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- PDB-6enj: Polyproline-stalled ribosome in the presence of A+P site tRNA and... -

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Entry
Database: PDB / ID: 6enj
TitlePolyproline-stalled ribosome in the presence of A+P site tRNA and elongation-factor P (EF-P)
DescriptorElongation factor P
(50S ribosomal protein ...) x 29
(30S ribosomal protein ...) x 20
KeywordsRIBOSOME / Polyproline stalled ribosome / cryo-em / elongation-factor P / EF-P / nascent chain
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (3.7 Å resolution / Particle / Single particle)
AuthorsHuter, P. / Wilson, D.N.
CitationMol. Cell, 2017, 68, 515-527.e6

Mol. Cell, 2017, 68, 515-527.e6 Yorodumi Papers
Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P.
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 5, 2017 / Release: Nov 22, 2017

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Assembly

Deposited unit
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
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
w: Elongation factor P
v: mRNA
x: Proline tRNA
7: 50S ribosomal protein L1
9: Proline tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,194,20257
Polyers2,194,08756
Non-polymers1151
Water0
#1


  • idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)275320
ΔGint (kcal/M)-2385
Surface area (Å2)807060
MethodPISA

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Components

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RNA chain , 5 types, 6 molecules ABavx9

#1: RNA chain23S Ribosomal RNA


Mass: 941306.250 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 802133627
#2: RNA chain5S Ribosomal RNA


Mass: 38813.133 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 1213441078
#31: RNA chain16S ribosomal RNA


Mass: 498725.406 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 1114277939
#53: RNA chainmRNA


Mass: 2821.751 Da / Num. of mol.: 1 / Source: (synth.) Escherichia coli
#54: RNA chainProline tRNA


Mass: 24846.746 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli / References: GenBank: 1229082179

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50S ribosomal protein ... , 29 types, 29 molecules CDEFGJKLMN...

#3: Polypeptide(L)50S ribosomal protein L2 / Large ribosomal subunit protein uL2


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 9057.423 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7L8
#22: Polypeptide(L)50S ribosomal protein L28 / Large ribosomal subunit protein bL28


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


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


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


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


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


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


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7Q1
#29: Polypeptide(L)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 / References: UniProt: P0A7Q6
#30: Polypeptide(L)50S ribosomal protein L31 / Large ribosomal subunit protein bL31-A


Mass: 7516.693 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7M9
#55: Polypeptide(L)50S ribosomal protein L1 / Large ribosomal subunit protein uL1


Mass: 23761.477 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7L0

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

#32: Polypeptide(L)30S ribosomal protein S2 / Small ribosomal subunit protein uS2


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 11546.442 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG59
#45: Polypeptide(L)30S ribosomal protein S15 / Small ribosomal subunit protein uS15


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


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


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


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


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


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


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

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Polypeptide(L) / Non-polymers , 2 types, 2 molecules w

#52: Polypeptide(L)Elongation factor P / EF-P


Mass: 20755.414 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0A6N4
#56: ChemicalChemComp-PRO / PROLINE


Mass: 115.130 Da / Num. of mol.: 1 / Formula: C5H9NO2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Polyproline-stalled ribosome in the presence of A+P site tRNA and elongation-factor P (EF-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, 54, 55
Source: NATURAL
Molecular weightValue: 3 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Escherichia 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 FIELD
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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 21655 / Symmetry type: POINT
Atomic model buildingRef space: REAL

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