SMTL ID : 7obr.1

RNC-SRP early complex

Coordinates

PDB Format

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-mer

Ligands

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

MG.1: 1 residues within 4Å: Chain B: U.2551 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain B: U.37, A.38, G.40, C.41 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain B: A.62, G.63, U.333 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: C.83, G.85, G.904, C.905 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain B: U.77 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: A.105, A.106 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: C.112, G.154, G.156 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain B: A.113, G.114 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: A.198, G.241 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain B: A.235 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: U.231, A.235 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: A.300 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain B: U.287, G.288 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain B: U.45, U.291 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain B: U.316, U.2861, U.2862 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Chain B: A.64 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain B: G.356, A.359 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain B: C.414, G.415, U.416, G.417 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain B: A.1678 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain B: C.1701, C.2125 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain B: C.1718, C.1719, A.1736 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain B: G.1729, C.1730, A.1731 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain B: U.1755, G.1818 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain B: G.1822, G.1824 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain B: A.1984, G.1985 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain B: G.1710, A.2091, C.2092 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain B: A.2097, G.2135, U.2136 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain B: C.2100 No protein-ligand interaction detected (PLIP) MG.29: 4 residues within 4Å: Chain B: A.1120, A.1121, G.2101, C.2102 No protein-ligand interaction detected (PLIP) MG.30: 4 residues within 4Å: Chain B: A.2152, A.2153, G.2156, G.2475 No protein-ligand interaction detected (PLIP) MG.31: 2 residues within 4Å: Chain B: C.2164, A.2165 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain B: A.2187, G.2264, A.2265 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain B: U.2267, C.2268, G.2442 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain B: G.2270, C.2272 No protein-ligand interaction detected (PLIP) MG.35: 4 residues within 4Å: Chain B: A.2278, A.2279, U.2280, U.2281 No protein-ligand interaction detected (PLIP) MG.36: 4 residues within 4Å: Chain B: C.2337, U.2340, G.2341, U.2381 No protein-ligand interaction detected (PLIP) MG.37: 5 residues within 4Å: Chain B: G.2325, A.2383, A.2384, C.2385, U.2454 No protein-ligand interaction detected (PLIP) MG.38: 1 residues within 4Å: Chain B: G.3049 No protein-ligand interaction detected (PLIP) MG.39: 2 residues within 4Å: Chain B: C.1199, G.2549 No protein-ligand interaction detected (PLIP) MG.40: 3 residues within 4Å: Chain B: U.2548, C.2701, U.2702 No protein-ligand interaction detected (PLIP) MG.41: 4 residues within 4Å: Chain B: G.40, C.41, U.2551, G.2552 No protein-ligand interaction detected (PLIP) MG.42: 2 residues within 4Å: Chain B: A.2553, U.2697 No protein-ligand interaction detected (PLIP) MG.43: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.44: 3 residues within 4Å: Chain B: U.2556, G.2692 Chain E: P.206 No protein-ligand interaction detected (PLIP) MG.45: 3 residues within 4Å: Chain B: U.35, G.2695, U.2696 No protein-ligand interaction detected (PLIP) MG.46: 4 residues within 4Å: Chain B: U.1238, U.2718, C.2719, A.2721 No protein-ligand interaction detected (PLIP) MG.47: 3 residues within 4Å: Chain B: A.2722, C.2723, G.2725 No protein-ligand interaction detected (PLIP) MG.48: 2 residues within 4Å: Chain B: A.2747 Chain H: A.32 No protein-ligand interaction detected (PLIP) MG.49: 1 residues within 4Å: Chain B: A.2789 No protein-ligand interaction detected (PLIP) MG.50: 1 residues within 4Å: Chain B: G.2837 No protein-ligand interaction detected (PLIP) MG.51: 1 residues within 4Å: Chain B: C.2894 No protein-ligand interaction detected (PLIP) MG.52: 2 residues within 4Å: Chain B: G.1154, G.3042 No protein-ligand interaction detected (PLIP) MG.53: 4 residues within 4Å: Chain B: A.1153, G.1154, A.3043 Chain E: N.205 No protein-ligand interaction detected (PLIP) MG.54: 2 residues within 4Å: Chain B: A.3041, G.3042 No protein-ligand interaction detected (PLIP) MG.55: 6 residues within 4Å: Chain B: G.2901, A.2902, U.2903, C.2951, C.2952, U.2953 No protein-ligand interaction detected (PLIP) MG.56: 3 residues within 4Å: Chain B: G.842, A.2902, U.2953 No protein-ligand interaction detected (PLIP) MG.57: 2 residues within 4Å: Chain B: A.2987, A.2988 No protein-ligand interaction detected (PLIP) MG.58: 3 residues within 4Å: Chain B: U.2468, C.2469, U.3005 No protein-ligand interaction detected (PLIP) MG.59: 4 residues within 4Å: Chain B: G.2959, G.3030, U.3064, U.3065 No protein-ligand interaction detected (PLIP) MG.60: 4 residues within 4Å: Chain B: C.2961, C.3027, G.3028, U.3029 No protein-ligand interaction detected (PLIP) MG.61: 1 residues within 4Å: Chain B: G.3023 No protein-ligand interaction detected (PLIP) MG.62: 5 residues within 4Å: Chain B: G.2534, G.2535, U.3029, G.3030, A.3031 No protein-ligand interaction detected (PLIP) MG.63: 2 residues within 4Å: Chain B: G.1113, U.3034 No protein-ligand interaction detected (PLIP) MG.64: 2 residues within 4Å: Chain B: G.3035, G.3036 No protein-ligand interaction detected (PLIP) MG.65: 2 residues within 4Å: Chain B: G.2451, G.3046 No protein-ligand interaction detected (PLIP) MG.66: 4 residues within 4Å: Chain B: U.1112, G.1113, C.1115, U.3064 No protein-ligand interaction detected (PLIP) MG.67: 1 residues within 4Å: Chain B: G.1116 No protein-ligand interaction detected (PLIP) MG.68: 3 residues within 4Å: Chain B: A.3189, U.3190, A.3215 No protein-ligand interaction detected (PLIP) MG.69: 3 residues within 4Å: Chain B: U.3190, A.3213, G.3214 No protein-ligand interaction detected (PLIP) MG.70: 2 residues within 4Å: Chain B: U.3193, C.3206 No protein-ligand interaction detected (PLIP) MG.71: 2 residues within 4Å: Chain B: G.3158, A.3159 No protein-ligand interaction detected (PLIP) MG.72: 4 residues within 4Å: Chain B: G.3259, U.3260, U.3370, C.3372 No protein-ligand interaction detected (PLIP) MG.73: 2 residues within 4Å: Chain B: G.1396, A.1397 No protein-ligand interaction detected (PLIP) MG.74: 2 residues within 4Å: Chain B: C.839, U.1177 No protein-ligand interaction detected (PLIP) MG.75: 2 residues within 4Å: Chain B: G.856, C.1654 No protein-ligand interaction detected (PLIP) MG.76: 4 residues within 4Å: Chain B: U.3135, A.3173, G.3174 Chain F: K.372 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:K.372 MG.77: 3 residues within 4Å: Chain B: G.850, C.2500, A.2501 No protein-ligand interaction detected (PLIP) MG.78: 2 residues within 4Å: Chain B: C.846, G.2516 No protein-ligand interaction detected (PLIP) MG.79: 2 residues within 4Å: Chain B: G.2533, G.2535 No protein-ligand interaction detected (PLIP) MG.80: 2 residues within 4Å: Chain B: A.1671, G.1672 No protein-ligand interaction detected (PLIP) MG.81: 1 residues within 4Å: Chain 3: I.21 No protein-ligand interaction detected (PLIP) MG.82: 3 residues within 4Å: Chain B: G.1033, C.1349, U.1350 No protein-ligand interaction detected (PLIP) MG.83: 3 residues within 4Å: Chain B: G.2413, G.2451, U.3047 No protein-ligand interaction detected (PLIP) MG.84: 4 residues within 4Å: Chain B: A.2542, G.2543, C.2955, G.2956 No protein-ligand interaction detected (PLIP) MG.85: 1 residues within 4Å: Chain B: G.1708 No protein-ligand interaction detected (PLIP) MG.86: 3 residues within 4Å: Chain B: U.2134, G.2135, G.2138 No protein-ligand interaction detected (PLIP) MG.87: 4 residues within 4Å: Chain B: G.1175, A.1200, G.1201, U.2550 No protein-ligand interaction detected (PLIP) MG.88: 2 residues within 4Å: Chain B: A.1239, A.1240 No protein-ligand interaction detected (PLIP) MG.89: 1 residues within 4Å: Chain B: U.2914 No protein-ligand interaction detected (PLIP) MG.90: 2 residues within 4Å: Chain B: A.1039, C.1042 No protein-ligand interaction detected (PLIP) MG.91: 2 residues within 4Å: Chain B: A.1044, G.1172 No protein-ligand interaction detected (PLIP) MG.92: 3 residues within 4Å: Chain 7: D.64 Chain B: U.838, A.843 No protein-ligand interaction detected (PLIP) MG.93: 6 residues within 4Å: Chain 7: I.63, D.64 Chain B: U.840, A.843, G.1381, C.1382 No protein-ligand interaction detected (PLIP) MG.94: 3 residues within 4Å: Chain B: U.1109, U.2281, A.2282 No protein-ligand interaction detected (PLIP) MG.95: 3 residues within 4Å: Chain B: C.1187, G.1188, G.1588 No protein-ligand interaction detected (PLIP) MG.96: 3 residues within 4Å: Chain B: C.1187, G.1210 Chain T: N.7 No protein-ligand interaction detected (PLIP) MG.97: 1 residues within 4Å: Chain B: G.1656 No protein-ligand interaction detected (PLIP)

