, W., Kuwasako, K., He, F., Takahashi, M., Tsuda, K., Nagata, T., Tanaka, A., Kobayashi, N., Kigawa, T., Guentert, P., Shirouzu, M., Yokoyama, S., Muto, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 400 
• Conformers Submitted: 20 
• Selection Criteria: structures with favorable non-bond energy 

Literature

1 H, 13 C, and 15 N resonance assignments and solution structure of the N-terminal divergent calponin homology (NN-CH) domain of human intraflagellar transport protein 54.

Kuwasako, K., Dang, W., He, F., Takahashi, M., Tsuda, K., Nagata, T., Tanaka, A., Kobayashi, N., Kigawa, T., Guntert, P., Shirouzu, M., Yokoyama, S., Muto, Y.

(2024) Biomol NMR Assign 18: 71-78

• PubMed: 38551798 
• DOI: https://doi.org/10.1007/s12104-024-10170-w
• Primary Citation Related Structures: 
  8KCQ


• PubMed Abstract: 
  

  The intraflagellar transport (IFT) machinery plays a crucial role in the bidirectional trafficking of components necessary for ciliary signaling, such as the Hedgehog, Wnt/PCR, and cAMP/PKA systems. Defects in some components of the IFT machinery cause dysfunction, leading to a wide range of human diseases and developmental disorders termed ciliopathies, such as nephronophthisis. The IFT machinery comprises three sub-complexes: BBsome, IFT-A, and IFT-B. The IFT protein 54 (IFT54) is an important component of the IFT-B sub-complex. In anterograde movement, IFT54 binds to active kinesin-II, walking along the cilia microtubule axoneme and carrying the dynein-2 complex in an inactive state, which works for retrograde movement. Several mutations in IFT54 are known to cause Senior-Loken syndrome, a ciliopathy. IFT54 possesses a divergent Calponin Homology (CH) domain termed as NN-CH domain at its N-terminus. However, several aspects of the function of the NN-CH domain of IFT54 are still obscure. Here, we report the ¹ H, ¹⁵ N, and ¹³ C resonance assignments of the NN-CH domain of human IFT54 and its solution structure. The NN-CH domain of human IFT54 adopts essentially the α1-α2-α3-α4-α5 topology as that of mouse IFT54, whose structure was determined by X-ray crystallographic study. The structural information and assignments obtained in this study shed light on the molecular function of the NN-CH domain in IFT54.

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Organizational Affiliation: 
• RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230- 0045, Japan.
Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan.
Institute of Advanced Energy, Graduate School of Energy Science, Kyoto University, Gokasho, Kyoto, Uji, 611-0011, Japan.
RIKEN Yokohama NMR Facility, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
Tatsuo Miyazawa Memorial Program, RIKEN Genomic Sciences Center, Yokohama, 230-0045, Japan.
Institute of Biophysical Chemistry, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany.
Institute of Molecular Physical Science, ETH Zurich, Vladimir-Prelog-Weg 2, Zurich, 8093, Switzerland.
Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192- 0397, Japan.
RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan. [e-mail].
RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan. [e-mail].
RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Yokohama, 230-0045, Japan. [e-mail].
RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan. [e-mail].
RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230- 0045, Japan. [e-mail].
Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.4 kDa 
• Atom Count: 1,075 
• Modeled Residue Count: 140 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAF3-interacting protein 1	A	140	Homo sapiens	Mutation(s): 0  Gene Names: TRAF3IP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDR0 (Homo sapiens) Explore Q8TDR0  Go to UniProtKB:  Q8TDR0
PHAROS:  Q8TDR0 GTEx:  ENSG00000204104

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 400 
• Conformers Submitted: 20 
• Selection Criteria: structures with favorable non-bond energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Dang, W., Kuwasako, K., He, F., Takahashi, M., Tsuda, K., Nagata, T., Tanaka, A., Kobayashi, N., Kigawa, T., Guentert, P., Shirouzu, M., Yokoyama, S., Muto, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release