Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A7B1C1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 236.49 kDa 
• Atom Count: 13122 
• Modelled Residue Count: 1203 
• Deposited 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

• PDB DOI: 10.2210/pdb6C0W/pdb
• EM Map EMD-7326:EMDBEMDataResource

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


• 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: 4.00 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:  
  6C0W, 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: 

Howard Hughes Medical Institute, Maryland, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3-like centromeric protein A	A, E	140	Homo sapiens	Mutation(s): 0  Gene Names: CENPA
UniProt & NIH Common Fund Data Resources
Find proteins for P49450 (Homo sapiens) Explore P49450  Go to UniProtKB:  P49450
PHAROS:  P49450 GTEx:  ENSG00000115163

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	102	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4, H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	130	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2AC, H2AFL, H2AC6
UniProt & NIH Common Fund Data Resources
Find proteins for Q93077 (Homo sapiens) Explore Q93077  Go to UniProtKB:  Q93077
PHAROS:  Q93077 GTEx:  ENSG00000180573

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	D, H	126	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H2BC, H2BFL, HIST1H2BE, H2BFH, HIST1H2BF, H2BFG, HIST1H2BG, H2BFA, HIST1H2BI, H2BFK, H2BC4, H2BC6, H2BC7, H2BC8, H2BC10
UniProt & NIH Common Fund Data Resources
Find proteins for P62807 (Homo sapiens) Explore P62807  Go to UniProtKB:  P62807
PHAROS:  P62807 GTEx:  ENSG00000180596 ENSG00000277224 ENSG00000278588 ENSG00000273802 ENSG00000274290

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein N	K	295	Homo sapiens	Mutation(s): 1  Gene Names: CENPN, C16orf60, ICEN32, BM-309
UniProt & NIH Common Fund Data Resources
Find proteins for Q96H22 (Homo sapiens) Explore Q96H22  Go to UniProtKB:  Q96H22
PHAROS:  Q96H22 GTEx:  ENSG00000166451

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

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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
  Changes: Author supporting evidence