National Center for
Biotechnology Information

8CDL: 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex

PDB ID:

8CDL Download

MMDB ID:

235745

PDB Deposition Date:

2023/1/31

Updated in MMDB:

2025/12

Experimental Method:

electron microscopy

Resolution:

2.72 Å

Source Organism:

Saccharomyces cerevisiae▼

Taxonomy	Molecule
Saccharomyces cerevisiae	0, 1, 2, 3, 4, 5, 6, 7, 8, A, AA, B, BB, Bb, C, CC, D, DD, Dd, E, EE , Ee, F, FF, G, GG, H, HH, I, II , J, JJ, K, KK, L, LL, M, MM, N, NN, O, OO, P, PP, Pp, Q, QQ, R, S, T, U, V, W, X, Y, Z, 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
Escherichia coli	Cc

Similar Structures:

Biological Unit for 8CDL: 83-meric; determined by author

Molecular Components in 8CDL
Label	Count	Molecule
Proteins (76 molecules)
0	1	40S Ribosomal Protein S24-a
1	1	40S Ribosomal Protein S25-a
2	1	40S Ribosomal Protein S26
3	1	40S Ribosomal Protein S27-a
4	1	40S Ribosomal Protein S28-a
5	1	Hlj1_g0030400.mrna.1.cds.1
6	1	40S Ribosomal Protein S30-a
7	1	Guanine Nucleotide-binding Protein Subunit Beta-like Protein
8	1	Ubiquitin-40s Ribosomal Protein S31
A	1	60S Ribosomal Protein L16-a
B	1	60S Ribosomal Protein L17-a
C	1	60S Ribosomal Protein L18-a
D	1	60S Ribosomal Protein L19-a
DD	1	60S Acidic Ribosomal Protein P0
E	1	60S Ribosomal Protein L20-a
EE	1	60S Ribosomal Protein L2-a
Ee	1	60S Ribosomal Protein L12-a
F	1	60S Ribosomal Protein L21-a
FF	1	60S Ribosomal Protein L3
G	1	60S Ribosomal Protein L22-a
GG	1	60S Ribosomal Protein L4-a
H	1	60S Ribosomal Protein L23-a
HH	1	60S Ribosomal Protein L5
I	1	60S Ribosomal Protein L24-a
II	1	60S Ribosomal Protein L6-a
J	1	60S Ribosomal Protein L25
JJ	1	60S Ribosomal Protein L7-a
K	1	60S Ribosomal Protein L26-a
KK	1	60S Ribosomal Protein L8-a
L	1	60S Ribosomal Protein L27-a
LL	1	60S Ribosomal Protein L9-a
M	1	60S Ribosomal Protein L28
MM	1	60S Ribosomal Protein L10
N	1	60S Ribosomal Protein L29
NN	1	60S Ribosomal Protein L11-a
O	1	60S Ribosomal Protein L30
OO	1	60S Ribosomal Protein L13-a
P	1	60S Ribosomal Protein L31-a
PP	1	60S Ribosomal Protein L14-a
Pp	1	Dipeptide
Q	1	60S Ribosomal Protein L32
QQ	1	60S Ribosomal Protein L15-a
R	1	60S Ribosomal Protein L33-a
S	1	60S Ribosomal Protein L34-a
T	1	60S Ribosomal Protein L35-a
U	1	60S Ribosomal Protein L36-a
V	1	60S Ribosomal Protein L37-a
W	1	60S Ribosomal Protein L38
X	1	60S Ribosomal Protein L39
Y	1	Ubiquitin-60s Ribosomal Protein L40
Z	1	60S Ribosomal Protein L41-a
a	1	60S Ribosomal Protein L42-a
b	1	60S Ribosomal Protein L43-a
d	1	40S Ribosomal Protein S0-a
e	1	40S Ribosomal Protein S1-a
f	1	40S Ribosomal Protein S2
g	1	Rps3 Isoform 1
h	1	40S Ribosomal Protein S4-a
i	1	40S Ribosomal Protein S5
j	1	40S Ribosomal Protein S6-a
k	1	40S Ribosomal Protein S7-a
l	1	40S Ribosomal Protein S8-b
m	1	40S Ribosomal Protein S9-a
n	1	40S Ribosomal Protein S10-a
o	1	40S Ribosomal Protein S11-a
p	1	40S Ribosomal Protein S13
q	1	40S Ribosomal Protein S14-a
r	1	40S Ribosomal Protein S15
s	1	40S Ribosomal Protein S16-a
t	1	40S Ribosomal Protein S17-a
u	1	40S Ribosomal Protein S18-a
v	1	40S Ribosomal Protein S19-a
w	1	40S Ribosomal Protein S20
x	1	40S Ribosomal Protein S21-a
y	1	40S Ribosomal Protein S22-a
z	1	40S Ribosomal Protein S23-a
Nucleotides(7 molecules)
AA	1	25S Ribosomal RNA
BB	1	5S Ribosomal RNA
Bb	1	Transfer RNA PHE
CC	1	5.8s Ribosomal RNA
Cc	1	Transfer RNA Fmet
Dd	1	Messenger RNA
c	1	18S Ribosomal RNA
Chemicals and Non-standard biopolymers (291 molecules)
1	8	ZINC ION
2	258	MAGNESIUM ION
3	21	POTASSIUM ION
4	4	SPERMIDINE

* 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