7OT5

CspA-70 cotranslational folding intermediate 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 


This is version 1.2 of the entry. See complete history


Literature

A switch from alpha-helical to beta-strand conformation during co-translational protein folding.

Agirrezabala, X.Samatova, E.Macher, M.Liutkute, M.Maiti, M.Gil-Carton, D.Novacek, J.Valle, M.Rodnina, M.V.

(2022) EMBO J 41: e109175-e109175

  • DOI: https://doi.org/10.15252/embj.2021109175
  • Primary Citation of Related Structures:  
    7NWW, 7OIF, 7OIG, 7OII, 7OT5

  • PubMed Abstract: 

    Cellular proteins begin to fold as they emerge from the ribosome. The folding landscape of nascent chains is not only shaped by their amino acid sequence but also by the interactions with the ribosome. Here, we combine biophysical methods with cryo-EM structure determination to show that folding of a β-barrel protein begins with formation of a dynamic α-helix inside the ribosome. As the growing peptide reaches the end of the tunnel, the N-terminal part of the nascent chain refolds to a β-hairpin structure that remains dynamic until its release from the ribosome. Contacts with the ribosome and structure of the peptidyl transferase center depend on nascent chain conformation. These results indicate that proteins may start out as α-helices inside the tunnel and switch into their native folds only as they emerge from the ribosome. Moreover, the correlation of nascent chain conformations with reorientation of key residues of the ribosomal peptidyl-transferase center suggest that protein folding could modulate ribosome activity.


