4P0T | pdb_00004p0t

Crystal structure of human centromere protein M

• PDB DOI: https://doi.org/10.2210/pdb4P0T/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-02-22 Released: 2014-07-09 
• Deposition Author(s): Basilico, F., Pasqualato, S., Musacchio, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.164 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.124 (Depositor), 0.125 (DCC) 
• R-Value Observed: 
  0.127 (Depositor) 

Literature

The pseudo GTPase CENP-M drives human kinetochore assembly.

Basilico, F., Maffini, S., Weir, J.R., Prumbaum, D., Rojas, A.M., Zimniak, T., De Antoni, A., Jeganathan, S., Voss, B., van Gerwen, S., Krenn, V., Massimiliano, L., Valencia, A., Vetter, I.R., Herzog, F., Raunser, S., Pasqualato, S., Musacchio, A.

(2014) Elife 3: e02978-e02978

• PubMed: 25006165 
• DOI: https://doi.org/10.7554/eLife.02978
• Primary Citation Related Structures: 
  4P0T


• PubMed Abstract: 
  

  Kinetochores, multi-subunit complexes that assemble at the interface with centromeres, bind spindle microtubules to ensure faithful delivery of chromosomes during cell division. The configuration and function of the kinetochore-centromere interface is poorly understood. We report that a protein at this interface, CENP-M, is structurally and evolutionarily related to small GTPases but is incapable of GTP-binding and conformational switching. We show that CENP-M is crucially required for the assembly and stability of a tetramer also comprising CENP-I, CENP-H, and CENP-K, the HIKM complex, which we extensively characterize through a combination of structural, biochemical, and cell biological approaches. A point mutant affecting the CENP-M/CENP-I interaction hampers kinetochore assembly and chromosome alignment and prevents kinetochore recruitment of the CENP-T/W complex, questioning a role of CENP-T/W as founder of an independent axis of kinetochore assembly. Our studies identify a single pathway having CENP-C as founder, and CENP-H/I/K/M and CENP-T/W as CENP-C-dependent followers.DOI: http://dx.doi.org/10.7554/eLife.02978.001.

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Organizational Affiliation: 
• Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany Department of Experimental Oncology, European Institute of Oncology, Milan, Italy.
Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
Computational Biology and Bioinformatics Group, Institute of Biomedicine of Seville, Campus Hospital Universitario Virgen del Rocio, Seville, Spain.
Department of Biochemistry and Gene Center, Ludwig-Maximilians-Universität, München, Munich, Germany.
Department of Experimental Oncology, European Institute of Oncology, Milan, Italy.
Structural Biology and Biocomputing Programme, Spanish National Cancer Centre-CNIO, Madrid, Spain.
Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.58 kDa 
• Atom Count: 2,610 
• Modeled Residue Count: 298 
• Deposited Residue Count: 352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein M	A, B	176	Homo sapiens	Mutation(s): 0  Gene Names: CENPM, C22orf18, ICEN39, PANE1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NSP4 (Homo sapiens) Explore Q9NSP4  Go to UniProtKB:  Q9NSP4
PHAROS:  Q9NSP4 GTEx:  ENSG00000100162

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.164 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.124 (Depositor), 0.125 (DCC) 
• R-Value Observed: 0.127 (Depositor) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.03	α = 90
b = 104.03	β = 90
c = 33.56	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
Coot	model building
xia2	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Basilico, F., Pasqualato, S., Musacchio, A.

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2014-07-23
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references