9EUF | pdb_00009euf

Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 baseplate in the pre-contraction state - complete

PDB DOI: https://doi.org/10.2210/pdb9EUF/pdb
EM Map EMD-19968: EMDB EMDataResource

Classification: VIRUS
Organism(s): Staphylococcus phage 812
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-03-27 Released: 2025-04-09
Deposition Author(s): Binovsky, J., Siborova, M., Baska, R., Pichel-Beleiro, A., Skubnik, K., Novacek, J., Benesik, M., van Raaij, M.J., Plevka, P.
Funding Organization(s): European Research Council (ERC), Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 7.30 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

Cell attachment and tail contraction of S. aureus phage phi812

Binovsky, J., Siborova, M., Baska, R., Pichel-Beleiro, A., Skubnik, K., Novacek, J., Benesik, M., van Raaij, M.J., Plevka, P.

To be published.

Macromolecule Content

Total Structure Weight: 3,795.97 kDa
Atom Count: 160,477
Modelled Residue Count: 30,231
Deposited Residue Count: 33,837
Unique protein chains: 14

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF4815 domain-containing protein	A [auth 0] B [auth 1] C [auth 2] D [auth 3] E [auth 4] A [auth 0], B [auth 1], C [auth 2], D [auth 3], E [auth 4], KB [auth z], SA [auth h], TA [auth i], UA [auth j], VA [auth k], WA [auth l], XA [auth m]	1,152	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A8E5NSA0 (Staphylococcus phage 812) Explore A0A8E5NSA0 Go to UniProtKB: A0A8E5NSA0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8E5NSA0
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor binding protein	AB [auth p] F [auth 5] G [auth 6] H [auth 7] YA [auth n] AB [auth p], F [auth 5], G [auth 6], H [auth 7], YA [auth n], ZA [auth o]	458	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1WIJ9 (Staphylococcus phage 812) Explore A0A0U1WIJ9 Go to UniProtKB: A0A0U1WIJ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U1WIJ9
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CBM-cenC domain-containing protein	BB [auth q] CB [auth r] DB [auth s] I [auth 8] J [auth 9] BB [auth q], CB [auth r], DB [auth s], I [auth 8], J [auth 9], L [auth AA]	640	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1UXW5 (Staphylococcus phage 812) Explore A0A0U1UXW5 Go to UniProtKB: A0A0U1UXW5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U1UXW5
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NlpC/P60 domain-containing protein	K [auth A]	295	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1UXW0 (Staphylococcus phage 812) Explore A0A0U1UXW0 Go to UniProtKB: A0A0U1UXW0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U1UXW0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
GP-PDE domain-containing protein	M [auth B]	848	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1WFD7 (Staphylococcus phage 812) Explore A0A0U1WFD7 Go to UniProtKB: A0A0U1WFD7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U1WFD7
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate component	N [auth C], O [auth D], T [auth I], V [auth K]	348	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1WF63 (Staphylococcus phage 812) Explore A0A0U1WF63 Go to UniProtKB: A0A0U1WF63
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U1WF63
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase C51 domain-containing protein	P [auth E]	808	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1X189 (Staphylococcus phage 812) Explore A0A0U1X189 Go to UniProtKB: A0A0U1X189
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U1X189
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate component	Q [auth F], R [auth G]	174	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1UXD6 (Staphylococcus phage 812) Explore A0A0U1UXD6 Go to UniProtKB: A0A0U1UXD6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U1UXD6
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
TmpF	S [auth H], U [auth J]	1,019	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1WGD3 (Staphylococcus phage 812) Explore A0A0U1WGD3 Go to UniProtKB: A0A0U1WGD3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U1WGD3
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge subunit	W [auth L], Z [auth O]	234	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1UXD7 (Staphylococcus phage 812) Explore A0A0U1UXD7 Go to UniProtKB: A0A0U1UXD7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U1UXD7
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative baseplate component	X [auth M], Y [auth N]	263	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1X2L4 (Staphylococcus phage 812) Explore A0A0U1X2L4 Go to UniProtKB: A0A0U1X2L4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U1X2L4
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Major tail sheath protein	AA [auth P] BA [auth Q] EA [auth T] FA [auth U] IA [auth X] AA [auth P], BA [auth Q], EA [auth T], FA [auth U], IA [auth X], JA [auth Y]	587	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1WZ79 (Staphylococcus phage 812) Explore A0A0U1WZ79 Go to UniProtKB: A0A0U1WZ79
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U1WZ79
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	CA [auth R] DA [auth S] GA [auth V] HA [auth W] KA [auth Z] CA [auth R], DA [auth S], GA [auth V], HA [auth W], KA [auth Z], LA [auth a]	142	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A1YTP2 (Staphylococcus phage 812) Explore A1YTP2 Go to UniProtKB: A1YTP2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1YTP2
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate protein	EB [auth t] FB [auth u] GB [auth v] HB [auth w] IB [auth x] EB [auth t], FB [auth u], GB [auth v], HB [auth w], IB [auth x], JB [auth y], MA [auth b], NA [auth c], OA [auth d], PA [auth e], QA [auth f], RA [auth g]	194	Staphylococcus phage 812	Mutation(s): 0 Gene Names: 812_119, 812_121, 812a_121, 812F1_121, K1/420_121, K1_121
UniProt
Find proteins for A0A0U1WGQ5 (Staphylococcus phage 812) Explore A0A0U1WGQ5 Go to UniProtKB: A0A0U1WGQ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U1WGQ5
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Reference Sequence