5 x ZN: ZINC ION(Non-covalent)

ZN.98: 5 residues within 4Å: Chain 9: S.56, C.58, C.61, C.95, C.98 4 PLIP interactions: 4 interactions with chain 9 Metal complexes: 9:S.56, 9:C.58, 9:C.95, 9:C.98 ZN.99: 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.100: 5 residues within 4Å: Chain f: C.20, C.23, C.34, C.39, T.42 4 PLIP interactions: 4 interactions with chain f Metal complexes: f:C.20, f:C.23, f:C.34, f:C.39 ZN.101: 5 residues within 4Å: Chain h: C.12, C.15, C.72, C.77, S.79 4 PLIP interactions: 4 interactions with chain h Metal complexes: h:C.12, h:C.15, h:C.72, h:C.77 ZN.102: 4 residues within 4Å: Chain i: C.39, C.42, C.57, C.60 4 PLIP interactions: 4 interactions with chain i Metal complexes: i:C.39, i:C.42, i:C.57, i:C.60

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.103: 16 residues within 4Å: Chain p: L.109, Q.110, G.111, S.112, G.113, K.114, T.115, T.116, K.120, R.141, K.249, D.251, G.274, T.275, G.276, E.277 14 PLIP interactions: 14 interactions with chain p Hydrogen bonds: p:G.111, p:S.112, p:G.113, p:K.114, p:T.115, p:T.115, p:T.116, p:K.120, p:R.141, p:K.249 Salt bridges: p:K.114, p:R.141, p:D.251, p:E.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jomaa, A. et al., Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle. Cell Rep (2021)

Release Date

2021-07-21

Peptides

60S ribosomal protein L8: 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
60S ribosomal protein L13a: R
uL22: S
eL18: T
60S RIBOSOMAL PROTEIN EL19: U
60S ribosomal protein L18a: 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
60S ribosomal protein L30: 5
eL31: 6
eL32: 7
eL33: 8
60S ribosomal protein L34: 9
uL29: a
60S ribosomal protein L36: 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: j
eL28: k
Dipeptidyl aminopeptidase B: l
Signal recognition particle 14 kDa protein: m
Signal recognition particle subunit SRP68: n
Signal recognition particle 9 kDa protein: o
Signal recognition particle 54 kDa protein: p
Signal recognition particle subunit SRP72: q

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
w

p
x

q
z

60S ribosomal protein L8

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

60S ribosomal protein L13a

uL22

eL18

60S RIBOSOMAL PROTEIN EL19

60S ribosomal protein L18a

eL21

Ribosomal protein L22

Ribosomal protein L23

Ribosomal protein L24

uL23

Ribosomal protein L26

60S ribosomal protein L27

uL15

60S ribosomal protein L29

60S ribosomal protein L30

eL31

eL32

eL33

60S ribosomal protein L34

uL29

60S ribosomal protein L36

Ribosomal protein L37

eL38

eL39

60S RIBOSOMAL PROTEIN EL40

60s ribosomal protein l41

eL42

eL43

Signal recognition particle 19

eL28

Dipeptidyl aminopeptidase B

Signal recognition particle 14 kDa protein

Signal recognition particle subunit SRP68

Signal recognition particle 9 kDa protein

Signal recognition particle 54 kDa protein

Signal recognition particle subunit SRP72

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