6TFL | pdb_00006tfl

Lsm protein (SmAP) from Halobacterium salinarum

PDB DOI: https://doi.org/10.2210/pdb6TFL/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Halobacterium salinarum R1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-11-14 Released: 2020-11-25
Deposition Author(s): Nikulin, A.D., Fando, M.S., Lekontseva, N.V.
Funding Organization(s): Russian Foundation for Basic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.231 (Depositor), 0.233 (DCC)
R-Value Work:
0.178 (Depositor), 0.185 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure and RNA-Binding Properties of Lsm Protein from Halobacterium salinarum.

Fando, M.S., Mikhaylina, A.O., Lekontseva, N.V., Tishchenko, S.V., Nikulin, A.D.

(2021) Biochemistry (Mosc) 86: 833-842

PubMed: 34284708 Search on PubMed
DOI: https://doi.org/10.1134/S000629792107004X
Primary Citation Related Structures:
6TFL

PubMed Abstract:
The structure and the RNA-binding properties of the Lsm protein from Halobacterium salinarum have been determined. A distinctive feature of this protein is the presence of a short L4 loop connecting the β3 and β4 strands. Since bacterial Lsm proteins (also called Hfq proteins) have a short L4 loop and form hexamers, whereas archaeal Lsm proteins (SmAP) have a long L4 loop and form heptamers, it has been suggested that the length of the L4 loop may affect the quaternary structure of Lsm proteins. Moreover, the L4 loop covers the region of SmAP corresponding to one of the RNA-binding sites in Hfq, and thus can affect the RNA-binding properties of the protein. Our results show that the SmAP from H. salinarum forms heptamers and possesses the same RNA-binding properties as homologous proteins with the long L4 loop. Therefore, the length of the L4 does not govern the number of monomers in the protein particles and does not affect the RNA-binding properties of Lsm proteins.

Organizational Affiliation

Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.

