Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer -A6B2C 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 236486.00 
• Atom Count: 13122 
• Residue Count: 1585 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

6C0W

Cryo-EM structure of human kinetochore protein CENP-N with the centromeric nucleosome containing CENP-A

• DOI: 10.2210/pdb6C0W/pdb
• EMDataResource: EMD-7326

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Escherichia coli str. 'clone D i2', Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG', Escherichia coli, Insect cell expression vector pTIE1


• Deposited: 2018-01-02 Released: 2018-01-17 
• Deposition Author(s): Zhou, K., Pentakota, S., Vetter, I.R., Morgan, G.P., Petrovic, A., Musacchio, A., Luger, K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS); Howard Hughes Medical Institute (HHMI) 

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Decoding the centromeric nucleosome through CENP-N.

Pentakota, S., Zhou, K., Smith, C., Maffini, S., Petrovic, A., Morgan, G.P., Weir, J.R., Vetter, I.R., Musacchio, A., Luger, K.

(2017) Elife 6: --

• PubMed: 29280735 
• DOI: 10.7554/eLife.33442
• Primary Citation of Related Structures:  
  6EQT


• PubMed Abstract: 
  

Centromere protein (CENP) A, a histone H3 variant, is a key epigenetic determinant of chromosome domains known as centromeres. Centromeres nucleate kinetochores, multi-subunit complexes that capture spindle microtubules to promote chromosome segregation during mitosis. Two kinetochore proteins, CENP-C and CENP-N, recognize CENP-A in the context of a rare CENP-A nucleosome. Here, we reveal the structural basis for the exquisite selectivity of CENP-N for centromeres. CENP-N uses charge and space complementarity to decode the L1 loop that is unique to CENP-A. It also engages in extensive interactions with a 15-base pair segment of the distorted nucleosomal DNA double helix, in a position predicted to exclude chromatin remodelling enzymes. Besides CENP-A, stable centromere recruitment of CENP-N requires a coincident interaction with a newly identified binding motif on nucleosome-bound CENP-C. Collectively, our studies clarify how CENP-N and CENP-C decode and stabilize the non-canonical CENP-A nucleosome to enforce epigenetic centromere specification and kinetochore assembly.

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Organizational Affiliation: 

Department of MCDB, University of Colorado at Boulder, Boulder, United States.,Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany.,Howard Hughes Medical Institute, Maryland, United States.,Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, United States.,Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, Dortmund, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3-like centromeric protein A	A, E	140	Homo sapiens	Mutation(s): 0  Gene Names: CENPA
Find proteins for P49450 (Homo sapiens) Go to Gene View: CENPA Go to UniProtKB:  P49450

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F	102	Homo sapiens	Mutation(s): 0  Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens) Go to UniProtKB:  P62805

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A	C, G	130	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2AC (H2AFL)
Find proteins for Q93077 (Homo sapiens) Go to Gene View: HIST1H2AC Go to UniProtKB:  Q93077

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B	D, H	126	Homo sapiens	Mutation(s): 0  Gene Names: H2BC4, H2BC6, H2BC7, H2BC8, H2BC10 (H2BFL, HIST1H2BC, H2BFH, HIST1H2BE, H2BFG, HIST1H2BF, H2BFA, HIST1H2BG, H2BFK, HIST1H2BI)
Find proteins for P62807 (Homo sapiens) Go to UniProtKB:  P62807

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
Centromere protein N	K	295	Homo sapiens	Mutation(s): 0  Gene Names: CENPN (C16orf60, ICEN32)
Find proteins for Q96H22 (Homo sapiens) Go to Gene View: CENPN Go to UniProtKB:  Q96H22

Entity ID: 5
Molecule	Chains	Length	Organism
147 mer DNA	I	147	Escherichia coli str. 'clone D i2'

Entity ID: 6
Molecule	Chains	Length	Organism
147 mer DNA	J	147	Escherichia coli str. 'clone D i2'

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-01-02 
• Released Date: 2018-01-17 
• Deposition Author(s): Zhou, K., Pentakota, S., Vetter, I.R., Morgan, G.P., Petrovic, A., Musacchio, A., Luger, K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM067777
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History 

• Version 1.0: 2018-01-17
  Type: Initial release
• Version 1.1: 2019-11-20
  Type: Author supporting evidence