6LT4 | pdb_00006lt4

AAA+ ATPase, ClpL from Streptococcus pneumoniae: ATPrS-bound

PDB DOI: https://doi.org/10.2210/pdb6LT4/pdb
EM Map EMD-0967: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Streptococcus pneumoniae D39
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-01-21 Released: 2021-01-27
Deposition Author(s): Kim, G., Lee, S.G., Han, S., Jung, J., Jeong, H.S., Hyun, J.K., Rhee, D.K., Kim, H.M., Lee, S.
Funding Organization(s): National Research Foundation (NRF, Korea), Rural Development Administration

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

ClpL is a functionally active tetradecameric AAA+ chaperone, distinct from hexameric/dodecameric ones.

Kim, G., Lee, S.G., Han, S., Jung, J., Jeong, H.S., Hyun, J.K., Rhee, D.K., Kim, H.M., Lee, S.

(2020) FASEB J 34: 14353-14370

PubMed: 32910525 Search on PubMed
DOI: https://doi.org/10.1096/fj.202000843R
Primary Citation Related Structures:
6LSY, 6LT4

PubMed Abstract:
AAA+ (ATPases associated with diverse cellular activities) chaperones are involved in a plethora of cellular activities to ensure protein homeostasis. The function of AAA+ chaperones is mostly modulated by their hexameric/dodecameric quaternary structures. Here we report the structural and biochemical characterizations of a tetradecameric AAA+ chaperone, ClpL from Streptococcus pneumoniae. ClpL exists as a tetradecamer in solution in the presence of ATP. The cryo-EM structure of ClpL at 4.5 Å resolution reveals a striking tetradecameric arrangement. Solution structures of ClpL derived from small-angle X-ray scattering data suggest that the tetradecameric ClpL could assume a spiral conformation found in active hexameric/dodecameric AAA+ chaperone structures. Vertical positioning of the middle domain accounts for the head-to-head arrangement of two heptameric rings. Biochemical activity assays with site-directed mutagenesis confirmed the critical roles of residues both in the integrity of the tetradecameric arrangement and activities of ClpL. Non-conserved Q321 and R670 are crucial in the heptameric ring assembly of ClpL. These results establish that ClpL is a functionally active tetradecamer, clearly distinct from hexameric/dodecameric AAA+ chaperones.

Organizational Affiliation

Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea.

