1M5Q

Crystal structure of a novel Sm-like archaeal protein from Pyrobaculum aerophilum

PDB DOI: https://doi.org/10.2210/pdb1M5Q/pdb

Classification: TRANSLATION
Organism(s): Pyrobaculum aerophilum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2002-07-09 Released: 2003-03-18
Deposition Author(s): Mura, C., Phillips, M., Kozhukhovsky, A., Eisenberg, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.236
R-Value Work: 0.191
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure and assembly of an augmented Sm-like archaeal protein 14-mer

Mura, C., Phillips, M., Kozhukhovsky, A., Eisenberg, D.

(2003) Proc Natl Acad Sci U S A 100: 4539-4544

PubMed: 12668760 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.0538042100
Primary Citation of Related Structures:
1M5Q

PubMed Abstract:
To better understand the roles of Sm proteins in forming the cores of many RNA-processing ribonucleoproteins, we determined the crystal structure of an atypical Sm-like archaeal protein (SmAP3) in which the conserved Sm domain is augmented by a previously uncharacterized, mixed alpha/beta C-terminal domain. The structure reveals an unexpected SmAP3 14-mer that is perforated by a cylindrical pore and is bound to 14 cadmium (Cd(2+)) ions. Individual heptamers adopt either "apical" or "equatorial" conformations that chelate Cd(2+) differently. SmAP3 forms supraheptameric oligomers (SmAP3)(n = 7,14,28) in solution, and assembly of the asymmetric 14-mer is modulated by differential divalent cation-binding in apical and equatorial subunits. Phylogenetic and sequence analyses substantiate SmAP3s as a unique subset of SmAPs. These results distinguish SmAP3s from other Sm proteins and provide a model for the structure and properties of Sm proteins >100 residues in length, e.g., several human Sm proteins.

Organizational Affiliation

Howard Hughes Medical Institute, Molecular Biology Institute, and Department of Energy Institute for Genomics and Proteomics, 201 Boyer Hall Molecular Biology Institute, University of California, Box 951570, Los Angeles, CA 90095-1570, USA.

