9B1E

Cryo-EM structure of native SWR1 bound to nucleosome (composite structure)

PDB DOI: https://doi.org/10.2210/pdb9B1E/pdb
EM Map EMD-44075: EMDB EMDataResource

Classification: GENE REGULATION
Organism(s): Saccharomyces cerevisiae W303, Saccharomyces cerevisiae, Drosophila melanogaster, synthetic construct
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-03-13 Released: 2024-10-09
Deposition Author(s): Louder, R.K., Park, G., Wu, C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler

Louder, R.K., Park, G., Ye, Z., Cha, J.S., Gardner, A.M., Lei, Q., Ranjan, A., Hollmuller, E., Stengel, F., Pugh, B.F., Wu, C.

(2024) Cell

DOI: https://doi.org/10.1016/j.cell.2024.09.007

Macromolecule Content

Total Structure Weight: 1,099.12 kDa
Atom Count: 49,842
Modelled Residue Count: 5,695
Deposited Residue Count: 9,038
Unique protein chains: 11
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase SWR1	A	1,544	Saccharomyces cerevisiae W303	Mutation(s): 0 EC: 3.6.4.12
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 72	B	795	Saccharomyces cerevisiae W303	Mutation(s): 0
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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-like protein ARP6	C	438	Saccharomyces cerevisiae W303	Mutation(s): 0
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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 71	D	280	Saccharomyces cerevisiae W303	Mutation(s): 0
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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like protein 1	E, G, I	837	Saccharomyces cerevisiae W303	Mutation(s): 0 EC: 3.6.4.12
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like protein 2	F, H, J	471	Saccharomyces cerevisiae W303	Mutation(s): 0 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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
SWR1-complex protein 3	K	625	Saccharomyces cerevisiae W303	Mutation(s): 0
UniProt
Find proteins for P31376 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P31376 Go to UniProtKB: P31376
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31376
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	L [auth Q], N [auth S]	132	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: HTA1, GI527_G0001155
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	M [auth R], O [auth T]	131	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: HTB1, GI527_G0001154
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	P [auth U], R [auth W]	136	Drosophila melanogaster	Mutation(s): 0 Gene Names: His3, His3:CG31613, CG31613, His3:CG33803, CG33803, His3:CG33806, CG33806, His3:CG33809, CG33809, His3:CG33812... 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02299
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	Q [auth V], S [auth X]	103	Drosophila melanogaster	Mutation(s): 0 Gene Names: His4r, BcDNA:RH52884, CG3379, Dmel\CG3379, FBtr0082962, H4r, His4-88CD, His4R, Dmel_CG3379
UniProt
Find proteins for A0A0B4KFZ9 (Drosophila melanogaster) Explore A0A0B4KFZ9 Go to UniProtKB: A0A0B4KFZ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0B4KFZ9
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Length	Organism	Image
DNA (214-MER)	T [auth Y]	214	synthetic construct
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Length	Organism	Image
DNA (214-MER)	U [auth Z]	214	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain FA [auth F] SDF format, chain HA [auth G] SDF format, chain JA [auth H] SDF format, chain LA [auth I] SDF format, chain NA [auth J] SDF format, chain V [auth A] SDF format, chain Y [auth C] MOL2 format, chain DA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain LA [auth I] MOL2 format, chain NA [auth J] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth C]	DA [auth E] FA [auth F] HA [auth G] JA [auth H] LA [auth I] DA [auth E], FA [auth F], HA [auth G], JA [auth H], LA [auth I], NA [auth J], V [auth A], Y [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain DA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain NA [auth J] Focus chain V [auth A] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain NA [auth J] Focus chain V [auth A] Focus chain Y [auth C]
BEF Query on BEF Download Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain Z [auth C] MOL2 format, chain W [auth A] MOL2 format, chain Z [auth C]	W [auth A], Z [auth C]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain W [auth A] Focus chain Z [auth C] Interactions & Density Focus chain W [auth A] Focus chain Z [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D]	BA [auth D], CA [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EA [auth E] SDF format, chain GA [auth F] SDF format, chain IA [auth G] SDF format, chain KA [auth H] SDF format, chain MA [auth I] SDF format, chain OA [auth J] SDF format, chain X [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain EA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain MA [auth I] MOL2 format, chain OA [auth J] MOL2 format, chain X [auth A]	AA [auth C] EA [auth E] GA [auth F] IA [auth G] KA [auth H] AA [auth C], EA [auth E], GA [auth F], IA [auth G], KA [auth H], MA [auth I], OA [auth J], X [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain MA [auth I] Focus chain OA [auth J] Focus chain X [auth A] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain MA [auth I] Focus chain OA [auth J] Focus chain X [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-10-09

Deposition Author(s):

Louder, R.K.

Park, G.

Wu, C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM149291
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM125831
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32GM133151

Revision History (Full details and data files)

Version 1.0: 2024-10-09
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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9B1E

Cryo-EM structure of native SWR1 bound to nucleosome (composite structure)

Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler

Entity ID: 1

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Sequence Annotations

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UniProt

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Entity ID: 13

Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)