1M5Q | pdb_00001m5q

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.236 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1M5Q

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

  • DOI: https://doi.org/10.1073/pnas.0538042100
  • Primary Citation 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 
  • Modeled Residue Count: 3,566 
  • Deposited Residue Count: 3,640 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
small nuclear ribonucleoprotein homolog
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
130Pyrobaculum aerophilumMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZVU2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD

Query on CD


Download:Ideal Coordinates CCD File
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
GOL

Query on GOL


Download:Ideal Coordinates CCD File
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
ACY

Query on ACY


Download:Ideal Coordinates CCD File
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
NA

Query on NA


Download:Ideal Coordinates CCD File
EA [auth A],
HA [auth B],
KB [auth R],
NB [auth S],
QB [auth V]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
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 LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.236 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.322α = 90
b = 172.427β = 90
c = 148.108γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
CNSrefinement

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

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