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5TGM: Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro

PDB ID:

5TGM Download

MMDB ID:

254046

PDB Deposition Date:

2016/9/28

Updated in MMDB:

2024/10

Experimental Method:

x-ray diffraction

Resolution:

3.5 Å

Source Organism:

Homo sapiens▼

Taxonomy

Molecule

Homo sapiens

P, p

Saccharomyces cerevisiae

2, S0, S1, S2, S3, S4, S5, S6, S7, S
8, S9, C0, C1, C2, C3, C4, C5, C
6, C7, C8, C9, D0, D1, D2, D3, D
4, D5, D6, D7, D8, D9, E0, E1, S
R, SM, 1, 3, 4, L2, L3, L4, L5,
L6, L7, L8, L9, M0, M1, M3, M4,
M5, M6, M7, M8, M9, N0, N1, N2,
N3, N4, N5, N6, N7, N8, N9, O0,
O1, O2, O3, O4, O5, O6, O7, O8,
O9, Q0, Q1, Q2, Q3, 6, s0, s1, s
2, s3, s4, s5, s6, s7, s8, s9, c
0, c1, c2, c3, c4, c5, c6, c7, c
8, c9, d0, d1, d2, d3, d4, d5, d
6, d7, d8, d9, e0, e1, sR, sM, 5
, 7, 8, l2, l3, l4, l5, l6, l7,
l8, l9, m0, m1, m2, m3, m4, m5,
m6, m7, m8, m9, n0, n1, n2, n3,
n4, n5, n6, n7, n8, n9, o0, o1,
o2, o3, o4, o5, o6, o7, o8, o9,
q0, q1, q2, q3, p0, p1, p2

Similar Structures:

Biological Unit for 5TGM: 164-meric; determined by author

Molecular Components in 5TGM
Label	Count	Molecule
Proteins (154 molecules)
S0 s0	2	40S Ribosomal Protein S0-a
S1 s1	2	40S Ribosomal Protein S1-a
S2 s2	2	40S Ribosomal Protein S2
S3 s3	2	40S Ribosomal Protein S3
S4 s4	2	40S Ribosomal Protein S4-a
S5 s5	2	40S Ribosomal Protein S5
S6 s6	2	40S Ribosomal Protein S6-a
S7 s7	2	40S Ribosomal Protein S7-a
S8 s8	2	40S Ribosomal Protein S8
S9 s9	2	40S Ribosomal Protein S9-a
C0	1	40S Ribosomal Protein S10-a,40s Ribosomal Protein S10
C1 c1	2	40S Ribosomal Protein S11-a,40s Ribosomal Protein S11
C2 c2	2	40S Ribosomal Protein S12,40s Ribosomal Protein S12
C3 c3	2	40S Ribosomal Protein S13
C4 c4	2	40S Ribosomal Protein S14-a
C5 c5	2	40S Ribosomal Protein S15,40s Ribosomal Protein S15,40s Ribosomal Protein S15
C6 c6	2	40S Ribosomal Protein S16-a
C7	1	Es17
C8 c8	2	40S Ribosomal Protein S18-a
C9 c9	2	40S Ribosomal Protein S19-a
D0 d0	2	40S Ribosomal Protein S20
D1 d1	2	40S Ribosomal Protein S21-a
D2 d2	2	40S Ribosomal Protein S22-a
D3 d3	2	40S Ribosomal Protein S23-a
D4 d4	2	40S Ribosomal Protein S24-a
D5 d5	2	40S Ribosomal Protein S25-a
D6 d6	2	40S Ribosomal Protein S26-b
D7 d7	2	40S Ribosomal Protein S27-a
D8 d8	2	40S Ribosomal Protein S28-a
D9 d9	2	40S Ribosomal Protein S29-a
E0 e0	2	40S Ribosomal Protein S30-a
E1 e1	2	Ubiquitin-40s Ribosomal Protein S31
SR	1	Guanine Nucleotide-binding Protein Subunit Beta-like Protein
SM	1	Ribosome-bound Protein Stm1,suppressor Protein Stm1,ribosome-bound Protein Stm1
L2 l2	2	60S Ribosomal Protein L2-a
L3 l3	2	60S Ribosomal Protein L3
L4 l4	2	60S Ribosomal Protein L4-a
L5 l5	2	60S Ribosomal Protein L5
L6 l6	2	60S Ribosomal Protein L6-a
L7 l7	2	60S Ribosomal Protein L7-a
L8	1	60S Ribosomal Protein L8-a
L9 l9	2	60S Ribosomal Protein L9-a
M0 m0	2	60S Ribosomal Protein L10
M1 m1	2	60S Ribosomal Protein L11-b
M3 m3	2	60S Ribosomal Protein L13-a
M4 m4	2	60S Ribosomal Protein L14-a
M5 m5	2	60S Ribosomal Protein L15-a
M6 m6	2	60S Ribosomal Protein L16-a
M7 m7	2	60S Ribosomal Protein L17-a
M8 m8	2	60S Ribosomal Protein L18-a
M9 m9	2	60S Ribosomal Protein L19-a
N0 n0	2	60S Ribosomal Protein L20-a
N1 n1	2	60S Ribosomal Protein L21-a
N2 n2	2	60S Ribosomal Protein L22-a
N3 n3	2	60S Ribosomal Protein L23-a
N4	1	60S Ribosomal Protein L24-a
N5 n5	2	60S Ribosomal Protein L25
N6 n6	2	60S Ribosomal Protein L26-a
N7 n7	2	60S Ribosomal Protein L27-a
N8 n8	2	60S Ribosomal Protein L28
N9 n9	2	60S Ribosomal Protein L29
O0 o0	2	60S Ribosomal Protein L30
O1 o1	2	60S Ribosomal Protein L31-a
O2 o2	2	60S Ribosomal Protein L32
O3 o3	2	60S Ribosomal Protein L33-a
O4 o4	2	60S Ribosomal Protein L34-a
O5 o5	2	60S Ribosomal Protein L35-a
O6 o6	2	60S Ribosomal Protein L36-a
O7 o7	2	60S Ribosomal Protein L37-a
O8 o8	2	60S Ribosomal Protein L38
O9 o9	2	60S Ribosomal Protein L39
Q0 q0	2	Ubiquitin-60s Ribosomal Protein L40
Q1 q1	2	60S Ribosomal Protein L41-a
Q2 q2	2	60S Ribosomal Protein L42-a
Q3 q3	2	60S Ribosomal Protein L43-a
c0	1	40S Ribosomal Protein S10-a,40s Ribosomal Protein S10
c7	1	Es17
sR	1	Guanine Nucleotide-binding Protein Subunit Beta-like Protein
sM	1	Suppressor Protein Stm1,ribosome-bound Protein Stm1
l8	1	60S Ribosomal Protein L8-a,60s Ribosomal Protein L8
m2	1	60S Ribosomal Protein L12
n4	1	60S Ribosomal Protein L24-a
p0	1	60S Ribosomal Protein P0
p1 p2	2	60S Ribosomal Protein P1/2
Nucleotides(10 molecules)
2	1	18S Ribosomal RNA
1	1	25S Ribosomal RNA
3 7	2	5S Ribosomal RNA
4 8	2	5.8s Ribosomal RNA
6	1	18S Ribosomal RNA
5	1	25S Ribosomal RNA
P p	2	Peptidyl-trna Analog Acca-leu-phe
Chemicals and Non-standard biopolymers (2310 molecules)
1	1095	osmium (III) hexammine
2	1191	MAGNESIUM ION
3	16	ZINC ION
4	2	PHENYLALANINE
5	2	LEUCINE
6	2	SPARSOMYCIN
7	2	3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate)

* 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