Macromolecule Content

Total Structure Weight: 425.49 kDa
Atom Count: 30,641
Modelled Residue Count: 3,566
Deposited Residue Count: 3,640
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
small nuclear ribonucleoprotein homolog	A AA [auth 1] B BA [auth 2] C A, AA [auth 1], B, BA [auth 2], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	130	Pyrobaculum aerophilum	Mutation(s): 0 Gene Names: SmAP3 gene (Pae2122)
UniProt
Find proteins for Q8ZVU2 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2)) Explore Q8ZVU2 Go to UniProtKB: Q8ZVU2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8ZVU2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain AB [auth L] SDF format, chain AC [auth Y] SDF format, chain BB [auth M] SDF format, chain CA [auth A] SDF format, chain CC [auth Z] SDF format, chain DA [auth A] SDF format, chain EC [auth 1] SDF format, chain FB [auth O] SDF format, chain GA [auth B] SDF format, chain GB [auth P] SDF format, chain HB [auth P] SDF format, chain HC [auth 2] SDF format, chain IA [auth D] SDF format, chain IB [auth Q] SDF format, chain JA [auth D] SDF format, chain JB [auth R] SDF format, chain KA [auth E] SDF format, chain LA [auth F] SDF format, chain MB [auth S] SDF format, chain OA [auth H] SDF format, chain OB [auth U] SDF format, chain PA [auth H] SDF format, chain PB [auth V] SDF format, chain TA [auth I] SDF format, chain TB [auth W] SDF format, chain WA [auth J] SDF format, chain XB [auth X] SDF format, chain YA [auth K] MOL2 format, chain AB [auth L] MOL2 format, chain AC [auth Y] MOL2 format, chain BB [auth M] MOL2 format, chain CA [auth A] MOL2 format, chain CC [auth Z] MOL2 format, chain DA [auth A] MOL2 format, chain EC [auth 1] MOL2 format, chain FB [auth O] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth P] MOL2 format, chain HB [auth P] MOL2 format, chain HC [auth 2] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth Q] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth R] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain MB [auth S] MOL2 format, chain OA [auth H] MOL2 format, chain OB [auth U] MOL2 format, chain PA [auth H] MOL2 format, chain PB [auth V] MOL2 format, chain TA [auth I] MOL2 format, chain TB [auth W] MOL2 format, chain WA [auth J] MOL2 format, chain XB [auth X] MOL2 format, chain YA [auth K] mmCIF format, chain AB [auth L] mmCIF format, chain AC [auth Y] mmCIF format, chain BB [auth M] mmCIF format, chain CA [auth A] mmCIF format, chain CC [auth Z] mmCIF format, chain DA [auth A] mmCIF format, chain EC [auth 1] mmCIF format, chain FB [auth O] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth P] mmCIF format, chain HB [auth P] mmCIF format, chain HC [auth 2] mmCIF format, chain IA [auth D] mmCIF format, chain IB [auth Q] mmCIF format, chain JA [auth D] mmCIF format, chain JB [auth R] mmCIF format, chain KA [auth E] mmCIF format, chain LA [auth F] mmCIF format, chain MB [auth S] mmCIF format, chain OA [auth H] mmCIF format, chain OB [auth U] mmCIF format, chain PA [auth H] mmCIF format, chain PB [auth V] mmCIF format, chain TA [auth I] mmCIF format, chain TB [auth W] mmCIF format, chain WA [auth J] mmCIF format, chain XB [auth X] mmCIF format, chain YA [auth K]	AB [auth L] AC [auth Y] BB [auth M] CA [auth A] CC [auth Z] AB [auth L], AC [auth Y], BB [auth M], CA [auth A], CC [auth Z], DA [auth A], EC [auth 1], FB [auth O], GA [auth B], GB [auth P], HB [auth P], HC [auth 2], IA [auth D], IB [auth Q], JA [auth D], JB [auth R], KA [auth E], LA [auth F], MB [auth S], OA [auth H], OB [auth U], PA [auth H], PB [auth V], TA [auth I], TB [auth W], WA [auth J], XB [auth X], YA [auth K]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain AB [auth L] Focus chain AC [auth Y] Focus chain BB [auth M] Focus chain CA [auth A] Focus chain CC [auth Z] Focus chain DA [auth A] Focus chain EC [auth 1] Focus chain FB [auth O] Focus chain GA [auth B] Focus chain GB [auth P] Focus chain HB [auth P] Focus chain HC [auth 2] Focus chain IA [auth D] Focus chain IB [auth Q] Focus chain JA [auth D] Focus chain JB [auth R] Focus chain KA [auth E] Focus chain LA [auth F] Focus chain MB [auth S] Focus chain OA [auth H] Focus chain OB [auth U] Focus chain PA [auth H] Focus chain PB [auth V] Focus chain TA [auth I] Focus chain TB [auth W] Focus chain WA [auth J] Focus chain XB [auth X] Focus chain YA [auth K] Interactions & Density Focus chain AB [auth L] Focus chain AC [auth Y] Focus chain BB [auth M] Focus chain CA [auth A] Focus chain CC [auth Z] Focus chain DA [auth A] Focus chain EC [auth 1] Focus chain FB [auth O] Focus chain GA [auth B] Focus chain GB [auth P] Focus chain HB [auth P] Focus chain HC [auth 2] Focus chain IA [auth D] Focus chain IB [auth Q] Focus chain JA [auth D] Focus chain JB [auth R] Focus chain KA [auth E] Focus chain LA [auth F] Focus chain MB [auth S] Focus chain OA [auth H] Focus chain OB [auth U] Focus chain PA [auth H] Focus chain PB [auth V] Focus chain TA [auth I] Focus chain TB [auth W] Focus chain WA [auth J] Focus chain XB [auth X] Focus chain YA [auth K]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CB [auth M] SDF format, chain FA [auth A] SDF format, chain FC [auth 1] SDF format, chain IC [auth 2] SDF format, chain LB [auth R] SDF format, chain NA [auth G] SDF format, chain QA [auth H] SDF format, chain RA [auth H] SDF format, chain RB [auth V] SDF format, chain UB [auth W] SDF format, chain XA [auth J] SDF format, chain YB [auth X] MOL2 format, chain CB [auth M] MOL2 format, chain FA [auth A] MOL2 format, chain FC [auth 1] MOL2 format, chain IC [auth 2] MOL2 format, chain LB [auth R] MOL2 format, chain NA [auth G] MOL2 format, chain QA [auth H] MOL2 format, chain RA [auth H] MOL2 format, chain RB [auth V] MOL2 format, chain UB [auth W] MOL2 format, chain XA [auth J] MOL2 format, chain YB [auth X] mmCIF format, chain CB [auth M] mmCIF format, chain FA [auth A] mmCIF format, chain FC [auth 1] mmCIF format, chain IC [auth 2] mmCIF format, chain LB [auth R] mmCIF format, chain NA [auth G] mmCIF format, chain QA [auth H] mmCIF format, chain RA [auth H] mmCIF format, chain RB [auth V] mmCIF format, chain UB [auth W] mmCIF format, chain XA [auth J] mmCIF format, chain YB [auth X]	CB [auth M] FA [auth A] FC [auth 1] IC [auth 2] LB [auth R] CB [auth M], FA [auth A], FC [auth 1], IC [auth 2], LB [auth R], NA [auth G], QA [auth H], RA [auth H], RB [auth V], UB [auth W], XA [auth J], YB [auth X]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CB [auth M] Focus chain FA [auth A] Focus chain FC [auth 1] Focus chain IC [auth 2] Focus chain LB [auth R] Focus chain NA [auth G] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain RB [auth V] Focus chain UB [auth W] Focus chain XA [auth J] Focus chain YB [auth X] Interactions & Density Focus chain CB [auth M] Focus chain FA [auth A] Focus chain FC [auth 1] Focus chain IC [auth 2] Focus chain LB [auth R] Focus chain NA [auth G] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain RB [auth V] Focus chain UB [auth W] Focus chain XA [auth J] Focus chain YB [auth X]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain BC [auth Y] SDF format, chain DB [auth M] SDF format, chain DC [auth Z] SDF format, chain EB [auth N] SDF format, chain GC [auth 1] SDF format, chain JC [auth 2] SDF format, chain MA [auth F] SDF format, chain SA [auth H] SDF format, chain SB [auth V] SDF format, chain UA [auth I] SDF format, chain VA [auth I] SDF format, chain VB [auth W] SDF format, chain WB [auth W] SDF format, chain ZA [auth K] SDF format, chain ZB [auth X] MOL2 format, chain BC [auth Y] MOL2 format, chain DB [auth M] MOL2 format, chain DC [auth Z] MOL2 format, chain EB [auth N] MOL2 format, chain GC [auth 1] MOL2 format, chain JC [auth 2] MOL2 format, chain MA [auth F] MOL2 format, chain SA [auth H] MOL2 format, chain SB [auth V] MOL2 format, chain UA [auth I] MOL2 format, chain VA [auth I] MOL2 format, chain VB [auth W] MOL2 format, chain WB [auth W] MOL2 format, chain ZA [auth K] MOL2 format, chain ZB [auth X] mmCIF format, chain BC [auth Y] mmCIF format, chain DB [auth M] mmCIF format, chain DC [auth Z] mmCIF format, chain EB [auth N] mmCIF format, chain GC [auth 1] mmCIF format, chain JC [auth 2] mmCIF format, chain MA [auth F] mmCIF format, chain SA [auth H] mmCIF format, chain SB [auth V] mmCIF format, chain UA [auth I] mmCIF format, chain VA [auth I] mmCIF format, chain VB [auth W] mmCIF format, chain WB [auth W] mmCIF format, chain ZA [auth K] mmCIF format, chain ZB [auth X]	BC [auth Y] DB [auth M] DC [auth Z] EB [auth N] GC [auth 1] BC [auth Y], DB [auth M], DC [auth Z], EB [auth N], GC [auth 1], JC [auth 2], MA [auth F], SA [auth H], SB [auth V], UA [auth I], VA [auth I], VB [auth W], WB [auth W], ZA [auth K], ZB [auth X]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain BC [auth Y] Focus chain DB [auth M] Focus chain DC [auth Z] Focus chain EB [auth N] Focus chain GC [auth 1] Focus chain JC [auth 2] Focus chain MA [auth F] Focus chain SA [auth H] Focus chain SB [auth V] Focus chain UA [auth I] Focus chain VA [auth I] Focus chain VB [auth W] Focus chain WB [auth W] Focus chain ZA [auth K] Focus chain ZB [auth X] Interactions & Density Focus chain BC [auth Y] Focus chain DB [auth M] Focus chain DC [auth Z] Focus chain EB [auth N] Focus chain GC [auth 1] Focus chain JC [auth 2] Focus chain MA [auth F] Focus chain SA [auth H] Focus chain SB [auth V] Focus chain UA [auth I] Focus chain VA [auth I] Focus chain VB [auth W] Focus chain WB [auth W] Focus chain ZA [auth K] Focus chain ZB [auth X]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain HA [auth B] SDF format, chain KB [auth R] SDF format, chain NB [auth S] SDF format, chain QB [auth V] MOL2 format, chain EA [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain KB [auth R] MOL2 format, chain NB [auth S] MOL2 format, chain QB [auth V] mmCIF format, chain EA [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain KB [auth R] mmCIF format, chain NB [auth S] mmCIF format, chain QB [auth V]	EA [auth A], HA [auth B], KB [auth R], NB [auth S], QB [auth V]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain HA [auth B] Focus chain KB [auth R] Focus chain NB [auth S] Focus chain QB [auth V] Interactions & Density Focus chain EA [auth A] Focus chain HA [auth B] Focus chain KB [auth R] Focus chain NB [auth S] Focus chain QB [auth V]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A AA [auth 1] B BA [auth 2] C A, AA [auth 1], B, BA [auth 2], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.236
R-Value Work: 0.191
R-Value Observed: 0.191
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.322	α = 90
b = 172.427	β = 90
c = 148.108	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
CNS	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-03-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-03-18
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-05-17
Changes: Structure summary
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary