7W91 | pdb_00007w91

Residues 440-490 of centrosomal protein 63

• PDB DOI: https://doi.org/10.2210/pdb7W91/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-12-09 Released: 2023-07-19 
• Deposition Author(s): Yun, H.Y., Ku, B.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 
  0.261 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Architectural basis for cylindrical self-assembly governing Plk4-mediated centriole duplication in human cells.

Il Ahn, J., Zhang, L., Ravishankar, H., Fan, L., Kirsch, K., Zeng, Y., Meng, L., Park, J.E., Yun, H.Y., Ghirlando, R., Ma, B., Ball, D., Ku, B., Nussinov, R., Schmit, J.D., Heinz, W.F., Kim, S.J., Karpova, T., Wang, Y.X., Lee, K.S.

(2023) Commun Biol 6: 712-712

• PubMed: 37433832 
• DOI: https://doi.org/10.1038/s42003-023-05067-8
• Primary Citation Related Structures: 
  7W91


• PubMed Abstract: 
  

  Proper organization of intracellular assemblies is fundamental for efficient promotion of biochemical processes and optimal assembly functionality. Although advances in imaging technologies have shed light on how the centrosome is organized, how its constituent proteins are coherently architected to elicit downstream events remains poorly understood. Using multidisciplinary approaches, we showed that two long coiled-coil proteins, Cep63 and Cep152, form a heterotetrameric building block that undergoes a stepwise formation into higher molecular weight complexes, ultimately generating a cylindrical architecture around a centriole. Mutants defective in Cep63•Cep152 heterotetramer formation displayed crippled pericentriolar Cep152 organization, polo-like kinase 4 (Plk4) relocalization to the procentriole assembly site, and Plk4-mediated centriole duplication. Given that the organization of pericentriolar materials (PCM) is evolutionarily conserved, this work could serve as a model for investigating the structure and function of PCM in other species, while offering a new direction in probing the organizational defects of PCM-related human diseases.

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Organizational Affiliation: 
• Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-ray Scattering Core Facility, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA.
School of Pharmacy, Shanghai Jiao Tong University, 200240, Shanghai, P R China.
Laboratory of Receptor Biology and Gene Expression, Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
Department of Physics, Kansas State University, Manhattan, KS, 66506, USA.
Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
Protein-Nucleic Acid Interaction Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 82.11 kDa 
• Atom Count: 5,084 
• Modeled Residue Count: 616 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Centrosomal protein of 63 kDa	A, B, C, D, E, F, G, H, I, J, K, L	56	Homo sapiens	Mutation(s): 0  Gene Names: CEP63
UniProt & NIH Common Fund Data Resources
Find proteins for Q96MT8 (Homo sapiens) Explore Q96MT8  Go to UniProtKB:  Q96MT8
PHAROS:  Q96MT8 GTEx:  ENSG00000182923

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free:  0.261 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.622	α = 65.33
b = 81.112	β = 60.07
c = 80.846	γ = 60.2

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-19 
Deposition Author(s): Yun, H.Y., Ku, B.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2019M3E5D6063955
National Research Foundation (NRF, Korea)	Korea, Republic Of	KGM9952112

Revision History  

• Version 1.0: 2023-07-19
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary