7OII image
Deposition Date 2021-05-11
Release Date 2022-01-19
Last Version Date 2025-03-12
Entry Detail
PDB ID:
7OII
Keywords:
RIBOSOME
Title:
CspA-70 cotranslational folding intermediate 2
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7OII validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:A (auth: 1)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:B (auth: 2)
Chain Length:1534
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:C (auth: 3)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:AB (auth: 4)
Chain Length:6
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cold-shock DNA-binding protein family
Gene (Uniprot):SAMN04489716_7730
Chain IDs:CB (auth: B)
Chain Length:39
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A1H2D2H5 Pfam ID:PF00313
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:D (auth: C)
Chain Length:271
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:E (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60438 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:F (auth: E)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60723 Pfam ID:PF00573
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:G (auth: F)
Chain Length:225
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:H (auth: G)
Chain Length:175
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:I (auth: H)
Chain Length:205
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:J (auth: I)
Chain Length:156
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AA10 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:K (auth: J)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY3 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:L (auth: K)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02413 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:M (auth: L)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY7 Pfam ID:PF00252
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:N (auth: M)
Chain Length:119
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:O (auth: N)
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:P (auth: O)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:Q (auth: P)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:R (auth: Q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG48 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:S (auth: R)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P61175 Pfam ID:PF00237
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:T (auth: S)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:U (auth: T)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:V (auth: U)
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P68919 Pfam ID:PF01386
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:W (auth: V)
Chain Length:66
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Chain IDs:X (auth: W)
Chain Length:83
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:Y (auth: X)
Chain Length:62
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:Z (auth: Y)
Chain Length:58
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:AA (auth: Z)
Chain Length:66
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A4P8CB21 Pfam ID:PF01197
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:BA (auth: a)
Chain Length:56
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:CA (auth: b)
Chain Length:39
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A1X3IVN5 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:DA (auth: c)
Chain Length:271
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7P5 Pfam ID:PF00468
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:EA (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:FA (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q6 Pfam ID:PF00444
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:GA (auth: f)
Chain Length:225
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:HA (auth: g)
Chain Length:175
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:IA (auth: h)
Chain Length:205
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:JA (auth: i)
Chain Length:156
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:KA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:LA (auth: k)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02359 Pfam ID:PF00177
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:MA (auth: l)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:NA (auth: m)
Chain Length:119
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:OA (auth: n)
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:PA (auth: o)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A5I5F5V9 Pfam ID:PF00411
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:QA (auth: p)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:RA (auth: q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:SA (auth: r)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:TA (auth: s)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:UA (auth: t)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SYP2 Pfam ID:PF00886
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:VA (auth: u)
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:WA (auth: v)
Chain Length:66
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:XA (auth: w)
Chain Length:83
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:YA (auth: x)
Chain Length:62
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Chain IDs:ZA (auth: y)
Chain Length:58
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:tRNA-Leu
Chain IDs:BB (auth: z)
Chain Length:66
Number of Molecules:1
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
0TD QA ASP modified residue
2MG B G modified residue
4OC B C modified residue
5MC B C modified residue
G7M B G modified residue
MA6 B A modified residue
PSU B U modified residue
UR3 B U modified residue
Ligand Molecules
MG
ZN
Primary Citation
A switch from alpha-helical to beta-strand conformation during co-translational protein folding.
Embo J. 41 e109175 e109175 (2022)
PMID: 34994471 DOI: 10.15252/embj.2021109175

Abstact

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.

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Protein

Chemical

Disease

Primary Citation of related structures
7OII