7AH9

Substrate-engaged type 3 secretion system needle complex from Salmonella enterica typhimurium - SpaR state 1

PDB DOI: https://doi.org/10.2210/pdb7AH9/pdb
EM Map EMD-11781: EMDB EMDataResource

Classification: PROTEIN TRANSPORT
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2020-09-24 Released: 2021-03-17
Deposition Author(s): Fahrenkamp, D., Goessweiner-Mohr, N., Miletic, S., Wald, J., Marlovits, T.
Funding Organization(s): Austrian Science Fund, German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 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

Substrate-engaged type III secretion system structures reveal gating mechanism for unfolded protein translocation

Miletic, S., Fahrenkamp, D., Goessweiner-Mohr, N., Wald, J., Pantel, M., Vesper, O., Kotov, V., Marlovits, T.C.

(2021) Nat Commun 12: 1546

DOI: https://doi.org/10.1038/s41467-021-21143-1

Macromolecule Content

Total Structure Weight: 3,649.17 kDa
Atom Count: 199,992
Modelled Residue Count: 25,300
Deposited Residue Count: 32,682
Unique protein chains: 9

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface presentation of antigens protein SpaP	A [auth 1A], B [auth 1B], C [auth 1C], D [auth 1D], E [auth 1E]	224	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P40700 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P40700 Go to UniProtKB: P40700
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40700
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface presentation of antigens protein SpaR	F [auth 1F]	263	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P40701 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P40701 Go to UniProtKB: P40701
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40701
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface presentation of antigens protein SpaQ	G [auth 1G], H [auth 1H], I [auth 1I], J [auth 1J]	86	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0A1L7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A1L7 Go to UniProtKB: P0A1L7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A1L7
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein PrgJ	K [auth 1K] L [auth 1L] M [auth 1M] N [auth 1N] O [auth 1O] K [auth 1K], L [auth 1L], M [auth 1M], N [auth 1N], O [auth 1O], P [auth 1P]	101	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0
UniProt
Find proteins for P41785 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P41785 Go to UniProtKB: P41785
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41785
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
SptP3x-GFP-FLAG	Q [auth 1Z]	141	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein PrgI	AA [auth 2J] AB [auth 3J] AC [auth 4J] BA [auth 2K] BB [auth 3K] AA [auth 2J], AB [auth 3J], AC [auth 4J], BA [auth 2K], BB [auth 3K], BC [auth 4K], CA [auth 2L], CB [auth 3L], CC [auth 4L], DA [auth 2M], DB [auth 3M], DC [auth 4M], EA [auth 2N], EB [auth 3N], EC [auth 4N], FA [auth 2O], FB [auth 3O], FC [auth 4O], GA [auth 2P], GB [auth 3P], GC [auth 4P], HA [auth 2Q], HB [auth 3Q], HC [auth 4Q], IA [auth 2R], IB [auth 3R], IC [auth 4R], JA [auth 2S], JB [auth 3S], JC [auth 4S], KA [auth 2T], KB [auth 3T], KC [auth 4T], LA [auth 2U], LB [auth 3U], MA [auth 2V], MB [auth 3V], NA [auth 2W], NB [auth 3W], OA [auth 2X], OB [auth 3X], PA [auth 2Y], PB [auth 3Y], QA [auth 2Z], QB [auth 3Z], R [auth 2A], RA [auth 3A], RB [auth 4A], S [auth 2B], SA [auth 3B], SB [auth 4B], T [auth 2C], TA [auth 3C], TB [auth 4C], U [auth 2D], UA [auth 3D], UB [auth 4D], V [auth 2E], VA [auth 3E], VB [auth 4E], W [auth 2F], WA [auth 3F], WB [auth 4F], X [auth 2G], XA [auth 3G], XB [auth 4G], Y [auth 2H], YA [auth 3H], YB [auth 4H], Z [auth 2I], ZA [auth 3I], ZB [auth 4I]	80	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0
UniProt
Find proteins for P41784 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P41784 Go to UniProtKB: P41784
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41784