  • Organizational Affiliation

    CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth C]271Escherichia coliMutation(s): 0 
Gene Names: rplB
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth D]209Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth E]201Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth F]177Escherichia coliMutation(s): 0 
Gene Names: rplE
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth G]175Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9I [auth H]149Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13J [auth I]142Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14K [auth J]123Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15L [auth K]144Escherichia coliMutation(s): 0 
UniProt
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16M [auth L]136Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17N [auth M]119Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18O [auth N]116Escherichia coliMutation(s): 0 
Gene Names: rplR
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19P [auth O]114Escherichia coliMutation(s): 0 
Gene Names: rplS
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20Q [auth P]117Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21R [auth Q]103Escherichia coliMutation(s): 0 
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Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22S [auth R]110Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23T [auth S]94Escherichia coliMutation(s): 0 
Gene Names: rplWECPG_02638
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24U [auth T]103Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25V [auth U]94Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27W [auth V]81Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28X [auth W]77Escherichia coliMutation(s): 0 
Gene Names: rpmB
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29Y [auth X]62Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Z [auth Y]58Escherichia coliMutation(s): 0 
Gene Names: rpmD
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31AA [auth Z]66Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32BA [auth a]56Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33CA [auth b]52Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34DA [auth c]46Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35EA [auth d]64Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36FA [auth e]38Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2GA [auth f]225Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3HA [auth g]208Escherichia coliMutation(s): 0 
Gene Names: rpsCG4V09_06545NCTC9094_00425
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4IA [auth h]205Escherichia coliMutation(s): 0 
Gene Names: rpsD
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5JA [auth i]156Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6KA [auth j]104Escherichia coliMutation(s): 0 
Gene Names: D9J60_11985
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7LA [auth k]151Escherichia coliMutation(s): 0 
Gene Names: rpsG
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8MA [auth l]129Escherichia coliMutation(s): 0 
Gene Names: rpsH
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9NA [auth m]127Escherichia coliMutation(s): 0 
Gene Names: rpsI
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10OA [auth n]99Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11PA [auth o]117Escherichia coliMutation(s): 0 
Gene Names: rpsK
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12QA [auth p]123Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13RA [auth q]116Escherichia coliMutation(s): 0 
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Find proteins for B7LHZ5 (Escherichia coli (strain 55989 / EAEC))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14SA [auth r]100Escherichia coliMutation(s): 0 
Gene Names: rpsN
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15TA [auth s]88Escherichia coliMutation(s): 0 
Gene Names: rpsO
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16UA [auth t]82Escherichia coliMutation(s): 0 
Gene Names: rpsP
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17VA [auth u]80Escherichia coliMutation(s): 0 
Gene Names: rpsQ
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18WA [auth v]66Escherichia coliMutation(s): 0 
Gene Names: rpsR
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S19XA [auth w]83Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20YA [auth x]86Escherichia coliMutation(s): 0 
Gene Names: rpsT
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21ZA [auth y]70Escherichia coliMutation(s): 0 
Gene Names: rpsU
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Cold shock protein CspBCB [auth B]66Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S rRNAA [auth 1]2,903Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
16S rRNAB [auth 2]1,534Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth 3]120Escherichia coli
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Entity ID: 53
MoleculeChains LengthOrganismImage
mRNAAB [auth 4]6Escherichia coli
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Entity ID: 54
MoleculeChains LengthOrganismImage
tRNA-LeuBB [auth z]85Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AQ [auth Z],
DQ [auth e]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth 1]
AD [auth 1]
AE [auth 1]
AF [auth 1]
AG [auth 1]
AC [auth 1],
AD [auth 1],
AE [auth 1],
AF [auth 1],
AG [auth 1],
AH [auth 1],
AI [auth 1],
AJ [auth 1],
AK [auth 1],
