SMTL ID : 8xi2.1

Cryo-EM structure of the Chlamydomonas C* complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.60 Å

Oligo State

hetero-1-1-1-4-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x C- C- G- A- A- C- G: RNA (5'-R(P*CP*CP*GP*AP*AP*CP*G)-3')(Non-covalent)

C-C-G-A-A-C-G.1: 20 residues within 4Å: Chain A: K.513, R.603, Y.656, R.657, Y.660, S.1369, K.1370, M.1371, P.1372, Y.1612, G.1628, K.1629 Chain B: U.42, U.43, U.44, U.45, A.46 Chain E: G.64, G.65 Ligands: MG.4 Protein-ligand interaction information (PLIP) not available

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

GTP.2: 21 residues within 4Å: Chain C: L.146, H.147, H.148, G.149, K.150, T.151, T.152, Q.177, R.179, A.191, M.192, S.193, G.220, K.272, D.274, R.275, E.279, A.327, A.328, Q.329 Ligands: MG.3 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:H.147, C:G.149, C:K.150, C:T.151, C:T.152, C:T.152, C:Q.177, C:D.182, C:S.193, C:G.220, C:K.272, C:K.272, C:E.279, C:Q.329, C:Q.329 Salt bridges: C:H.147, C:K.150, C:K.150, C:R.179, C:D.274

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

MG.3: 5 residues within 4Å: Chain C: T.151, D.182, S.193, D.217 Ligands: GTP.2 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.151, C:S.193 MG.4: 4 residues within 4Å: Chain E: G.47, G.65, U.67 Ligands: C-C-G-A-A-C-G.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain E: A.46, G.47, U.67 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain E: G.68 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain E: G.64, G.65, G.68 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain E: C.48, A.49, U.67 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain E: G.47, C.48, G.64 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain E: A.21 Chain V: C.166, C.174, C.180, H.184 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.166, V:C.174, V:C.180, V:H.184 ZN.11: 4 residues within 4Å: Chain V: C.23, C.26, C.80, C.83 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:C.26, V:C.80, V:C.83 ZN.12: 4 residues within 4Å: Chain W: C.102, C.120, C.141, C.144 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:C.102, W:C.120, W:C.141, W:C.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, Y. et al., Structure of a Step II catalytically activated spliceosome form Chlamydomonas reinhardtii. To Be Published

Release Date

2024-10-09

Peptides

MPN domain-containing protein: A
Elongation factor Tu, chloroplastic: C
U5-40K: D
Pre-mRNA-processing factor 19: FGHI
Small nuclear ribonucleoprotein Sm D3: J
Small nuclear ribonucleoprotein G: K
Small nuclear ribonucleoprotein E: L
Sm protein F: M
Small nuclear ribonucleoprotein Sm D2: N
Small nuclear ribonucleoprotein Sm D1: O
Sm domain-containing protein: P
Syf1: Q
Crooked neck protein: R
Cwf15/Cwc15 cell cycle control protein: S
PPIase cyclophilin-type domain-containing protein: T
PLRG1: U
Rbm22: V
G10 protein: W
SKI-interacting protein SKIP SNW domain-containing protein: X
Peptidyl-prolyl cis-trans isomerase: Z
Prp17: 0
Cdc5L: 1
Pre-mRNA-splicing factor SPF27: 2
CWF21 domain-containing protein: 3
MI domain-containing protein: 4
Intron-binding protein aquarius: 5

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
E

F
q

G
r

H
s

I
t

J
a

K
g

L
e

M
f

N
d

O
c

P
b

Q
I

R
J

S
P

T
M

U
T

V
O

W
N

X
R

Z
S

0
W

1
L

2
K

3
U

4
V

5
Q

MPN domain-containing protein

Elongation factor Tu, chloroplastic

U5-40K

Pre-mRNA-processing factor 19

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein E

Sm protein F

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein Sm D1

Sm domain-containing protein

Syf1

Crooked neck protein

Cwf15/Cwc15 cell cycle control protein

PPIase cyclophilin-type domain-containing protein

PLRG1

Rbm22

G10 protein

SKI-interacting protein SKIP SNW domain-containing protein

Peptidyl-prolyl cis-trans isomerase

Prp17

Cdc5L

Pre-mRNA-splicing factor SPF27

CWF21 domain-containing protein

MI domain-containing protein

Intron-binding protein aquarius