National Center for
Biotechnology Information

8V84: 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)

PDB ID:

8V84 Download

MMDB ID:

246210

PDB Deposition Date:

2023/12/4

Updated in MMDB:

2024/05

Experimental Method:

electron microscopy

Resolution:

2.7 Å

Source Organism:

Saccharomyces cerevisiae BY4741-AV16▼

Taxonomy	Molecule
Saccharomyces cerevisiae BY4741-AV16	B
Saccharomyces cerevisiae BY4741	1, 2, 3, 6, 7, 8, A, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, W, Y, Z, a, b, e, f, h , i, j, l, m, n, o, q, r, t, u, v, w, x, y

Similar Structures:

Biological Unit for 8V84: 49-meric; determined by author

Molecular Components in 8V84
Label	Count	Molecule
Proteins (46 molecules)
3	1	Atp-dependent RNA Helicase Dbp10
7	1	60S Ribosomal Subunit Assembly/export Protein Loc1
8	1	Ribosomal RNA-processing Protein 14
A	1	Ribosome Biogenesis Protein Brx1
B	1	Large Ribosomal Subunit Protein UL3
C	1	60S Ribosomal Protein L4-a
D	1	Atp-dependent RNA Helicase Has1
E	1	60S Ribosomal Protein L6-a
F	1	60S Ribosomal Protein L7-a
G	1	Large Ribosomal Subunit Protein El8a
H	1	Large Ribosomal Subunit Protein Ul6a
I	1	Ribosome Biogenesis Protein Nsa1
J	1	rRNA-processing Protein Ebp2
K	1	Proteasome-interacting Protein Cic1
L	1	60S Ribosomal Protein L13-a
M	1	60S Ribosomal Protein L14-a
N	1	Large Ribosomal Subunit Protein El15a
O	1	Large Ribosomal Subunit Protein Ul13a
P	1	60S Ribosomal Protein L17-a
Q	1	60S Ribosomal Protein L18-a
R	1	Protein Mak16
S	1	Large Ribosomal Subunit Protein El20a
T	1	Ribosomal RNA-processing Protein 15
V	1	60S Ribosomal Protein L23-a
W	1	Ribosome Assembly Factor Mrt4
Y	1	60S Ribosomal Protein L26-a
Z	1	Ribosome Biogenesis Protein Ssf1
a	1	Large Ribosomal Subunit Protein Ul1a
b	1	Nucleolar Gtp-binding Protein 1
e	1	60S Ribosomal Protein L32
f	1	60S Ribosomal Protein L33-a
h	1	60S Ribosomal Protein L35-a
i	1	60S Ribosomal Protein L36-a
j	1	60S Ribosomal Protein L37-a
l	1	60S Ribosome Subunit Biogenesis Protein Nip7
m	1	Ribosome Biogenesis Protein Erb1
n	1	Pescadillo Homolog
o	1	Ribosome Biogenesis Protein 15
q	1	25S rRNA (Cytosine(2870)-c(5))-methyltransferase
r	1	Ribosome Biogenesis Protein Nsa2
t	1	Ribosome Biogenesis Protein Rlp7
u	1	Ribosome Biogenesis Protein Rlp24
v	1	Nucleolar Protein 16
w	1	Ribosomal RNA-processing Protein 1
x	1	Ribosome Production Factor 1
y	1	Eukaryotic Translation Initiation Factor 6
Nucleotides(3 molecules)
1	1	Saccharomyces Cerevisiae 25S Ribosomal RNA
2	1	Saccharomyces Cerevisiae 5.8s Ribosomal RNA
6	1	Its2 RNA
Chemicals and Non-standard biopolymers (4 molecules)
1	1	GUANOSINE-5'-DIPHOSPHATE
2	1	MAGNESIUM ION
3	2	ZINC ION

* 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