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Cryo-EM structure of small subunit of giardia lamblia ribosome at 2.9 a resolution

Analyse Cryo-EM structure of small subunit of giardia lamblia ribosome at 2.9 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PWF
Type: protein + RNA
Length: 5,320 residues
Chains: 32
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosomal protein S29A; Ribosomal protein S19E; Ribosomal protein S13; Ribosomal protein…
UniProt: A8B7H6, A0A644F964, A8BE02, A8BKS8, A8B8Z2, A8BS96, A8BZ58, A8BKC6, A8BMZ1, A8BE86, A8BS79, A8B593, A8BJL1, A8BQZ7, A8B8H7, A8B484, A8BBP3, A8BRG5, A8BRX3, A8B252, A0A644F843, A8B4F3, E2RU83, E2RU77, A8BFE3, V6TVJ7, A8B4G0, A8B6L8, A8BZD3
Ligands: K, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 32 distinct chains · 30% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
d	Ribosomal protein S29A	protein	48	29% helix, 13% strand	A8B7H6
T	Ribosomal protein S19E	protein	130	43% helix, 11% strand	A0A644F964
N	Ribosomal protein S13	protein	152	52% helix, 0% strand	A8BE02
J	Ribosomal protein S9	protein	166	49% helix, 6% strand	A8BKS8
D	Ribosomal protein S3	protein	182	36% helix, 27% strand	A8B8Z2
X	Ribosomal protein S23	protein	142	25% helix, 29% strand	A8BS96
S	Ribosomal protein S18	protein	133	37% helix, 6% strand	A8BZ58
Q	Ribosomal protein S16	protein	125	30% helix, 19% strand	A8BKC6
C	Ribosomal protein S2	protein	212	31% helix, 28% strand	A8BMZ1
A	40S ribosomal protein sa	protein	194	38% helix, 14% strand	A8BE86
B	40S ribosomal protein S3A	protein	218	30% helix, 33% strand	A8BS79
Y	Ribosomal protein S24	protein	90	16% helix, 40% strand	A8B593
b	Ribosomal protein S27	protein	79	6% helix, 20% strand	A8BJL1
a	40S ribosomal protein S26	protein	97	16% helix, 24% strand	A8BQZ7
Z	40S ribosomal protein S25	protein	59	41% helix, 19% strand	A8B8H7
V	40S ribosomal protein S21	protein	82	17% helix, 20% strand	A8B484
P	Ribosomal protein S15	protein	105	22% helix, 12% strand	A8BBP3
R	Ribosomal protein S17	protein	101	50% helix, 1% strand	A8BRG5
K	Ribosomal protein S10B	protein	83	41% helix, 19% strand	A8BRX3
I	40S ribosomal protein S8	protein	163	23% helix, 33% strand	A8B252
e	40S ribosomal protein S30	protein	37	41% helix, 0% strand	A0A644F843
H	Ribosomal protein ES7	protein	162	29% helix, 22% strand	—
n	Ribosomal protein EL41	protein	24	83% helix, 0% strand	—
c	Ribosomal protein S28	protein	55	0% helix, 53% strand	A8B4F3
O	Ribosomal protein S14	protein	126	25% helix, 27% strand	E2RU83
W	Ribosomal protein S15A	protein	129	33% helix, 27% strand	E2RU77
E	40S ribosomal protein S4	protein	258	12% helix, 32% strand	A8BFE3
2	RRNA 18S	rna	1355	—	—
L	Ssu ribosomal protein S17P	protein	181	11% helix, 26% strand	V6TVJ7
U	Ribosomal protein S20	protein	74	12% helix, 42% strand	A8B4G0
G	40S ribosomal protein S6	protein	197	20% helix, 19% strand	A8B6L8
F	Ribosomal protein S5	protein	161	52% helix, 5% strand	A8BZD3

Ligands and binding sites

K · Potassium ion · metal · 266 copies · chains d, 2, N, S, Z, A, b, R, O, a, W, E, J, Q, U, B, I, n, G, X, L, C
MG · Magnesium ion · metal · 37 copies · chains N, 2, I, E, G, X, a, b

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	922	0.88	0.90	103	K
2	1165	0.88	0.90	106	K, MG
3	815	0.87	0.90	73	empty
4	1027	0.86	0.87	82	K
5	1090	0.86	0.87	84	K

Interfaces

80 interfaces between chains.

E–2 · 4002 Å² buried · 64 hydrogen bonds · protein-nucleic
2–L · 3498 Å² buried · 72 hydrogen bonds · protein-nucleic
X–2 · 3386 Å² buried · 63 hydrogen bonds · protein-nucleic
2–G · 3380 Å² buried · 67 hydrogen bonds · protein-nucleic
I–2 · 3198 Å² buried · 62 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 15 modified, 1 disulfide (nucleotide modification, disulfide).

Compared structures

7PWF · Cryo-EM structure of small subunit of Giardia lamblia ribosome at 2.9 A resolution · the same entry in another collection · chain B against B, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A8B7H6
Every structure of UniProt A0A644F964
Every structure of UniProt A8BE02
Every structure of UniProt A8BKS8
Every structure of UniProt A8B8Z2
Every structure of UniProt A8BS96
Every structure of UniProt A8BZ58
Every structure of UniProt A8BKC6
Every structure of UniProt A8BMZ1
Every structure of UniProt A8BE86
Every structure of UniProt A8BS79
Every structure of UniProt A8B593
Every structure of UniProt A8BJL1
Every structure of UniProt A8BQZ7
Every structure of UniProt A8B8H7
Every structure of UniProt A8B484
Every structure of UniProt A8BBP3
Every structure of UniProt A8BRG5
Every structure of UniProt A8BRX3
Every structure of UniProt A8B252
Every structure of UniProt A0A644F843
Every structure of UniProt A8B4F3
Every structure of UniProt E2RU83
Every structure of UniProt E2RU77
Every structure of UniProt A8BFE3
Every structure of UniProt V6TVJ7
Every structure of UniProt A8B4G0
Every structure of UniProt A8B6L8
Every structure of UniProt A8BZD3
Elsewhere: RCSB PDB 7PWF · PDBe 7PWF · UniProt A8B7H6 · UniProt A0A644F964 · UniProt A8BE02 · UniProt A8BKS8 · UniProt A8B8Z2 · UniProt A8BS96 · UniProt A8BZ58 · UniProt A8BKC6 · UniProt A8BMZ1 · UniProt A8BE86 · UniProt A8BS79 · UniProt A8B593 · UniProt A8BJL1 · UniProt A8BQZ7 · UniProt A8B8H7 · UniProt A8B484 · UniProt A8BBP3 · UniProt A8BRG5 · UniProt A8BRX3 · UniProt A8B252 · UniProt A0A644F843 · UniProt A8B4F3 · UniProt E2RU83 · UniProt E2RU77 · UniProt A8BFE3 · UniProt V6TVJ7 · UniProt A8B4G0 · UniProt A8B6L8 · UniProt A8BZD3

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