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Type 3 secretion system secretin	AD [auth 5P] LC [auth 5A] MC [auth 5B] NC [auth 5C] OC [auth 5D] AD [auth 5P], LC [auth 5A], MC [auth 5B], NC [auth 5C], OC [auth 5D], PC [auth 5E], QC [auth 5F], RC [auth 5G], SC [auth 5H], TC [auth 5I], UC [auth 5J], VC [auth 5K], WC [auth 5L], XC [auth 5M], YC [auth 5N], ZC [auth 5O]	562	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P35672 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P35672 Go to UniProtKB: P35672
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35672
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein PrgK	BD [auth 6A] CD [auth 6B] DD [auth 6C] ED [auth 6D] FD [auth 6E] BD [auth 6A], CD [auth 6B], DD [auth 6C], ED [auth 6D], FD [auth 6E], GD [auth 6F], HD [auth 6G], ID [auth 6H], JD [auth 6I], KD [auth 6J], LD [auth 6K], MD [auth 6L], ND [auth 6M], OD [auth 6N], PD [auth 6O], QD [auth 6P], RD [auth 6Q], SD [auth 6R], TD [auth 6S], UD [auth 6T], VD [auth 6U], WD [auth 6V], XD [auth 6W], YD [auth 6X]	252	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P41786 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P41786 Go to UniProtKB: P41786
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41786
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein PrgH	AE [auth 7B] BE [auth 7C] CE [auth 7D] DE [auth 7E] EE [auth 7F] AE [auth 7B], BE [auth 7C], CE [auth 7D], DE [auth 7E], EE [auth 7F], FE [auth 7G], GE [auth 7H], HE [auth 7I], IE [auth 7J], JE [auth 7K], KE [auth 7L], LE [auth 7M], ME [auth 7N], NE [auth 7O], OE [auth 7P], PE [auth 7Q], QE [auth 7R], RE [auth 7S], SE [auth 7T], TE [auth 7U], UE [auth 7V], VE [auth 7W], WE [auth 7X], ZD [auth 7A]	392	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P41783 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P41783 Go to UniProtKB: P41783
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41783
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PH Query on 3PH Download Ideal Coordinates CCD File SDF format, chain HF [auth 1L] SDF format, chain IF [auth 1M] SDF format, chain JF [auth 1N] SDF format, chain KF [auth 1P] SDF format, chain XE [auth 1A] MOL2 format, chain HF [auth 1L] MOL2 format, chain IF [auth 1M] MOL2 format, chain JF [auth 1N] MOL2 format, chain KF [auth 1P] MOL2 format, chain XE [auth 1A]	HF [auth 1L], IF [auth 1M], JF [auth 1N], KF [auth 1P], XE [auth 1A]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C₃₉ H₇₇ O₈ P YFWHNAWEOZTIPI-DIPNUNPCSA-N		Interactions Focus chain HF [auth 1L] Focus chain IF [auth 1M] Focus chain JF [auth 1N] Focus chain KF [auth 1P] Focus chain XE [auth 1A] Interactions & Density Focus chain HF [auth 1L] Focus chain IF [auth 1M] Focus chain JF [auth 1N] Focus chain KF [auth 1P] Focus chain XE [auth 1A]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain AF [auth 1G] SDF format, chain BF [auth 1H] SDF format, chain CF [auth 1I] SDF format, chain DF [auth 1I] SDF format, chain EF [auth 1I] SDF format, chain FF [auth 1J] SDF format, chain GF [auth 1J] SDF format, chain YE [auth 1A] SDF format, chain ZE [auth 1D] MOL2 format, chain AF [auth 1G] MOL2 format, chain BF [auth 1H] MOL2 format, chain CF [auth 1I] MOL2 format, chain DF [auth 1I] MOL2 format, chain EF [auth 1I] MOL2 format, chain FF [auth 1J] MOL2 format, chain GF [auth 1J] MOL2 format, chain YE [auth 1A] MOL2 format, chain ZE [auth 1D]	AF [auth 1G] BF [auth 1H] CF [auth 1I] DF [auth 1I] EF [auth 1I] AF [auth 1G], BF [auth 1H], CF [auth 1I], DF [auth 1I], EF [auth 1I], FF [auth 1J], GF [auth 1J], YE [auth 1A], ZE [auth 1D]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain AF [auth 1G] Focus chain BF [auth 1H] Focus chain CF [auth 1I] Focus chain DF [auth 1I] Focus chain EF [auth 1I] Focus chain FF [auth 1J] Focus chain GF [auth 1J] Focus chain YE [auth 1A] Focus chain ZE [auth 1D] Interactions & Density Focus chain AF [auth 1G] Focus chain BF [auth 1H] Focus chain CF [auth 1I] Focus chain DF [auth 1I] Focus chain EF [auth 1I] Focus chain FF [auth 1J] Focus chain GF [auth 1J] Focus chain YE [auth 1A] Focus chain ZE [auth 1D]