SMTL ID : 7bhp.1

Cryo-EM structure of the human Ebp1 - 80S ribosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

41 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: A.3917, G.4187, U.4188 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: G.85, G.1383, C.1384 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: C.111, C.112, G.156 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: A.113, G.114 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: G.213 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: U.45, U.291 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain A: G.48, U.291 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: U.316, U.4353, U.4354 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain A: A.407, G.409, A.410 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain A: C.414, G.415, U.416, G.417 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain A: G.731, A.732, A.733 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain A: G.369, G.2793 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain A: A.353, U.354 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain A: G.1592, C.1594, U.4556 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain A: G.1633, G.1641, G.4534 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain A: U.1677, C.1678 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain A: C.1879, U.1882 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain A: G.2421, C.2422, A.2423 Chain R: R.127 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain A: A.2551, A.2553 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain A: C.2392, C.2818, U.2819 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain A: U.3778, G.3815 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain A: G.3815, G.4538 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain A: U.3920, G.4184 Chain D: P.206 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain A: A.3902, U.4450, G.4451 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain A: A.2360, C.4560, C.4561 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain A: A.4664, A.4665, G.4666 Chain E: K.373 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain A: G.1864, G.1865 Chain L: N.14 No protein-ligand interaction detected (PLIP) MG.30: 3 residues within 4Å: Chain 5: R.16, T.17 Chain A: G.2320 No protein-ligand interaction detected (PLIP) MG.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain A: A.3903, G.3904 No protein-ligand interaction detected (PLIP) MG.33: 4 residues within 4Å: Chain A: G.1887, A.1888, U.1889, G.1890 No protein-ligand interaction detected (PLIP) MG.34: 1 residues within 4Å: Chain B: A.83 No protein-ligand interaction detected (PLIP) MG.35: 2 residues within 4Å: Chain B: G.64, G.65 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain B: G.41, A.42 No protein-ligand interaction detected (PLIP) MG.37: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.38: 3 residues within 4Å: Chain A: U.2293 Chain C: C.19, A.20 No protein-ligand interaction detected (PLIP) MG.39: 1 residues within 4Å: Chain C: G.15 No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain C: U.100, C.101 No protein-ligand interaction detected (PLIP) MG.42: 2 residues within 4Å: Chain A: C.2792 Chain c: K.48 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.41: 5 residues within 4Å: Chain a: C.19, R.21, C.22, C.34, C.37 5 PLIP interactions: 5 interactions with chain a Metal complexes: a:C.19, a:R.21, a:C.22, a:C.34, a:C.37 ZN.43: 4 residues within 4Å: Chain d: C.96, C.99, C.110, C.115 3 PLIP interactions: 3 interactions with chain d Metal complexes: d:C.96, d:C.110, d:C.115 ZN.44: 5 residues within 4Å: Chain e: C.12, C.15, Q.19, C.72, C.77 3 PLIP interactions: 3 interactions with chain e Metal complexes: e:C.12, e:C.72, e:C.77 ZN.45: 5 residues within 4Å: Chain f: C.39, C.42, C.57, S.59, C.60 4 PLIP interactions: 4 interactions with chain f Metal complexes: f:C.42, f:C.57, f:S.59, f:C.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhaskar, V. et al., Dynamic association of human Ebp1 with the ribosome. Rna (2021)

Release Date

2021-02-03

Peptides

60S ribosomal protein L8: D
60S ribosomal protein L3: E
60S ribosomal protein L4: F
60S ribosomal protein L5: G
60S ribosomal protein L6: H
60S ribosomal protein L7: I
60S ribosomal protein L7a: J
60S ribosomal protein L9: K
60S ribosomal protein L10-like: L
60S ribosomal protein L11: M
60S ribosomal protein L13: N
60S ribosomal protein L14: O
60S ribosomal protein L15: P
60S ribosomal protein L13a: Q
60S ribosomal protein L17: R
60S ribosomal protein L18: S
60S ribosomal protein L19: T
60S ribosomal protein L18a: U
60S ribosomal protein L21: V
60S ribosomal protein L22: W
60S ribosomal protein L24: X
60S ribosomal protein L23a: Y
60S ribosomal protein L26: Z
60S ribosomal protein L27: 0
60S ribosomal protein L27a: 1
60S ribosomal protein L29: 2
60S ribosomal protein L30: 3
60S ribosomal protein L31: 4
60S ribosomal protein L32: 5
60S ribosomal protein L35a: 6
60S ribosomal protein L34: 7
60S ribosomal protein L35: 8
60S ribosomal protein L36: 9
60S ribosomal protein L37: a
60S ribosomal protein L38: b
60S ribosomal protein L39: c
Ubiquitin-60S ribosomal protein L40: d
60S ribosomal protein L36a: e
60S ribosomal protein L37a: f
60S ribosomal protein L28: g
Proliferation-associated protein 2G4: h

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
LA

E
LB

F
LC

G
LD

H
LE

I
LF

J
LG

K
LH

L
LI

M
LJ

N
LL

O
LM

P
LN

Q
LO

R
LP

S
LQ

T
LR

U
LS

V
LT

W
LU

X
LW

Y
LX

Z
LY

0
LZ

1
La

2
Lb

3
Lc

4
Ld

5
Le

6
Lf

7
Lg

8
Lh

9
Li

a
Lj

b
Lk

c
Ll

d
Lm

e
Lo

f
Lp

g
Lr

h
A

60S ribosomal protein L8

60S ribosomal protein L3

60S ribosomal protein L4

60S ribosomal protein L5

60S ribosomal protein L6

60S ribosomal protein L7

60S ribosomal protein L7a

60S ribosomal protein L9

60S ribosomal protein L10-like

60S ribosomal protein L11

60S ribosomal protein L13

60S ribosomal protein L14

60S ribosomal protein L15

60S ribosomal protein L13a

60S ribosomal protein L17

60S ribosomal protein L18

60S ribosomal protein L19

60S ribosomal protein L18a

60S ribosomal protein L21

60S ribosomal protein L22

60S ribosomal protein L24

60S ribosomal protein L23a

60S ribosomal protein L26

60S ribosomal protein L27

60S ribosomal protein L27a

60S ribosomal protein L29

60S ribosomal protein L30

60S ribosomal protein L31

60S ribosomal protein L32

60S ribosomal protein L35a

60S ribosomal protein L34

60S ribosomal protein L35

60S ribosomal protein L36

60S ribosomal protein L37

60S ribosomal protein L38

60S ribosomal protein L39

Ubiquitin-60S ribosomal protein L40

60S ribosomal protein L36a

60S ribosomal protein L37a

60S ribosomal protein L28

Proliferation-associated protein 2G4

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