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- PDB-6enf: Cryo-EM structure of a polyproline-stalled ribosome in the absenc... -

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Entry
Database: PDB / ID: 6enf
TitleCryo-EM structure of a polyproline-stalled ribosome in the absence of EF-P
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • RNA (5'-R(P*CP*CP*G)-3'), mRNA
  • proline tRNA
KeywordsRIBOSOME / Proline / EF-P / ribosome / nascent chain
Function / homologyRibosomal protein L4 domain superfamily / Ribosomal protein L15 / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L25 / Ribosomal protein L29/L35 superfamily ...Ribosomal protein L4 domain superfamily / Ribosomal protein L15 / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L25 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L21-like / Ribosomal protein L31 type A / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein L28/L24 / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S8 superfamily / L21-like superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein L33 superfamily / Ribosomal protein L14P, conserved site / Ribosomal protein L25, short-form / Ribosomal protein L6, alpha-beta domain / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L18e/L15P / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Ribosomal protein L34, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L16, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S21 superfamily / Ribosomal protein L19 superfamily / Ribosomal protein S5 signature. / Ribosomal protein S20 / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / KH domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal L32p protein family / Ribosomal protein L35 / Ribosomal protein S7 signature. / S4 domain / Ribosomal L25p family / Ribosomal protein S6 / Ribosomal protein L19 / Ribosomal protein L31 / Ribosomal protein L17 / Ribosomal protein S21 / Ribosomal protein L23 signature. / Ribosomal protein S8 signature. / Ribosomal L27 protein / Ribosomal protein L22 signature. / Ribosomal protein L29 signature.
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsHuter, P. / Arenz, S. / Wilson, D.N.
CitationJournal: Mol. Cell / Year: 2017
Title: Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P.
Authors: Paul Huter / Stefan Arenz / Lars V Bock / Michael Graf / Jan Ole Frister / Andre Heuer / Lauri Peil / Agata L Starosta / Ingo Wohlgemuth / Frank Peske / Jiří Nováček / Otto Berninghausen / Helmut Grubmüller / Tanel Tenson / Roland Beckmann / Marina V Rodnina / Andrea C Vaiana / Daniel N Wilson
Abstract: Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or ...Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyl-tRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 4, 2017 / Release: Nov 22, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 22, 2017Structure modelrepositoryInitial release
1.1Jan 31, 2018Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
a: 16S ribosomal RNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
u: 30S ribosomal protein S21
v: RNA (5'-R(P*CP*CP*G)-3'), mRNA
A: 23S ribosomal RNA
B: 5S ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
6: 50S ribosomal protein L31
x: proline tRNA


Theoretical massNumber of molelcules
Total (without water)2,122,17453
Polyers2,122,17453
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)256490
ΔGint (kcal/M)-2193
Surface area (Å2)771850
MethodPISA

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Components

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RNA chain , 5 types, 5 molecules avABx

#1: RNA chain 16S ribosomal RNA /


Mass: 498725.406 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1114277939
#22: RNA chain RNA (5'-R(P*CP*CP*G)-3'), mRNA


Mass: 910.612 Da / Num. of mol.: 1 / Source: (synth.) Escherichia coli (E. coli)
#23: RNA chain 23S ribosomal RNA /


Mass: 941305.250 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 802133627
#24: RNA chain 5S ribosomal RNA /


Mass: 38813.133 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1213441078
#53: RNA chain proline tRNA


Mass: 24846.746 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1231762938

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30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu

#2: Protein/peptide 30S ribosomal protein S2 / / Small ribosomal subunit protein uS2


Mass: 24253.943 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V0
#3: Protein/peptide 30S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 23078.785 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V3
#4: Protein/peptide 30S ribosomal protein S4 / / Small ribosomal subunit protein uS4


Mass: 23383.002 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V8
#5: Protein/peptide 30S ribosomal protein S5 / / Small ribosomal subunit protein uS5


Mass: 16532.088 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W1
#6: Protein/peptide 30S ribosomal protein S6 / / Small ribosomal subunit protein bS6


Mass: 11669.371 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#7: Protein/peptide 30S ribosomal protein S7 / / Small ribosomal subunit protein uS7


Mass: 16861.523 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359
#8: Protein/peptide 30S ribosomal protein S8 / / Small ribosomal subunit protein uS8


Mass: 14015.361 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W7
#9: Protein/peptide 30S ribosomal protein S9 / / Small ribosomal subunit protein uS9


Mass: 14554.882 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7X3
#10: Protein/peptide 30S ribosomal protein S10 / / Small ribosomal subunit protein uS10


Mass: 11196.988 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R5
#11: Protein/peptide 30S ribosomal protein S11 / / Small ribosomal subunit protein uS11


Mass: 12388.068 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9
#12: Protein/peptide 30S ribosomal protein S12 / / Small ribosomal subunit protein uS12


Mass: 13636.961 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3
#13: Protein/peptide 30S ribosomal protein S13 / / Small ribosomal subunit protein uS13


Mass: 12625.753 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S9
#14: Protein/peptide 30S ribosomal protein S14 / / Small ribosomal subunit protein uS14


Mass: 11546.442 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsN, b3307, JW3269 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG59
#15: Protein/peptide 30S ribosomal protein S15 / / Small ribosomal subunit protein uS15


Mass: 10159.621 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ4
#16: Protein/peptide 30S ribosomal protein S16 / / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T3
#17: Protein/peptide 30S ribosomal protein S17 / / Small ribosomal subunit protein uS17


Mass: 9263.946 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG63
#18: Protein/peptide 30S ribosomal protein S18 / / Small ribosomal subunit protein bS18


Mass: 7606.768 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T7
#19: Protein/peptide 30S ribosomal protein S19 / / Small ribosomal subunit protein uS19


Mass: 9057.626 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U3
#20: Protein/peptide 30S ribosomal protein S20 / / Small ribosomal subunit protein bS20


Mass: 9506.190 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U7
#21: Protein/peptide 30S ribosomal protein S21 / / Small ribosomal subunit protein bS21


Mass: 7763.073 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68679

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50S ribosomal protein ... , 28 types, 28 molecules CDEFGJKLMNOPQRSTUVWXYZ012346

#25: Protein/peptide 50S ribosomal protein L2 / / Large ribosomal subunit protein uL2


Mass: 29663.244 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60422
#26: Protein/peptide 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#27: Protein/peptide 50S ribosomal protein L4 / / Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60723
#28: Protein/peptide 50S ribosomal protein L5 / / Large ribosomal subunit protein uL5


Mass: 20073.234 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P62399
#29: Protein/peptide 50S ribosomal protein L6 / / Large ribosomal subunit protein uL6


Mass: 18801.598 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG55
#30: Protein/peptide 50S ribosomal protein L13 / / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AA10
#31: Protein/peptide 50S ribosomal protein L14 / / Large ribosomal subunit protein uL14


Mass: 13451.910 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY3
#32: Protein/peptide 50S ribosomal protein L15 / / Large ribosomal subunit protein uL15


Mass: 14877.273 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02413
#33: Protein/peptide 50S ribosomal protein L16 / / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY7
#34: Protein/peptide 50S ribosomal protein L17 / / Large ribosomal subunit protein bL17


Mass: 13721.938 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG44
#35: Protein/peptide 50S ribosomal protein L18 / / Large ribosomal subunit protein uL18


Mass: 12663.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0C018
#36: Protein/peptide 50S ribosomal protein L19 / / Large ribosomal subunit protein bL19


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7K6
#37: Protein/peptide 50S ribosomal protein L20 / / Large ribosomal subunit protein bL20


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L3
#38: Protein/peptide 50S ribosomal protein L21 / / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG48
#39: Protein/peptide 50S ribosomal protein L22 / / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P61175
#40: Protein/peptide 50S ribosomal protein L23 / / Large ribosomal subunit protein uL23


Mass: 10546.472 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#41: Protein/peptide 50S ribosomal protein L24 / / Large ribosomal subunit protein uL24


Mass: 11078.874 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60624
#42: Protein/peptide 50S ribosomal protein L25 / / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68919
#43: Protein/peptide 50S ribosomal protein L27 / / Large ribosomal subunit protein bL27


Mass: 8419.629 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8
#44: Protein/peptide 50S ribosomal protein L28 / / Large ribosomal subunit protein bL28


Mass: 8896.354 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M2
#45: Protein/peptide 50S ribosomal protein L29 / / Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M6
#46: Protein/peptide 50S ribosomal protein L30 / / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG51
#47: Protein/peptide 50S ribosomal protein L32 / / Large ribosomal subunit protein bL32


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N4
#48: Protein/peptide 50S ribosomal protein L33 / / Large ribosomal subunit protein bL33


Mass: 5814.842 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N9
#49: Protein/peptide 50S ribosomal protein L34 / / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7P5
#50: Protein/peptide 50S ribosomal protein L35 / / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#51: Protein/peptide 50S ribosomal protein L36 / / Large ribosomal subunit protein bL36-A / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q6
#52: Protein/peptide 50S ribosomal protein L31 / / Large ribosomal subunit protein bL31-A


Mass: 7516.693 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Polyproline stalled ribosome in the absence of elongation factor P
Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53
Source: NATURAL
Molecular weightValue: 3 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 75089 / Symmetry type: POINT
Atomic model buildingRef space: REAL

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