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5T62: Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex

PDB ID:

5T62 Download

MMDB ID:

171341

PDB Deposition Date:

2016/9/1

Updated in MMDB:

2022/11

Experimental Method:

electron microscopy

Resolution:

3.1 Å

Source Organism:

Saccharomyces cerevisiae S288C▼

Taxonomy	Molecule
Saccharomyces cerevisiae S288C	X, A, D, E, F, G, H, I, J, K, L, M, N, O, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t , u, v, w, x, y, z, Q, R, V, W
Saccharomyces cerevisiae	B, C, S

Similar Structures:

Biological Unit for 5T62: 47-meric; determined by author

Molecular Components in 5T62
Label	Count	Molecule
Proteins (44 molecules)
X	1	Eukaryotic Translation Initiation Factor 6
D	1	60S Ribosomal Protein L2-a
E	1	60S Ribosomal Protein L3
F	1	60S Ribosomal Protein L4-a
G	1	60S Ribosomal Protein L5
H	1	60S Ribosomal Protein L6-a
I	1	60S Ribosomal Protein L7-a
J	1	60S Ribosomal Protein L8-a
K	1	60S Ribosomal Protein L9-a
L	1	60S Ribosomal Protein L10
M	1	60S Ribosomal Protein L11-a
N	1	60S Ribosomal Protein L13-a
O	1	60S Ribosomal Protein L14-a
a	1	60S Ribosomal Protein L15-a
b	1	60S Ribosomal Protein L16-a
c	1	60S Ribosomal Protein L17-a
d	1	60S Ribosomal Protein L18-a
e	1	60S Ribosomal Protein L19-a
f	1	60S Ribosomal Protein L20-a
g	1	60S Ribosomal Protein L21-a
h	1	60S Ribosomal Protein L22-a
i	1	60S Ribosomal Protein L23-a
j	1	60S Ribosomal Protein L24-a
k	1	60S Ribosomal Protein L25
l	1	60S Ribosomal Protein L26-a
m	1	60S Ribosomal Protein L27-a
n	1	60S Ribosomal Protein L28
o	1	60S Ribosomal Protein L29
p	1	60S Ribosomal Protein L30
q	1	60S Ribosomal Protein L31-a
r	1	60S Ribosomal Protein L32
s	1	60S Ribosomal Protein L33-a
t	1	60S Ribosomal Protein L34-a
u	1	60S Ribosomal Protein L35-a
v	1	60S Ribosomal Protein L36-a
w	1	60S Ribosomal Protein L37-a
x	1	60S Ribosomal Protein L38
y	1	60S Ribosomal Protein L39
z	1	Ubiquitin-60s Ribosomal Protein L40
Q	1	60S Ribosomal Protein L42-a
R	1	60S Ribosomal Protein L43-a
S	1	Ribosomal Protein UL1
V	1	60S Ribosomal Export Protein Nmd3
W	1	Large Subunit Gtpase 1
Nucleotides(3 molecules)
A	1	25S Ribosomal RNA
B	1	5S Ribosomal RNA
C	1	5.8s Ribosomal RNA
Chemicals and Non-standard biopolymers (163 molecules)
1	160	MAGNESIUM ION (Link to PubChem not yet available)
2	2	POTASSIUM ION (Link to PubChem not yet available)
3	1	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (Link to PubChem not yet available)

* Click molecule labels to explore molecular sequence information.

Citing MMDB

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303