Macromolecule Content

Total Structure Weight: 1,101.72 kDa
Atom Count: 68,432
Modeled Residue Count: 8,722
Deposited Residue Count: 9,814
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease, ATP-binding subunit	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	701	Streptococcus pneumoniae D39	Mutation(s): 2 Gene Names: clpL, SPD_0308
UniProt
Find proteins for A0A0H2ZMB9 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore A0A0H2ZMB9 Go to UniProtKB: A0A0H2ZMB9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2ZMB9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download:Ideal Coordinates CCD File SDF format, chain ZA [auth J] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain WA [auth I] SDF format, chain VA [auth I] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain SA [auth H] SDF format, chain RA [auth H] SDF format, chain QB [auth N] SDF format, chain Q [auth A] SDF format, chain PB [auth N] SDF format, chain P [auth A] SDF format, chain OA [auth G] SDF format, chain NA [auth G] SDF format, chain MB [auth M] SDF format, chain LB [auth M] SDF format, chain KA [auth F] SDF format, chain JA [auth F] SDF format, chain IB [auth L] SDF format, chain HB [auth L] SDF format, chain GA [auth E] SDF format, chain FA [auth E] SDF format, chain EB [auth K] SDF format, chain DB [auth K] SDF format, chain CA [auth D] SDF format, chain BA [auth D] SDF format, chain AB [auth J] MOL2 format, chain ZA [auth J] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain WA [auth I] MOL2 format, chain VA [auth I] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth H] MOL2 format, chain RA [auth H] MOL2 format, chain QB [auth N] MOL2 format, chain Q [auth A] MOL2 format, chain PB [auth N] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain MB [auth M] MOL2 format, chain LB [auth M] MOL2 format, chain KA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain IB [auth L] MOL2 format, chain HB [auth L] MOL2 format, chain GA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain EB [auth K] MOL2 format, chain DB [auth K] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain AB [auth J] mmCIF format, chain ZA [auth J] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain WA [auth I] mmCIF format, chain VA [auth I] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth H] mmCIF format, chain RA [auth H] mmCIF format, chain QB [auth N] mmCIF format, chain Q [auth A] mmCIF format, chain PB [auth N] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth G] mmCIF format, chain NA [auth G] mmCIF format, chain MB [auth M] mmCIF format, chain LB [auth M] mmCIF format, chain KA [auth F] mmCIF format, chain JA [auth F] mmCIF format, chain IB [auth L] mmCIF format, chain HB [auth L] mmCIF format, chain GA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain EB [auth K] mmCIF format, chain DB [auth K] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain AB [auth J]	AB [auth J] BA [auth D] CA [auth D] DB [auth K] EB [auth K] AB [auth J], BA [auth D], CA [auth D], DB [auth K], EB [auth K], FA [auth E], GA [auth E], HB [auth L], IB [auth L], JA [auth F], KA [auth F], LB [auth M], MB [auth M], NA [auth G], OA [auth G], P [auth A], PB [auth N], Q [auth A], QB [auth N], RA [auth H], SA [auth H], T [auth B], U [auth B], VA [auth I], WA [auth I], X [auth C], Y [auth C], ZA [auth J]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain AB [auth J] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DB [auth K] Focus chain EB [auth K] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HB [auth L] Focus chain IB [auth L] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain LB [auth M] Focus chain MB [auth M] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain P [auth A] Focus chain PB [auth N] Focus chain Q [auth A] Focus chain QB [auth N] Focus chain RA [auth H] Focus chain SA [auth H] Focus chain T [auth B] Focus chain U [auth B] Focus chain VA [auth I] Focus chain WA [auth I] Focus chain X [auth C] Focus chain Y [auth C] Focus chain ZA [auth J] Interactions & Density Focus chain AB [auth J] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DB [auth K] Focus chain EB [auth K] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HB [auth L] Focus chain IB [auth L] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain LB [auth M] Focus chain MB [auth M] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain P [auth A] Focus chain PB [auth N] Focus chain Q [auth A] Focus chain QB [auth N] Focus chain RA [auth H] Focus chain SA [auth H] Focus chain T [auth B] Focus chain U [auth B] Focus chain VA [auth I] Focus chain WA [auth I] Focus chain X [auth C] Focus chain Y [auth C] Focus chain ZA [auth J]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain YA [auth J] SDF format, chain XA [auth I] SDF format, chain W [auth C] SDF format, chain V [auth B] SDF format, chain UA [auth I] SDF format, chain TA [auth H] SDF format, chain S [auth B] SDF format, chain RB [auth N] SDF format, chain R [auth A] SDF format, chain QA [auth H] SDF format, chain PA [auth G] SDF format, chain OB [auth N] SDF format, chain O [auth A] SDF format, chain NB [auth M] SDF format, chain MA [auth G] SDF format, chain LA [auth F] SDF format, chain KB [auth M] SDF format, chain JB [auth L] SDF format, chain IA [auth F] SDF format, chain HA [auth E] SDF format, chain GB [auth L] SDF format, chain FB [auth K] SDF format, chain EA [auth E] SDF format, chain DA [auth D] SDF format, chain CB [auth K] SDF format, chain BB [auth J] SDF format, chain AA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain YA [auth J] MOL2 format, chain XA [auth I] MOL2 format, chain W [auth C] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth I] MOL2 format, chain TA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain RB [auth N] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth H] MOL2 format, chain PA [auth G] MOL2 format, chain OB [auth N] MOL2 format, chain O [auth A] MOL2 format, chain NB [auth M] MOL2 format, chain MA [auth G] MOL2 format, chain LA [auth F] MOL2 format, chain KB [auth M] MOL2 format, chain JB [auth L] MOL2 format, chain IA [auth F] MOL2 format, chain HA [auth E] MOL2 format, chain GB [auth L] MOL2 format, chain FB [auth K] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth D] MOL2 format, chain CB [auth K] MOL2 format, chain BB [auth J] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain YA [auth J] mmCIF format, chain XA [auth I] mmCIF format, chain W [auth C] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth I] mmCIF format, chain TA [auth H] mmCIF format, chain S [auth B] mmCIF format, chain RB [auth N] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth H] mmCIF format, chain PA [auth G] mmCIF format, chain OB [auth N] mmCIF format, chain O [auth A] mmCIF format, chain NB [auth M] mmCIF format, chain MA [auth G] mmCIF format, chain LA [auth F] mmCIF format, chain KB [auth M] mmCIF format, chain JB [auth L] mmCIF format, chain IA [auth F] mmCIF format, chain HA [auth E] mmCIF format, chain GB [auth L] mmCIF format, chain FB [auth K] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth D] mmCIF format, chain CB [auth K] mmCIF format, chain BB [auth J] mmCIF format, chain AA [auth D]	AA [auth D] BB [auth J] CB [auth K] DA [auth D] EA [auth E] AA [auth D], BB [auth J], CB [auth K], DA [auth D], EA [auth E], FB [auth K], GB [auth L], HA [auth E], IA [auth F], JB [auth L], KB [auth M], LA [auth F], MA [auth G], NB [auth M], O [auth A], OB [auth N], PA [auth G], QA [auth H], R [auth A], RB [auth N], S [auth B], TA [auth H], UA [auth I], V [auth B], W [auth C], XA [auth I], YA [auth J], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BB [auth J] Focus chain CB [auth K] Focus chain DA [auth D] Focus chain EA [auth E] Focus chain FB [auth K] Focus chain GB [auth L] Focus chain HA [auth E] Focus chain IA [auth F] Focus chain JB [auth L] Focus chain KB [auth M] Focus chain LA [auth F] Focus chain MA [auth G] Focus chain NB [auth M] Focus chain O [auth A] Focus chain OB [auth N] Focus chain PA [auth G] Focus chain QA [auth H] Focus chain R [auth A] Focus chain RB [auth N] Focus chain S [auth B] Focus chain TA [auth H] Focus chain UA [auth I] Focus chain V [auth B] Focus chain W [auth C] Focus chain XA [auth I] Focus chain YA [auth J] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BB [auth J] Focus chain CB [auth K] Focus chain DA [auth D] Focus chain EA [auth E] Focus chain FB [auth K] Focus chain GB [auth L] Focus chain HA [auth E] Focus chain IA [auth F] Focus chain JB [auth L] Focus chain KB [auth M] Focus chain LA [auth F] Focus chain MA [auth G] Focus chain NB [auth M] Focus chain O [auth A] Focus chain OB [auth N] Focus chain PA [auth G] Focus chain QA [auth H] Focus chain R [auth A] Focus chain RB [auth N] Focus chain S [auth B] Focus chain TA [auth H] Focus chain UA [auth I] Focus chain V [auth B] Focus chain W [auth C] Focus chain XA [auth I] Focus chain YA [auth J] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-01-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2018R1A2B6004367
National Research Foundation (NRF, Korea)	Korea, Republic Of	2017R1A5A1014560
Rural Development Administration	Korea, Republic Of	PJ01367602