8QKU

SWR1-nucleosome complex in configuration 1

PDB DOI: https://doi.org/10.2210/pdb8QKU/pdb
EM Map EMD-18471: EMDB EMDataResource
NAKB: 8QKU

Classification: DNA BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae S288C, synthetic construct
Expression System: Escherichia coli, Trichoplusia ni
Mutation(s): No

Deposited: 2023-09-18 Released: 2024-10-02
Deposition Author(s): Jalal, A.S.B., Wigley, D.B.
Funding Organization(s): Wellcome Trust, Cancer Research UK, Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Nucleosome flipping drives kinetic proof reading and processivity of histone exchange by yeast SWR1 complex

Girvan, P., Jalal, A.S.B., McCormack, E.A., Skehan, M.T., Wigley, D.B., Rueda, D.S.

To be published.

Macromolecule Content

Total Structure Weight: 814.96 kDa
Atom Count: 45,395
Modelled Residue Count: 5,217
Deposited Residue Count: 6,624
Unique protein chains: 10
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A, B	136	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P61830 Go to UniProtKB: P61830
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61830
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	C, D	103	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: HHF1
UniProt
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02309 Go to UniProtKB: P02309
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02309
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A.2	E, F	158	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: HTA2
UniProt
Find proteins for P04912 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04912 Go to UniProtKB: P04912
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04912
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B.1	G, H	131	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: HTB1
UniProt
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02293 Go to UniProtKB: P02293
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02293
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase SWR1	K [auth M]	1,514	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: SWR1 EC: 3.6.4.12
UniProt
Find proteins for Q05471 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05471 Go to UniProtKB: Q05471
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05471
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-like protein ARP6	L [auth R]	438	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: ARP6
UniProt
Find proteins for Q12509 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12509 Go to UniProtKB: Q12509
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12509
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 71	M [auth S]	280	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: VPS71
UniProt
Find proteins for Q03433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03433 Go to UniProtKB: Q03433
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03433
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like protein 1	N [auth T], P [auth V], R [auth X]	463	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RVB1 EC: 3.6.4.12
UniProt
Find proteins for Q03940 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03940 Go to UniProtKB: Q03940
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03940
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like protein 2	O [auth U], Q [auth W], S [auth Y]	471	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RVB2 EC: 3.6.4.12
UniProt
Find proteins for Q12464 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12464 Go to UniProtKB: Q12464
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12464
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 72	T [auth Z]	180	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: VPS72, SWC2, YDR485C
UniProt
Find proteins for Q03388 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03388 Go to UniProtKB: Q03388
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03388
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (177-MER)	I	177	synthetic construct
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (177-MER)	J	177	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain CA [auth T] SDF format, chain EA [auth U] SDF format, chain GA [auth V] SDF format, chain IA [auth W] SDF format, chain KA [auth X] SDF format, chain MA [auth Y] SDF format, chain U [auth M] SDF format, chain X [auth R] MOL2 format, chain CA [auth T] MOL2 format, chain EA [auth U] MOL2 format, chain GA [auth V] MOL2 format, chain IA [auth W] MOL2 format, chain KA [auth X] MOL2 format, chain MA [auth Y] MOL2 format, chain U [auth M] MOL2 format, chain X [auth R] mmCIF format, chain CA [auth T] mmCIF format, chain EA [auth U] mmCIF format, chain GA [auth V] mmCIF format, chain IA [auth W] mmCIF format, chain KA [auth X] mmCIF format, chain MA [auth Y] mmCIF format, chain U [auth M] mmCIF format, chain X [auth R]	CA [auth T] EA [auth U] GA [auth V] IA [auth W] KA [auth X] CA [auth T], EA [auth U], GA [auth V], IA [auth W], KA [auth X], MA [auth Y], U [auth M], X [auth R]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain CA [auth T] Focus chain EA [auth U] Focus chain GA [auth V] Focus chain IA [auth W] Focus chain KA [auth X] Focus chain MA [auth Y] Focus chain U [auth M] Focus chain X [auth R] Interactions & Density Focus chain CA [auth T] Focus chain EA [auth U] Focus chain GA [auth V] Focus chain IA [auth W] Focus chain KA [auth X] Focus chain MA [auth Y] Focus chain U [auth M] Focus chain X [auth R]
BEF (Subject of Investigation/LOI) Query on BEF Download Ideal Coordinates CCD File SDF format, chain V [auth M] SDF format, chain Y [auth R] MOL2 format, chain V [auth M] MOL2 format, chain Y [auth R] mmCIF format, chain V [auth M] mmCIF format, chain Y [auth R]	V [auth M], Y [auth R]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain V [auth M] Focus chain Y [auth R] Interactions & Density Focus chain V [auth M] Focus chain Y [auth R]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth S] SDF format, chain BA [auth S] MOL2 format, chain AA [auth S] MOL2 format, chain BA [auth S] mmCIF format, chain AA [auth S] mmCIF format, chain BA [auth S]	AA [auth S], BA [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth S] Focus chain BA [auth S] Interactions & Density Focus chain AA [auth S] Focus chain BA [auth S]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain DA [auth U] SDF format, chain FA [auth U] SDF format, chain HA [auth V] SDF format, chain JA [auth W] SDF format, chain LA [auth X] SDF format, chain NA [auth Y] SDF format, chain W [auth M] SDF format, chain Z [auth R] MOL2 format, chain DA [auth U] MOL2 format, chain FA [auth U] MOL2 format, chain HA [auth V] MOL2 format, chain JA [auth W] MOL2 format, chain LA [auth X] MOL2 format, chain NA [auth Y] MOL2 format, chain W [auth M] MOL2 format, chain Z [auth R] mmCIF format, chain DA [auth U] mmCIF format, chain FA [auth U] mmCIF format, chain HA [auth V] mmCIF format, chain JA [auth W] mmCIF format, chain LA [auth X] mmCIF format, chain NA [auth Y] mmCIF format, chain W [auth M] mmCIF format, chain Z [auth R]	DA [auth U] FA [auth U] HA [auth V] JA [auth W] LA [auth X] DA [auth U], FA [auth U], HA [auth V], JA [auth W], LA [auth X], NA [auth Y], W [auth M], Z [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth U] Focus chain FA [auth U] Focus chain HA [auth V] Focus chain JA [auth W] Focus chain LA [auth X] Focus chain NA [auth Y] Focus chain W [auth M] Focus chain Z [auth R] Interactions & Density Focus chain DA [auth U] Focus chain FA [auth U] Focus chain HA [auth V] Focus chain JA [auth W] Focus chain LA [auth X] Focus chain NA [auth Y] Focus chain W [auth M] Focus chain Z [auth R]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-02

Deposition Author(s):

Jalal, A.S.B.

Wigley, D.B.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	095519/Z/11/Z and 209327/Z/17/Z
Cancer Research UK	United Kingdom	C6913/A21608
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N009258/1 and MR/R009023/1

Revision History (Full details and data files)

Version 1.0: 2024-10-02
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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Help and Resources

8QKU

SWR1-nucleosome complex in configuration 1

Nucleosome flipping drives kinetic proof reading and processivity of histone exchange by yeast SWR1 complex

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

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Entity ID: 3

UniProt

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Entity ID: 4

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Entity ID: 7

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Entity ID: 8

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Entity ID: 9

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Entity ID: 10

UniProt

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Entity ID: 11

UniProt

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Entity ID: 12

UniProt

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Entity ID: 5

Sequence Annotations

Entity ID: 6

Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)