Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A8B1 

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

Macromolecule Content

• Total Structure Weight: 214.68 kDa 
• Atom Count: 11919 
• Residue Count: 1041 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

6SEF

Class2C : CENP-A nucleosome in complex with CENP-C central region

• DOI: 10.2210/pdb6SEF/pdb
• EMDataResource: EMD-10154

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-29 Released: 2019-08-14 
• Deposition Author(s): Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N.
• Funding Organization(s): Research Council of Norway, European Research Council

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail.

Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N.

(2019) EMBO Rep 20: e48913-e48913

• PubMed: 31475439 
• DOI: 10.15252/embr.201948913
• Primary Citation of Related Structures:  
  6SEE, 6SEG, 6SEF, 6SE0, 6SE6


• PubMed Abstract: 
  

Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is considered to be a central organizer of the CCAN. We provide new molecular insights into the structure of human CENP-A nucleosomes, in isolation and in complex with the CENP-C central region (CENP-C ^CR ), the main CENP-A binding module of human CENP-C. We establish that the short αN helix of CENP-A promotes DNA flexibility at the nucleosome ends, independently of the sequence it wraps. Furthermore, we show that, in vitro, two regions of human CENP-C (CENP-C ^CR and CENP-C ^motif ) both bind exclusively to the CENP-A nucleosome. We find CENP-C ^CR to bind with high affinity due to an extended hydrophobic area made up of CENP-A ^{V 532} and CENP-A ^{V 533} . Importantly, we identify two key conformational changes within the CENP-A nucleosome upon CENP-C binding. First, the loose DNA wrapping of CENP-A nucleosomes is further exacerbated, through destabilization of the H2A C-terminal tail. Second, CENP-C ^CR rigidifies the N-terminal tail of H4 in the conformation favoring H4 ^K20 monomethylation, essential for a functional centromere.

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Organizational Affiliation: 

Department of Chemistry, University of Oslo, Oslo, Norway.

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
Find proteins for P49450 (Homo sapiens) Explore P49450  Go to UniProtKB:  P49450
NIH Common Fund Data Resources
PHAROS:  P49450 GTEx:  ENSG00000115163

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	103	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
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS:  P62805 GTEx:  ENSG00000274618ENSG00000197238ENSG00000197837ENSG00000158406ENSG00000278705ENSG00000197061ENSG00000270882ENSG00000270276ENSG00000273542ENSG00000277157ENSG00000276966ENSG00000276180ENSG00000278637ENSG00000275126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 2-A	C, G	130	Homo sapiens	Mutation(s): 0  Gene Names: HIST2H2AA3, H2AFO, HIST2H2AA, HIST2H2AA4, H2AC18, H2AC19
Find proteins for Q6FI13 (Homo sapiens) Explore Q6FI13  Go to UniProtKB:  Q6FI13
NIH Common Fund Data Resources
PHAROS:  Q6FI13 GTEx:  ENSG00000203812ENSG00000272196

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-C/E/F/G/I	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
Find proteins for P62807 (Homo sapiens) Explore P62807  Go to UniProtKB:  P62807
NIH Common Fund Data Resources
PHAROS:  P62807 GTEx:  ENSG00000180596ENSG00000277224ENSG00000278588ENSG00000273802ENSG00000274290

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein C	V	124	Homo sapiens	Mutation(s): 0  Gene Names: CENPC, CENPC1, ICEN7
Find proteins for Q03188 (Homo sapiens) Explore Q03188  Go to UniProtKB:  Q03188
NIH Common Fund Data Resources
PHAROS:  Q03188 GTEx:  ENSG00000145241

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	I	145	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	J	145	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-07-29 
• Released Date: 2019-08-14 
Deposition Author(s): Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N.

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Funding Organization	Location	Grant Number
Research Council of Norway	Norway	263195
European Research Council	Germany	ERC-smallRNAhet-309584

Revision History 

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2019-09-11
  Changes: Data collection, Database references
• Version 1.2: 2019-10-16
  Changes: Data collection, Database references
• Version 1.3: 2019-10-23
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2019-11-06
  Changes: Data collection, Refinement description