5M86 | pdb_00005m86

Crystal Structure of the Thermoplasma acidophilum Protein Ta1207

PDB DOI: https://doi.org/10.2210/pdb5M86/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Thermoplasma acidophilum DSM 1728
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-10-28 Released: 2017-06-14
Deposition Author(s): Pathare, G.R., Nagy, I., Bracher, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.203 (Depositor), 0.209 (DCC)
R-Value Work:
0.176 (Depositor), 0.186 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the Thermoplasma acidophilum protein Ta1207.

Pathare, G.R., Nagy, I., Hubert, A., Thomas, D.R., Bracher, A.

(2017) Acta Crystallogr F Struct Biol Commun 73: 328-335

PubMed: 28580920 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X17007087
Primary Citation Related Structures:
5M86

PubMed Abstract:
The crystal structure of the Ta1207 protein from Thermoplasma acidophilum is reported. Ta1207 was identified in a screen for high-molecular-weight protein complexes in T. acidophilum. In solution, Ta1207 forms homopentamers of 188 kDa. The crystal structure of recombinant Ta1207 solved by Se-MAD at 2.4 Å resolution revealed a complex with fivefold symmetry. In the crystal lattice, calcium ions induce the formation of a nanocage from two pentamers. The Ta1207 protomers comprise two domains with the same novel α/β topology. A deep pocket with a binding site for a negatively charged group suggests that Ta1207 functions as an intracellular receptor for an unknown ligand. Homologues of Ta1207 occur only in Thermoplasmatales and its function might be related to the extreme lifestyle of these archaea. The thermostable Ta1207 complex might provide a useful fivefold-symmetric scaffold for future nanotechnological applications.

Organizational Affiliation

Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

Macromolecule Content

Total Structure Weight: 395.69 kDa
Atom Count: 27,183
Modeled Residue Count: 3,210
Deposited Residue Count: 3,330
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ta1207	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	333	Thermoplasma acidophilum DSM 1728	Mutation(s): 0 Gene Names: Ta1207
UniProt
Find proteins for Q9HIW9 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HIW9 Go to UniProtKB: Q9HIW9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HIW9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain HA [auth H] SDF format, chain M [auth A] SDF format, chain Y [auth E] SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain NA [auth J] SDF format, chain KA [auth I] SDF format, chain EA [auth G] MOL2 format, chain BA [auth F] MOL2 format, chain HA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain NA [auth J] MOL2 format, chain KA [auth I] MOL2 format, chain EA [auth G] mmCIF format, chain BA [auth F] mmCIF format, chain HA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain NA [auth J] mmCIF format, chain KA [auth I] mmCIF format, chain EA [auth G]	BA [auth F] EA [auth G] HA [auth H] KA [auth I] M [auth A] BA [auth F], EA [auth G], HA [auth H], KA [auth I], M [auth A], NA [auth J], P [auth B], S [auth C], V [auth D], Y [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain IA [auth I] SDF format, chain LA [auth J] SDF format, chain Q [auth C] SDF format, chain Z [auth F] SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain FA [auth H] SDF format, chain CA [auth G] MOL2 format, chain IA [auth I] MOL2 format, chain LA [auth J] MOL2 format, chain Q [auth C] MOL2 format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain FA [auth H] MOL2 format, chain CA [auth G] mmCIF format, chain IA [auth I] mmCIF format, chain LA [auth J] mmCIF format, chain Q [auth C] mmCIF format, chain Z [auth F] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain FA [auth H] mmCIF format, chain CA [auth G]	CA [auth G] FA [auth H] IA [auth I] K [auth A] LA [auth J] CA [auth G], FA [auth H], IA [auth I], K [auth A], LA [auth J], N [auth B], Q [auth C], T [auth D], W [auth E], Z [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain IA [auth I] Focus chain K [auth A] Focus chain LA [auth J] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain IA [auth I] Focus chain K [auth A] Focus chain LA [auth J] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain JA [auth I] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain MA [auth J] SDF format, chain L [auth A] SDF format, chain GA [auth H] SDF format, chain DA [auth G] SDF format, chain AA [auth F] MOL2 format, chain JA [auth I] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain MA [auth J] MOL2 format, chain L [auth A] MOL2 format, chain GA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain JA [auth I] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain MA [auth J] mmCIF format, chain L [auth A] mmCIF format, chain GA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] DA [auth G] GA [auth H] JA [auth I] L [auth A] AA [auth F], DA [auth G], GA [auth H], JA [auth I], L [auth A], MA [auth J], O [auth B], R [auth C], U [auth D], X [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain JA [auth I] Focus chain L [auth A] Focus chain MA [auth J] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain JA [auth I] Focus chain L [auth A] Focus chain MA [auth J] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.203 (Depositor), 0.209 (DCC)
R-Value Work: 0.176 (Depositor), 0.186 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 228.639	α = 90
b = 112.821	β = 118.7
c = 221.328	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
RESOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
SHELXD	phasing
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-06-14

Deposition Author(s):

Pathare, G.R.

Nagy, I.

Bracher, A.

Revision History (Full details and data files)

Version 1.0: 2017-06-14
Type: Initial release
Version 1.1: 2017-06-21
Changes: Database references, Structure summary
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary