4X23

CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE

• PDB DOI:  https://doi.org/10.2210/pdb4X23/pdb
• Entry: 4X23 supersedes: 4INM
• NAKB: 4X23

• Classification: structural protein/dna
• Organism(s): Homo sapiens, Drosophila melanogaster, Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-25 Released: 2014-12-10 
• Deposition Author(s): Jiang, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.286 
• R-Value Work: 0.236 
• R-Value Observed: 0.238 

Literature

A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C.

Kato, H., Jiang, J.S., Zhou, B.R., Rozendaal, M., Feng, H., Ghirlando, R., Xiao, T.S., Straight, A.F., Bai, Y.

(2013) Science 340: 1110-1113

• PubMed: 23723239 
• DOI: https://doi.org/10.1126/science.1235532
• Primary Citation of Related Structures:  
  4X23


• PubMed Abstract: 
  

Chromosome segregation during mitosis requires assembly of the kinetochore complex at the centromere. Kinetochore assembly depends on specific recognition of the histone variant CENP-A in the centromeric nucleosome by centromere protein C (CENP-C). We have defined the determinants of this recognition mechanism and discovered that CENP-C binds a hydrophobic region in the CENP-A tail and docks onto the acidic patch of histone H2A and H2B. We further found that the more broadly conserved CENP-C motif uses the same mechanism for CENP-A nucleosome recognition. Our findings reveal a conserved mechanism for protein recruitment to centromeres and a histone recognition mode whereby a disordered peptide binds the histone tail through hydrophobic interactions facilitated by nucleosome docking.

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Organizational Affiliation: 

Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A7B1C1D1 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 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A8B1C1 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 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 359.94 kDa 
• Atom Count: 23,974 
• Modelled Residue Count: 2,103 
• Deposited Residue Count: 2,164 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	C [auth A], G [auth E], O [auth K], S [auth O]	98	Drosophila melanogaster	Mutation(s): 0  Gene Names:  His3, His3:CG31613, CG31613, His3:CG33803, CG33803, His3:CG33806, CG33806, His3:CG33809, CG33809, His3:CG33812, CG33812, His3:CG33815, CG33815, His3:CG33818, CG33818, His3:CG33821, CG33821, His3:CG33824, CG33824, His3:CG33827, CG33827, His3:CG33830, CG33830, His3:CG33833, CG33833, His3:CG33836, CG33836, His3:CG33839, CG33839, His3:CG33842, CG33842, His3:CG33845, CG33845, His3:CG33848, CG33848, His3:CG33851, CG33851, His3:CG33854, CG33854, His3:CG33857, CG33857, His3:CG33860, CG33860, His3:CG33863, CG33863, His3:CG33866, CG33866
UniProt
Find proteins for P02299 (Drosophila melanogaster) Explore P02299  Go to UniProtKB:  P02299

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D [auth B], H [auth F], P [auth L], T [auth P]	79	Drosophila melanogaster	Mutation(s): 0  Gene Names:  His4, H4, His4r, H4r, CG3379, His4:CG31611, CG31611, His4:CG33869, CG33869, His4:CG33871, CG33871, His4:CG33873, CG33873, His4:CG33875, CG33875, His4:CG33877, CG33877, His4:CG33879, CG33879, His4:CG33881, CG33881, His4:CG33883, CG33883, His4:CG33885, CG33885, His4:CG33887, CG33887, His4:CG33889, CG33889, His4:CG33891, CG33891, His4:CG33893, CG33893, His4:CG33895, CG33895, His4:CG33897, CG33897, His4:CG33899, CG33899, His4:CG33901, CG33901, His4:CG33903, CG33903, His4:CG33905, CG33905, His4:CG33907, CG33907, His4:CG33909, CG33909
UniProt
Find proteins for P84040 (Drosophila melanogaster) Explore P84040  Go to UniProtKB:  P84040

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	E [auth C], I [auth G], Q [auth M], U [auth Q]	102	Drosophila melanogaster	Mutation(s): 0  Gene Names:  His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A:CG33829, CG33829, His2A:CG33832, CG33832, His2A:CG33835, CG33835, His2A:CG33838, CG33838, His2A:CG33841, CG33841, His2A:CG33844, CG33844, His2A:CG33847, CG33847, His2A:CG33850, CG33850, His2A:CG33862, CG33862, His2A:CG33865, CG33865
UniProt
Find proteins for P84051 (Drosophila melanogaster) Explore P84051  Go to UniProtKB:  P84051

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	F [auth D], J [auth H], R [auth N], V [auth R]	90	Drosophila melanogaster	Mutation(s): 0  Gene Names:  His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, CG33880, His2B:CG33882, CG33882, His2B:CG33884, CG33884, His2B:CG33886, CG33886, His2B:CG33888, CG33888, His2B:CG33890, CG33890, His2B:CG33892, CG33892, His2B:CG33894, CG33894, His2B:CG33896, CG33896, His2B:CG33898, CG33898, His2B:CG33900, CG33900, His2B:CG33902, CG33902, His2B:CG33904, CG33904, His2B:CG33906, CG33906, His2B:CG33908, CG33908, His2B:CG33910, CG33910
UniProt
Find proteins for P02283 (Drosophila melanogaster) Explore P02283  Go to UniProtKB:  P02283

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
CENP-C	K [auth V], L [auth U], W [auth X], X [auth W]	25	Rattus norvegicus	Mutation(s): 0  Gene Names: Cenpc, Cenpc1
UniProt
Find proteins for Q66LH7 (Rattus norvegicus) Explore Q66LH7  Go to UniProtKB:  Q66LH7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (147-MER)	A [auth I], M [auth S]	147	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (147-MER)	B [auth J], N [auth T]	147	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.286 
• R-Value Work: 0.236 
• R-Value Observed: 0.238 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.994	α = 90
b = 176.102	β = 90
c = 208.846	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
Blu-Ice	data collection
CBASS	data collection
HKL-2000	data scaling
CNS	refinement
PHASER	phasing
XDS	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Jiang, J.S.
• This entry supersedes: 4INM

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Derived calculations
• Version 1.2: 2016-07-13
  Changes: Derived calculations
• Version 1.3: 2017-11-22
  Changes: Advisory, Derived calculations, Refinement description