AL [auth 1],
AM [auth 2],
AN [auth 2],
AO [auth 2],
AP [auth 2],
BC [auth 1],
BD [auth 1],
BE [auth 1],
BF [auth 1],
BG [auth 1],
BH [auth 1],
BI [auth 1],
BJ [auth 1],
BK [auth 1],
BL [auth 1],
BM [auth 2],
BN [auth 2],
BO [auth 2],
BP [auth 2],
BQ [auth a],
CC [auth 1],
CD [auth 1],
CE [auth 1],
CF [auth 1],
CG [auth 1],
CH [auth 1],
CI [auth 1],
CJ [auth 1],
CK [auth 1],
CL [auth 1],
CM [auth 2],
CN [auth 2],
CO [auth 2],
CP [auth 2],
CQ [auth a],
DB [auth 1],
DC [auth 1],
DD [auth 1],
DE [auth 1],
DF [auth 1],
DG [auth 1],
DH [auth 1],
DI [auth 1],
DJ [auth 1],
DK [auth 1],
DL [auth 1],
DM [auth 2],
DN [auth 2],
DO [auth 2],
DP [auth 2],
EB [auth 1],
EC [auth 1],
ED [auth 1],
EE [auth 1],
EF [auth 1],
EG [auth 1],
EH [auth 1],
EI [auth 1],
EJ [auth 1],
EK [auth 1],
EL [auth 2],
EM [auth 2],
EN [auth 2],
EO [auth 2],
EP [auth 2],
EQ [auth h],
FB [auth 1],
FC [auth 1],
FD [auth 1],
FE [auth 1],
FF [auth 1],
FG [auth 1],
FH [auth 1],
FI [auth 1],
FJ [auth 1],
FK [auth 1],
FL [auth 2],
FM [auth 2],
FN [auth 2],
FO [auth 2],
FP [auth 2],
FQ [auth m],
GB [auth 1],
GC [auth 1],
GD [auth 1],
GE [auth 1],
GF [auth 1],
GG [auth 1],
GH [auth 1],
GI [auth 1],
GJ [auth 1],
GK [auth 1],
GL [auth 2],
GM [auth 2],
GN [auth 2],
GO [auth 2],
GP [auth 2],
GQ [auth q],
HB [auth 1],
HC [auth 1],
HD [auth 1],
HE [auth 1],
HF [auth 1],
HG [auth 1],
HH [auth 1],
HI [auth 1],
HJ [auth 1],
HK [auth 1],
HL [auth 2],
HM [auth 2],
HN [auth 2],
HO [auth 2],
HP [auth 2],
HQ [auth z],
IB [auth 1],
IC [auth 1],
ID [auth 1],
IE [auth 1],
IF [auth 1],
IG [auth 1],
IH [auth 1],
II [auth 1],
IJ [auth 1],
IK [auth 1],
IL [auth 2],
IM [auth 2],
IN [auth 2],
IO [auth 2],
IP [auth 2],
IQ [auth z],
JB [auth 1],
JC [auth 1],
JD [auth 1],
JE [auth 1],
JF [auth 1],
JG [auth 1],
JH [auth 1],
JI [auth 1],
JJ [auth 1],
JK [auth 1],
JL [auth 2],
JM [auth 2],
JN [auth 2],
JO [auth 2],
JP [auth 2],
KB [auth 1],
KC [auth 1],
KD [auth 1],
KE [auth 1],
KF [auth 1],
KG [auth 1],
KH [auth 1],
KI [auth 1],
KJ [auth 1],
KK [auth 1],
KL [auth 2],
KM [auth 2],
KN [auth 2],
KO [auth 2],
KP [auth 2],
LB [auth 1],
LC [auth 1],
LD [auth 1],
LE [auth 1],
LF [auth 1],
LG [auth 1],
LH [auth 1],
LI [auth 1],
LJ [auth 1],
LK [auth 1],
LL [auth 2],
LM [auth 2],
LN [auth 2],
LO [auth 2],
LP [auth 2],
MB [auth 1],
MC [auth 1],
MD [auth 1],
ME [auth 1],
MF [auth 1],
MG [auth 1],
MH [auth 1],
MI [auth 1],
MJ [auth 1],
MK [auth 1],
ML [auth 2],
MM [auth 2],
MN [auth 2],
MO [auth 2],
MP [auth 2],
NB [auth 1],
NC [auth 1],
ND [auth 1],
NE [auth 1],
NF [auth 1],
NG [auth 1],
NH [auth 1],
NI [auth 1],
NJ [auth 1],
NK [auth 1],
NL [auth 2],
NM [auth 2],
NN [auth 2],
NO [auth 2],
NP [auth 3],
OB [auth 1],
OC [auth 1],
OD [auth 1],
OE [auth 1],
OF [auth 1],
OG [auth 1],
OH [auth 1],
OI [auth 1],
OJ [auth 1],
OK [auth 1],
OL [auth 2],
OM [auth 2],
ON [auth 2],
OO [auth 2],
OP [auth 3],
PB [auth 1],
PC [auth 1],
PD [auth 1],
PE [auth 1],
PF [auth 1],
PG [auth 1],
PH [auth 1],
PI [auth 1],
PJ [auth 1],
PK [auth 1],
PL [auth 2],
PM [auth 2],
PN [auth 2],
PO [auth 2],
PP [auth 3],
QB [auth 1],
QC [auth 1],
QD [auth 1],
QE [auth 1],
QF [auth 1],
QG [auth 1],
QH [auth 1],
QI [auth 1],
QJ [auth 1],
QK [auth 1],
QL [auth 2],
QM [auth 2],
QN [auth 2],
QO [auth 2],
QP [auth 3],
RB [auth 1],
RC [auth 1],
RD [auth 1],
RE [auth 1],
RF [auth 1],
RG [auth 1],
RH [auth 1],
RI [auth 1],
RJ [auth 1],
RK [auth 1],
RL [auth 2],
RM [auth 2],
RN [auth 2],
RO [auth 2],
RP [auth 3],
SB [auth 1],
SC [auth 1],
SD [auth 1],
SE [auth 1],
SF [auth 1],
SG [auth 1],
SH [auth 1],
SI [auth 1],
SJ [auth 1],
SK [auth 1],
SL [auth 2],
SM [auth 2],
SN [auth 2],
SO [auth 2],
SP [auth 3],
TB [auth 1],
TC [auth 1],
TD [auth 1],
TE [auth 1],
TF [auth 1],
TG [auth 1],
TH [auth 1],
TI [auth 1],
TJ [auth 1],
TK [auth 1],
TL [auth 2],
TM [auth 2],
TN [auth 2],
TO [auth 2],
TP [auth 3],
UB [auth 1],
UC [auth 1],
UD [auth 1],
UE [auth 1],
UF [auth 1],
UG [auth 1],
UH [auth 1],
UI [auth 1],
UJ [auth 1],
UK [auth 1],
UL [auth 2],
UM [auth 2],
UN [auth 2],
UO [auth 2],
UP [auth 3],
VB [auth 1],
VC [auth 1],
VD [auth 1],
VE [auth 1],
VF [auth 1],
VG [auth 1],
VH [auth 1],
VI [auth 1],
VJ [auth 1],
VK [auth 1],
VL [auth 2],
VM [auth 2],
VN [auth 2],
VO [auth 2],
VP [auth C],
WB [auth 1],
WC [auth 1],
WD [auth 1],
WE [auth 1],
WF [auth 1],
WG [auth 1],
WH [auth 1],
WI [auth 1],
WJ [auth 1],
WK [auth 1],
WL [auth 2],
WM [auth 2],
WN [auth 2],
WO [auth 2],
WP [auth D],
XB [auth 1],
XC [auth 1],
XD [auth 1],
XE [auth 1],
XF [auth 1],
XG [auth 1],
XH [auth 1],
XI [auth 1],
XJ [auth 1],
XK [auth 1],
XL [auth 2],
XM [auth 2],
XN [auth 2],
XO [auth 2],
XP [auth D],
YB [auth 1],
YC [auth 1],
YD [auth 1],
YE [auth 1],
YF [auth 1],
YG [auth 1],
YH [auth 1],
YI [auth 1],
YJ [auth 1],
YK [auth 1],
YL [auth 2],
YM [auth 2],
YN [auth 2],
YO [auth 2],
YP [auth P],
ZB [auth 1],
ZC [auth 1],
ZD [auth 1],
ZE [auth 1],
ZF [auth 1],
ZG [auth 1],
ZH [auth 1],
ZI [auth 1],
ZJ [auth 1],
ZK [auth 1],
ZL [auth 2],
ZM [auth 2],
ZN [auth 2],
ZO [auth 2],
ZP [auth T]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
0TD
Query on 0TD
QA [auth p]L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.07
MODEL REFINEMENTPHENIX1.18

Structure Validation



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Economy and Competitiveness (MINECO)SpainCTQ2015-73560-JIN
European Research Council (ERC)European Union787926
Ministry of Economy and Competitiveness (MINECO)SpainPGC2018-098996-B-I00

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2024-04-24
    Changes: Data collection, Refinement description