Macromolecule Content

Total Structure Weight: 99.38 kDa
Atom Count: 7,184
Modeled Residue Count: 868
Deposited Residue Count: 868
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein Lsm	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	62	Halobacterium salinarum R1	Mutation(s): 0 Gene Names: lsm, snp, OE_3142R
UniProt
Find proteins for B0R5R2 (Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1)) Explore B0R5R2 Go to UniProtKB: B0R5R2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0R5R2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URI Query on URI Download:Ideal Coordinates CCD File SDF format, chain ZA [auth M] SDF format, chain Z [auth D] SDF format, chain XA [auth L] SDF format, chain U [auth C] SDF format, chain TA [auth K] SDF format, chain T [auth B] SDF format, chain QA [auth J] SDF format, chain Q [auth A] SDF format, chain OA [auth I] SDF format, chain KA [auth H] SDF format, chain GA [auth G] SDF format, chain EB [auth N] SDF format, chain EA [auth F] SDF format, chain CA [auth E] MOL2 format, chain ZA [auth M] MOL2 format, chain Z [auth D] MOL2 format, chain XA [auth L] MOL2 format, chain U [auth C] MOL2 format, chain TA [auth K] MOL2 format, chain T [auth B] MOL2 format, chain QA [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain OA [auth I] MOL2 format, chain KA [auth H] MOL2 format, chain GA [auth G] MOL2 format, chain EB [auth N] MOL2 format, chain EA [auth F] MOL2 format, chain CA [auth E] mmCIF format, chain ZA [auth M] mmCIF format, chain Z [auth D] mmCIF format, chain XA [auth L] mmCIF format, chain U [auth C] mmCIF format, chain TA [auth K] mmCIF format, chain T [auth B] mmCIF format, chain QA [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain OA [auth I] mmCIF format, chain KA [auth H] mmCIF format, chain GA [auth G] mmCIF format, chain EB [auth N] mmCIF format, chain EA [auth F] mmCIF format, chain CA [auth E]	CA [auth E] EA [auth F] EB [auth N] GA [auth G] KA [auth H] CA [auth E], EA [auth F], EB [auth N], GA [auth G], KA [auth H], OA [auth I], Q [auth A], QA [auth J], T [auth B], TA [auth K], U [auth C], XA [auth L], Z [auth D], ZA [auth M]	URIDINE C₉ H₁₂ N₂ O₆ DRTQHJPVMGBUCF-XVFCMESISA-N		Interactions Focus chain CA [auth E] Focus chain EA [auth F] Focus chain EB [auth N] Focus chain GA [auth G] Focus chain KA [auth H] Focus chain OA [auth I] Focus chain Q [auth A] Focus chain QA [auth J] Focus chain T [auth B] Focus chain TA [auth K] Focus chain U [auth C] Focus chain XA [auth L] Focus chain Z [auth D] Focus chain ZA [auth M] Interactions & Density Focus chain CA [auth E] Focus chain EA [auth F] Focus chain EB [auth N] Focus chain GA [auth G] Focus chain KA [auth H] Focus chain OA [auth I] Focus chain Q [auth A] Focus chain QA [auth J] Focus chain T [auth B] Focus chain TA [auth K] Focus chain U [auth C] Focus chain XA [auth L] Focus chain Z [auth D] Focus chain ZA [auth M]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain FA [auth G] MOL2 format, chain FA [auth G] mmCIF format, chain FA [auth G]	FA [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth G] Interactions & Density Focus chain FA [auth G]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain YA [auth M] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain WA [auth L] SDF format, chain W [auth D] SDF format, chain VA [auth L] SDF format, chain V [auth D] SDF format, chain UA [auth L] SDF format, chain SA [auth K] SDF format, chain S [auth B] SDF format, chain RA [auth K] SDF format, chain R [auth B] SDF format, chain PA [auth J] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain NA [auth I] SDF format, chain MA [auth I] SDF format, chain LA [auth I] SDF format, chain JA [auth H] SDF format, chain IA [auth H] SDF format, chain HA [auth H] SDF format, chain DB [auth N] SDF format, chain DA [auth F] SDF format, chain CB [auth N] SDF format, chain BB [auth N] SDF format, chain BA [auth E] SDF format, chain AB [auth N] SDF format, chain AA [auth E] MOL2 format, chain YA [auth M] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain WA [auth L] MOL2 format, chain W [auth D] MOL2 format, chain VA [auth L] MOL2 format, chain V [auth D] MOL2 format, chain UA [auth L] MOL2 format, chain SA [auth K] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth K] MOL2 format, chain R [auth B] MOL2 format, chain PA [auth J] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth I] MOL2 format, chain MA [auth I] MOL2 format, chain LA [auth I] MOL2 format, chain JA [auth H] MOL2 format, chain IA [auth H] MOL2 format, chain HA [auth H] MOL2 format, chain DB [auth N] MOL2 format, chain DA [auth F] MOL2 format, chain CB [auth N] MOL2 format, chain BB [auth N] MOL2 format, chain BA [auth E] MOL2 format, chain AB [auth N] MOL2 format, chain AA [auth E] mmCIF format, chain YA [auth M] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain WA [auth L] mmCIF format, chain W [auth D] mmCIF format, chain VA [auth L] mmCIF format, chain V [auth D] mmCIF format, chain UA [auth L] mmCIF format, chain SA [auth K] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth K] mmCIF format, chain R [auth B] mmCIF format, chain PA [auth J] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth I] mmCIF format, chain MA [auth I] mmCIF format, chain LA [auth I] mmCIF format, chain JA [auth H] mmCIF format, chain IA [auth H] mmCIF format, chain HA [auth H] mmCIF format, chain DB [auth N] mmCIF format, chain DA [auth F] mmCIF format, chain CB [auth N] mmCIF format, chain BB [auth N] mmCIF format, chain BA [auth E] mmCIF format, chain AB [auth N] mmCIF format, chain AA [auth E]	AA [auth E] AB [auth N] BA [auth E] BB [auth N] CB [auth N] AA [auth E], AB [auth N], BA [auth E], BB [auth N], CB [auth N], DA [auth F], DB [auth N], HA [auth H], IA [auth H], JA [auth H], LA [auth I], MA [auth I], NA [auth I], O [auth A], P [auth A], PA [auth J], R [auth B], RA [auth K], S [auth B], SA [auth K], UA [auth L], V [auth D], VA [auth L], W [auth D], WA [auth L], X [auth D], Y [auth D], YA [auth M]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain AB [auth N] Focus chain BA [auth E] Focus chain BB [auth N] Focus chain CB [auth N] Focus chain DA [auth F] Focus chain DB [auth N] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth J] Focus chain R [auth B] Focus chain RA [auth K] Focus chain S [auth B] Focus chain SA [auth K] Focus chain UA [auth L] Focus chain V [auth D] Focus chain VA [auth L] Focus chain W [auth D] Focus chain WA [auth L] Focus chain X [auth D] Focus chain Y [auth D] Focus chain YA [auth M] Interactions & Density Focus chain AA [auth E] Focus chain AB [auth N] Focus chain BA [auth E] Focus chain BB [auth N] Focus chain CB [auth N] Focus chain DA [auth F] Focus chain DB [auth N] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth J] Focus chain R [auth B] Focus chain RA [auth K] Focus chain S [auth B] Focus chain SA [auth K] Focus chain UA [auth L] Focus chain V [auth D] Focus chain VA [auth L] Focus chain W [auth D] Focus chain WA [auth L] Focus chain X [auth D] Focus chain Y [auth D] Focus chain YA [auth M]