SMTL ID : 7nfx.1

Mammalian ribosome nascent chain complex with SRP and SRP receptor in early state A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain 9: S.56, C.58, V.60, C.61, C.95, C.98 4 PLIP interactions: 4 interactions with chain 9 Metal complexes: 9:C.58, 9:C.61, 9:C.95, 9:C.98 ZN.2: 4 residues within 4Å: Chain c: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain c Metal complexes: c:C.19, c:C.22, c:C.34, c:C.37 ZN.3: 4 residues within 4Å: Chain f: C.20, C.23, C.34, C.39 4 PLIP interactions: 4 interactions with chain f Metal complexes: f:C.20, f:C.23, f:C.34, f:C.39 ZN.4: 5 residues within 4Å: Chain h: C.12, C.15, Q.19, C.72, C.77 4 PLIP interactions: 4 interactions with chain h Metal complexes: h:C.12, h:C.15, h:C.72, h:C.77 ZN.5: 5 residues within 4Å: Chain i: C.39, C.42, C.57, S.59, C.60 4 PLIP interactions: 4 interactions with chain i Metal complexes: i:C.39, i:C.42, i:C.57, i:C.60

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Ligands: GTP.7 Chain o: T.78, Q.93, S.95 2 PLIP interactions: 2 interactions with chain o Metal complexes: o:T.78, o:S.95 MG.9: 4 residues within 4Å: Ligands: GNP.8 Chain q: K.114, T.115, D.138 1 PLIP interactions: 1 interactions with chain q Metal complexes: q:T.115

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.7: 22 residues within 4Å: Ligands: MG.6 Chain o: L.72, C.73, D.74, S.75, G.76, K.77, T.78, L.79, T.92, Q.93, T.94, S.95, G.120, N.180, K.181, D.183, S.247, A.248, K.249, G.250, G.251 21 PLIP interactions: 21 interactions with chain o Hydrogen bonds: o:D.74, o:S.75, o:G.76, o:K.77, o:T.78, o:T.92, o:Q.93, o:S.95, o:G.120, o:N.180, o:K.181, o:S.247, o:A.248, o:K.249, o:K.249, o:K.249, o:G.250, o:G.251 Salt bridges: o:K.77, o:K.77, o:D.183

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.8: 16 residues within 4Å: Ligands: MG.9 Chain q: L.109, Q.110, G.111, S.112, G.113, K.114, T.115, T.116, R.141, G.193, K.249, G.274, T.275, G.276, E.277 14 PLIP interactions: 14 interactions with chain q Hydrogen bonds: q:G.111, q:S.112, q:G.113, q:K.114, q:K.114, q:K.114, q:T.115, q:T.115, q:T.116, q:G.193, q:K.249, q:T.275, q:T.275, q:E.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, J.H. et al., Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER. Sci Adv (2021)

Release Date

2021-06-02

Peptides

uL2: E
uL3: F
60S ribosomal protein L4: G
60S ribosomal protein L5: H
60S ribosomal protein L6: I
uL30: J
60S ribosomal protein L7a: K
60S ribosomal protein L9: L
60S ribosomal protein L10: M
Ribosomal protein L11: N
60S ribosomal protein L13: O
60S ribosomal protein L14: P
Ribosomal protein L15: Q
uL13: R
uL22: S
eL18: T
60S RIBOSOMAL PROTEIN EL19: U
eL20: V
eL21: W
Ribosomal protein L22: X
Ribosomal protein L23: Y
Ribosomal protein L24: Z
uL23: 0
Ribosomal protein L26: 1
60S ribosomal protein L27: 2
uL15: 3
60S ribosomal protein L29: 4
eL30: 5
eL31: 6
eL32: 7
eL33: 8
60S ribosomal protein L34: 9
uL29: a
eL36: b
Ribosomal protein L37: c
eL38: d
eL39: e
60S RIBOSOMAL PROTEIN EL40: f
60s ribosomal protein l41: g
eL42: h
eL43: i
Signal recognition particle 19 kDa protein: j
eL28: k
Signal Sequence: l
Signal recognition particle 14 kDa protein: m
Signal recognition particle subunit SRP68: n
Signal recognition particle receptor subunit beta: o
Signal recognition particle 9 kDa protein: p
Signal recognition particle 54 kDa protein: q
Signal recognition particle receptor subunit alpha: r
Signal recognition particle subunit SRP72: s

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

E
A

F
B

G
C

H
D

I
E

J
F

K
G

L
H

M
I

N
J

O
L

P
M

Q
N

R
O

S
P

T
Q

U
R

V
S

W
T

X
U

Y
V

Z
W

0
X

1
Y

2
Z

3
a

4
b

5
c

6
d

7
e

8
f

9
g

a
h

b
i

c
j

d
k

e
l

f
m

g
n

h
o

i
p

j
q

k
r

l
s

m
t

n
u

o
v

p
w

q
x

r
y

s
z

uL2

uL3

60S ribosomal protein L4

60S ribosomal protein L5

60S ribosomal protein L6

uL30

60S ribosomal protein L7a

60S ribosomal protein L9

60S ribosomal protein L10

Ribosomal protein L11

60S ribosomal protein L13

60S ribosomal protein L14

Ribosomal protein L15

uL13

uL22

eL18

60S RIBOSOMAL PROTEIN EL19

eL20

eL21

Ribosomal protein L22

Ribosomal protein L23

Ribosomal protein L24

uL23

Ribosomal protein L26

60S ribosomal protein L27

uL15

60S ribosomal protein L29

eL30

eL31

eL32

eL33

60S ribosomal protein L34

uL29

eL36

Ribosomal protein L37

eL38

eL39

60S RIBOSOMAL PROTEIN EL40

60s ribosomal protein l41

eL42

eL43

Signal recognition particle 19 kDa protein

eL28

Signal Sequence

Signal recognition particle 14 kDa protein

Signal recognition particle subunit SRP68

Signal recognition particle receptor subunit beta

Signal recognition particle 9 kDa protein

Signal recognition particle 54 kDa protein

Signal recognition particle receptor subunit alpha

Signal recognition particle subunit SRP72

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