6KW5

The ClassC RSC-Nucleosome Complex

• PDB DOI: https://doi.org/10.2210/pdb6KW5/pdb
• EM Map EMD-0779: EMDB EMDataResource
• NAKB: 6KW5

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Saccharomyces cerevisiae S288C, Xenopus laevis, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-06 Released: 2020-09-09 
• Deposition Author(s): Ye, Y.P., Wu, H., Chen, K.J., Verma, N., Cairns, B., Gao, N., Chen, Z.C.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 10.1 Å
• Aggregation State: CELL 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the RSC complex bound to the nucleosome

Ye, Y.P., Wu, H., Chen, K.J., Verma, N., Cairns, B., Gao, N., Chen, Z.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 26-mer - A2B2C2D2E2F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 26-mer - A8B2C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - B2C2D2E2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - B2C2D2E2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 1,598.36 kDa 
• Atom Count: 45,484 
• Modelled Residue Count: 5,169 
• Deposited Residue Count: 13,403 
• Unique protein chains: 19
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin structure-remodeling complex subunit RSC7	A [auth F]	435	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P32832 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32832  Go to UniProtKB:  P32832

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin structure-remodeling complex protein RSC8	B [auth H], C [auth D]	557	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P43609 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43609  Go to UniProtKB:  P43609

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin structure-remodeling complex subunit RSC9	D [auth M]	581	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q03124 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03124  Go to UniProtKB:  Q03124

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin structure-remodeling complex protein RSC6	E [auth I]	483	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P25632 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25632  Go to UniProtKB:  P25632

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin structure-remodeling complex subunit SFH1	F [auth G]	426	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q06168 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06168  Go to UniProtKB:  Q06168

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin structure-remodeling complex protein RSC58	G [auth A]	502	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q07979 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q07979  Go to UniProtKB:  Q07979

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear protein STH1/NPS1	AA [auth P], BA [auth Q], H [auth J]	1,359	Saccharomyces cerevisiae S288C	Mutation(s): 0  EC: 3.6.4.12
UniProt
Find proteins for P32597 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32597  Go to UniProtKB:  P32597

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
High temperature lethal protein 1	I [auth E]	78	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q9URQ5 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q9URQ5  Go to UniProtKB:  Q9URQ5

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin structure-remodeling complex protein RSC30	J [auth C]	883	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P38781 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38781  Go to UniProtKB:  P38781

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin structure-remodeling complex protein RSC3	K	885	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q06639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06639  Go to UniProtKB:  Q06639

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin structure-remodeling complex subunit RSC4	L [auth X]	625	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q02206 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02206  Go to UniProtKB:  Q02206

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin structure-remodeling complex subunit RSC2	M [auth L]	889	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q06488 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06488  Go to UniProtKB:  Q06488

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	N [auth W], R [auth S]	103	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 7	O [auth f]	477	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12406  Go to UniProtKB:  Q12406

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulator of Ty1 transposition protein 102	P [auth h]	157	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P53330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53330  Go to UniProtKB:  P53330

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	Q [auth R], T [auth V]	136	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	S [auth T], U [auth O]	130	Xenopus laevis	Mutation(s): 0  Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897  Go to UniProtKB:  P06897

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	V [auth U], W [auth Y]	126	Xenopus laevis	Mutation(s): 0  Gene Names: XELAEV_18028549mg

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-like protein ARP9	X [auth g]	467	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q05123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05123  Go to UniProtKB:  Q05123

Entity ID: 20
Molecule	Chains	Length	Organism	Image
DNA 167	Y [auth B]	167	Homo sapiens

Entity ID: 21
Molecule	Chains	Length	Organism	Image
DNA 167	Z [auth N]	167	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	CA [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 10.1 Å
• Aggregation State: CELL 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): Ye, Y.P., Wu, H., Chen, K.J., Verma, N., Cairns, B., Gao, N., Chen, Z.C.

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references