7XYG

Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome

• PDB DOI: https://doi.org/10.2210/pdb7XYG/pdb
• EM Map EMD-33521: EMDB EMDataResource
• NAKB: 7XYG

• Classification: DNA BINDING PROTEIN
• Organism(s): Drosophila melanogaster, synthetic construct, Schizosaccharomyces pombe 972h-
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-06-01 Released: 2023-12-06 
• Deposition Author(s): Nan, Z., Tao, J., Yangao, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome (Class II Fft3-nucleosome complex)

Nan, Z., Tao, J., Yangao, H.

To be published.

Biological Assembly 1  

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

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

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

Biological Assembly Evidence: cross-linking

Macromolecule Content

• Total Structure Weight: 315.11 kDa 
• Atom Count: 17,273 
• Modelled Residue Count: 1,704 
• Deposited Residue Count: 2,224 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	A [auth C], B [auth G]	123	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	C [auth D], D [auth H]	123	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent helicase fft3	G [auth K]	922	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: fft3, snf2SR, SPAC25A8.01c EC: 3.6.4.12
UniProt
Find proteins for O42861 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O42861  Go to UniProtKB:  O42861

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	H [auth A], I [auth E]	135	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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	J [auth B], K [auth F]	103	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: 3
Molecule	Chains	Length	Organism	Image
DNA (167-MER)	E [auth J]	167	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (167-MER)	F [auth I]	167	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-06 
Deposition Author(s): Nan, Z., Tao, J., Yangao, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31800632

Revision History  

• Version 1.0: 2023-12-06
  Type: Initial release
  
• Version 2.0: 2024-06-12
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Data processing, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary