8AKR | pdb_00008akr

200 A SynPspA rod after incubation with ATP

PDB DOI: https://doi.org/10.2210/pdb8AKR/pdb
EM Map EMD-15490: EMDB EMDataResource

Classification: LIPID BINDING PROTEIN
Organism(s): Synechocystis sp. PCC 6803
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-31 Released: 2024-02-14
Deposition Author(s): Junglas, B., Hudina, E., Schoennenbeck, P., Ritter, I., Santiago-Schuebel, B., Huesgen, P., Sachse, C.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

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

Literature

Structural plasticity of bacterial ESCRT-III protein PspA in higher-order assemblies.

Junglas, B., Hudina, E., Schonnenbeck, P., Ritter, I., Heddier, A., Santiago-Schubel, B., Huesgen, P.F., Schneider, D., Sachse, C.

(2024) Nat Struct Mol Biol

PubMed: 39152237 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-024-01359-7
Primary Citation Related Structures:
8AKQ, 8AKR, 8AKS, 8AKT, 8AKU, 8AKV, 8AKW, 8AKX, 8AKY, 8AKZ, 8AL0

PubMed Abstract:
Eukaryotic members of the endosome sorting complex required for transport-III (ESCRT-III) family have been shown to form diverse higher-order assemblies. The bacterial phage shock protein A (PspA) has been identified as a member of the ESCRT-III superfamily, and PspA homo-oligomerizes to form rod-shaped assemblies. As observed for eukaryotic ESCRT-III, PspA forms tubular assemblies of varying diameters. Using electron cryo-electron microscopy, we determined 61 Synechocystis PspA structures and observed in molecular detail how the structural plasticity of PspA rods is mediated by conformational changes at three hinge regions in the monomer and by the fixed and changing molecular contacts between protomers. Moreover, we reduced and increased the structural plasticity of PspA rods by removing the loop connecting helices α3/α4 and the addition of nucleotides, respectively. Based on our analysis of PspA-mediated membrane remodeling, we suggest that the observed mode of structural plasticity is a prerequisite for the biological function of ESCRT-III members.

Organizational Affiliation

Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany.

Macromolecule Content

Total Structure Weight: 1,711.5 kDa
Atom Count: 96,240
Modeled Residue Count: 11,760
Deposited Residue Count: 14,760
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloroplast membrane-associated 30 kD protein	A [auth H] AA [auth a] AB [auth 0] B [auth A] BA [auth b] A [auth H], AA [auth a], AB [auth 0], B [auth A], BA [auth b], BB [auth 1], C [auth B], CA [auth c], CB [auth 2], D [auth C], DA [auth d], DB [auth 3], E [auth D], EA [auth e], EB [auth 4], F [auth E], FA [auth f], FB [auth 5], G [auth F], GA [auth g], GB [auth 6], H [auth G], HA [auth h], HB [auth 7], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth y], Z, ZA [auth z]	246	Synechocystis sp. PCC 6803	Mutation(s): 0 Gene Names: im30
UniProt
Find proteins for P74717 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P74717 Go to UniProtKB: P74717
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P74717
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 AC [auth R] SDF format, chain AD [auth r] SDF format, chain BC [auth S] SDF format, chain BD [auth s] SDF format, chain CC [auth T] SDF format, chain CD [auth t] SDF format, chain DC [auth U] SDF format, chain DD [auth u] SDF format, chain EC [auth V] SDF format, chain ED [auth v] SDF format, chain FC [auth W] SDF format, chain FD [auth w] SDF format, chain GC [auth X] SDF format, chain GD [auth y] SDF format, chain HC [auth Y] SDF format, chain HD [auth z] SDF format, chain IB [auth H] SDF format, chain IC [auth Z] SDF format, chain ID [auth 0] SDF format, chain JB [auth A] SDF format, chain JC [auth a] SDF format, chain JD [auth 1] SDF format, chain KB [auth B] SDF format, chain KC [auth b] SDF format, chain KD [auth 2] SDF format, chain LB [auth C] SDF format, chain LC [auth c] SDF format, chain LD [auth 3] SDF format, chain MB [auth D] SDF format, chain MC [auth d] SDF format, chain MD [auth 4] SDF format, chain NB [auth E] SDF format, chain NC [auth e] SDF format, chain ND [auth 5] SDF format, chain OB [auth F] SDF format, chain OC [auth f] SDF format, chain OD [auth 6] SDF format, chain PB [auth G] SDF format, chain PC [auth g] SDF format, chain PD [auth 7] SDF format, chain QB [auth I] SDF format, chain QC [auth h] SDF format, chain RB [auth J] SDF format, chain RC [auth i] SDF format, chain SB [auth K] SDF format, chain SC [auth j] SDF format, chain TB [auth L] SDF format, chain TC [auth k] SDF format, chain UB [auth M] SDF format, chain UC [auth l] SDF format, chain VB [auth N] SDF format, chain VC [auth m] SDF format, chain WB [auth O] SDF format, chain WC [auth n] SDF format, chain XB [auth P] SDF format, chain XC [auth o] SDF format, chain YB [auth P] SDF format, chain YC [auth p] SDF format, chain ZB [auth Q] SDF format, chain ZC [auth q] MOL2 format, chain AC [auth R] MOL2 format, chain AD [auth r] MOL2 format, chain BC [auth S] MOL2 format, chain BD [auth s] MOL2 format, chain CC [auth T] MOL2 format, chain CD [auth t] MOL2 format, chain DC [auth U] MOL2 format, chain DD [auth u] MOL2 format, chain EC [auth V] MOL2 format, chain ED [auth v] MOL2 format, chain FC [auth W] MOL2 format, chain FD [auth w] MOL2 format, chain GC [auth X] MOL2 format, chain GD [auth y] MOL2 format, chain HC [auth Y] MOL2 format, chain HD [auth z] MOL2 format, chain IB [auth H] MOL2 format, chain IC [auth Z] MOL2 format, chain ID [auth 0] MOL2 format, chain JB [auth A] MOL2 format, chain JC [auth a] MOL2 format, chain JD [auth 1] MOL2 format, chain KB [auth B] MOL2 format, chain KC [auth b] MOL2 format, chain KD [auth 2] MOL2 format, chain LB [auth C] MOL2 format, chain LC [auth c] MOL2 format, chain LD [auth 3] MOL2 format, chain MB [auth D] MOL2 format, chain MC [auth d] MOL2 format, chain MD [auth 4] MOL2 format, chain NB [auth E] MOL2 format, chain NC [auth e] MOL2 format, chain ND [auth 5] MOL2 format, chain OB [auth F] MOL2 format, chain OC [auth f] MOL2 format, chain OD [auth 6] MOL2 format, chain PB [auth G] MOL2 format, chain PC [auth g] MOL2 format, chain PD [auth 7] MOL2 format, chain QB [auth I] MOL2 format, chain QC [auth h] MOL2 format, chain RB [auth J] MOL2 format, chain RC [auth i] MOL2 format, chain SB [auth K] MOL2 format, chain SC [auth j] MOL2 format, chain TB [auth L] MOL2 format, chain TC [auth k] MOL2 format, chain UB [auth M] MOL2 format, chain UC [auth l] MOL2 format, chain VB [auth N] MOL2 format, chain VC [auth m] MOL2 format, chain WB [auth O] MOL2 format, chain WC [auth n] MOL2 format, chain XB [auth P] MOL2 format, chain XC [auth o] MOL2 format, chain YB [auth P] MOL2 format, chain YC [auth p] MOL2 format, chain ZB [auth Q] MOL2 format, chain ZC [auth q] mmCIF format, chain AC [auth R] mmCIF format, chain AD [auth r] mmCIF format, chain BC [auth S] mmCIF format, chain BD [auth s] mmCIF format, chain CC [auth T] mmCIF format, chain CD [auth t] mmCIF format, chain DC [auth U] mmCIF format, chain DD [auth u] mmCIF format, chain EC [auth V] mmCIF format, chain ED [auth v] mmCIF format, chain FC [auth W] mmCIF format, chain FD [auth w] mmCIF format, chain GC [auth X] mmCIF format, chain GD [auth y] mmCIF format, chain HC [auth Y] mmCIF format, chain HD [auth z] mmCIF format, chain IB [auth H] mmCIF format, chain IC [auth Z] mmCIF format, chain ID [auth 0] mmCIF format, chain JB [auth A] mmCIF format, chain JC [auth a] mmCIF format, chain JD [auth 1] mmCIF format, chain KB [auth B] mmCIF format, chain KC [auth b] mmCIF format, chain KD [auth 2] mmCIF format, chain LB [auth C] mmCIF format, chain LC [auth c] mmCIF format, chain LD [auth 3] mmCIF format, chain MB [auth D] mmCIF format, chain MC [auth d] mmCIF format, chain MD [auth 4] mmCIF format, chain NB [auth E] mmCIF format, chain NC [auth e] mmCIF format, chain ND [auth 5] mmCIF format, chain OB [auth F] mmCIF format, chain OC [auth f] mmCIF format, chain OD [auth 6] mmCIF format, chain PB [auth G] mmCIF format, chain PC [auth g] mmCIF format, chain PD [auth 7] mmCIF format, chain QB [auth I] mmCIF format, chain QC [auth h] mmCIF format, chain RB [auth J] mmCIF format, chain RC [auth i] mmCIF format, chain SB [auth K] mmCIF format, chain SC [auth j] mmCIF format, chain TB [auth L] mmCIF format, chain TC [auth k] mmCIF format, chain UB [auth M] mmCIF format, chain UC [auth l] mmCIF format, chain VB [auth N] mmCIF format, chain VC [auth m] mmCIF format, chain WB [auth O] mmCIF format, chain WC [auth n] mmCIF format, chain XB [auth P] mmCIF format, chain XC [auth o] mmCIF format, chain YB [auth P] mmCIF format, chain YC [auth p] mmCIF format, chain ZB [auth Q] mmCIF format, chain ZC [auth q]	AC [auth R] AD [auth r] BC [auth S] BD [auth s] CC [auth T] AC [auth R], AD [auth r], BC [auth S], BD [auth s], CC [auth T], CD [auth t], DC [auth U], DD [auth u], EC [auth V], ED [auth v], FC [auth W], FD [auth w], GC [auth X], GD [auth y], HC [auth Y], HD [auth z], IB [auth H], IC [auth Z], ID [auth 0], JB [auth A], JC [auth a], JD [auth 1], KB [auth B], KC [auth b], KD [auth 2], LB [auth C], LC [auth c], LD [auth 3], MB [auth D], MC [auth d], MD [auth 4], NB [auth E], NC [auth e], ND [auth 5], OB [auth F], OC [auth f], OD [auth 6], PB [auth G], PC [auth g], PD [auth 7], QB [auth I], QC [auth h], RB [auth J], RC [auth i], SB [auth K], SC [auth j], TB [auth L], TC [auth k], UB [auth M], UC [auth l], VB [auth N], VC [auth m], WB [auth O], WC [auth n], XB [auth P], XC [auth o], YB [auth P], YC [auth p], ZB [auth Q], ZC [auth q]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AC [auth R] Focus chain AD [auth r] Focus chain BC [auth S] Focus chain BD [auth s] Focus chain CC [auth T] Focus chain CD [auth t] Focus chain DC [auth U] Focus chain DD [auth u] Focus chain EC [auth V] Focus chain ED [auth v] Focus chain FC [auth W] Focus chain FD [auth w] Focus chain GC [auth X] Focus chain GD [auth y] Focus chain HC [auth Y] Focus chain HD [auth z] Focus chain IB [auth H] Focus chain IC [auth Z] Focus chain ID [auth 0] Focus chain JB [auth A] Focus chain JC [auth a] Focus chain JD [auth 1] Focus chain KB [auth B] Focus chain KC [auth b] Focus chain KD [auth 2] Focus chain LB [auth C] Focus chain LC [auth c] Focus chain LD [auth 3] Focus chain MB [auth D] Focus chain MC [auth d] Focus chain MD [auth 4] Focus chain NB [auth E] Focus chain NC [auth e] Focus chain ND [auth 5] Focus chain OB [auth F] Focus chain OC [auth f] Focus chain OD [auth 6] Focus chain PB [auth G] Focus chain PC [auth g] Focus chain PD [auth 7] Focus chain QB [auth I] Focus chain QC [auth h] Focus chain RB [auth J] Focus chain RC [auth i] Focus chain SB [auth K] Focus chain SC [auth j] Focus chain TB [auth L] Focus chain TC [auth k] Focus chain UB [auth M] Focus chain UC [auth l] Focus chain VB [auth N] Focus chain VC [auth m] Focus chain WB [auth O] Focus chain WC [auth n] Focus chain XB [auth P] Focus chain XC [auth o] Focus chain YB [auth P] Focus chain YC [auth p] Focus chain ZB [auth Q] Focus chain ZC [auth q] Interactions & Density Focus chain AC [auth R] Focus chain AD [auth r] Focus chain BC [auth S] Focus chain BD [auth s] Focus chain CC [auth T] Focus chain CD [auth t] Focus chain DC [auth U] Focus chain DD [auth u] Focus chain EC [auth V] Focus chain ED [auth v] Focus chain FC [auth W] Focus chain FD [auth w] Focus chain GC [auth X] Focus chain GD [auth y] Focus chain HC [auth Y] Focus chain HD [auth z] Focus chain IB [auth H] Focus chain IC [auth Z] Focus chain ID [auth 0] Focus chain JB [auth A] Focus chain JC [auth a] Focus chain JD [auth 1] Focus chain KB [auth B] Focus chain KC [auth b] Focus chain KD [auth 2] Focus chain LB [auth C] Focus chain LC [auth c] Focus chain LD [auth 3] Focus chain MB [auth D] Focus chain MC [auth d] Focus chain MD [auth 4] Focus chain NB [auth E] Focus chain NC [auth e] Focus chain ND [auth 5] Focus chain OB [auth F] Focus chain OC [auth f] Focus chain OD [auth 6] Focus chain PB [auth G] Focus chain PC [auth g] Focus chain PD [auth 7] Focus chain QB [auth I] Focus chain QC [auth h] Focus chain RB [auth J] Focus chain RC [auth i] Focus chain SB [auth K] Focus chain SC [auth j] Focus chain TB [auth L] Focus chain TC [auth k] Focus chain UB [auth M] Focus chain UC [auth l] Focus chain VB [auth N] Focus chain VC [auth m] Focus chain WB [auth O] Focus chain WC [auth n] Focus chain XB [auth P] Focus chain XC [auth o] Focus chain YB [auth P] Focus chain YC [auth p] Focus chain ZB [auth Q] Focus chain ZC [auth q]