6KW5 | pdb_00006kw5

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.

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32832
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Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43609
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Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03124
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Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25632
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Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06168
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Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07979
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Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32597
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Reference Sequence

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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
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9URQ5
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Reference Sequence

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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
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UniProt Group	P38781
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Reference Sequence

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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
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06639
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Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02206
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Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06488
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Reference Sequence

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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
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62799
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Reference Sequence

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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
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UniProt Group	Q12406
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Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53330
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Reference Sequence

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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
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84233
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Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06897
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Reference Sequence

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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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05123
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 20
DNA 167	Y [auth B]	167	Homo sapiens
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Molecule	Chains	Length	Organism
Entity ID: 21
DNA 167	Z [auth N]	167	Homo sapiens
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain CA [auth H] MOL2 format, chain CA [auth H] mmCIF format, chain CA [auth H]	CA [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth H] Interactions & Density Focus chain CA [auth H]