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- PDB-5u4i: Structural Basis of Co-translational Quality Control by ArfA and ... -

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Entry
Database: PDB / ID: 5u4i
TitleStructural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome
DescriptorRibosome
KeywordsRIBOSOME / Ribosome / ArfA / RF2 / nonstop translation
Specimen sourceEscherichia coli (strain k12) / bacteria /
Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (3.5 A resolution / Single particle)
AuthorsZeng, F. / Chen, Y. / Remis, J. / Shekhar, M. / Phillips, J.C. / Tajkhorshid, E. / Jin, H.
CitationNature, 2017, 541, 554-557

Nature, 2017, 541, 554-557 StrPapers
Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome.
Fuxing Zeng / Yanbo Chen / Jonathan Remis / Mrinal Shekhar / James C Phillips / Emad Tajkhorshid / Hong Jin

DateDeposition: Dec 4, 2016 / Release: Jan 11, 2017 / Last modification: Feb 8, 2017

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Assembly

Deposited unit
A: 23S rRNA
B: 5S rRNA
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
H: 50S ribosomal protein L9
J: 50S ribosomal protein L11
K: 50S ribosomal protein L13
L: 50S ribosomal protein L14
M: 50S ribosomal protein L15
N: 50S ribosomal protein L16
O: 50S ribosomal protein L17
P: 50S ribosomal protein L18
Q: 50S ribosomal protein L19
R: 50S ribosomal protein L20
S: 50S ribosomal protein L21
T: 50S ribosomal protein L22
U: 50S ribosomal protein L23
V: 50S ribosomal protein L24
W: 50S ribosomal protein L25
X: 50S ribosomal protein L27
Y: 50S ribosomal protein L28
Z: 50S ribosomal protein L29
0: 50S ribosomal protein L30
1: 50S ribosomal protein L32
2: 50S ribosomal protein L33
3: 50S ribosomal protein L34
4: 50S ribosomal protein L35
5: 50S ribosomal protein L36
a: 16S rRNA
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: Peptide chain release factor 2
w: Alternative ribosome-rescue factor A
x: P-site or E-site fMet-tRNA(fMet)
y: P-site or E-site fMet-tRNA(fMet)
z: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,249,304182
Polyers2,246,22557
Non-polymers3,079125
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (A2)325460
ΔGint (kcal/M)-3695
Surface area (A2)762030

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Components

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RNA chain , 5 types, 6 molecules ABaxyz

#1: RNA chain23S rRNA


Mass: 941761.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 42756
#2: RNA chain5S rRNA


Mass: 38177.762 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 1036415628
#32: RNA chain16S rRNA


Mass: 497044.750 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 817573384
#55: RNA chainP-site or E-site fMet-tRNA(fMet)


Mass: 24802.785 Da / Num. of mol.: 2 / Source: (synth.) Escherichia coli / References: GenBank: 1062469497
#56: RNA chainmRNA


Mass: 5922.644 Da / Num. of mol.: 1 / Source: (synth.) Escherichia coli

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

#3: Polypeptide(L)50S ribosomal protein L2


Mass: 29923.619 Da / Num. of mol.: 1 / Details: Gene Name(s): rplB b3317 JW3279 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P60422

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)50S ribosomal protein L3


Mass: 22277.535 Da / Num. of mol.: 1 / Details: Gene Name(s): rplC b3320 JW3282 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P60438

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Details: Gene Name(s): rplD eryA b3319 JW3281 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P60723

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1 / Details: Gene Name(s): rplE b3308 JW3270 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P62399

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)50S ribosomal protein L6


Mass: 18932.791 Da / Num. of mol.: 1 / Details: Gene Name(s): rplF b3305 JW3267 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0AG55

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Details: Gene Name(s): rplI b4203 JW4161 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7R1

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)50S ribosomal protein L11


Mass: 14894.362 Da / Num. of mol.: 1 / Details: Gene Name(s): rplK relC b3983 JW3946 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7J7

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Details: Gene Name(s): rplM b3231 JW3200 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0AA10

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Details: Gene Name(s): rplN b3310 JW3272 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0ADY3

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1 / Details: Gene Name(s): rplO b3301 JW3263 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P02413

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)50S ribosomal protein L16


Mass: 15312.269 Da / Num. of mol.: 1 / Details: Gene Name(s): rplP b3313 JW3275 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0ADY7

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 1 / Details: Gene Name(s): rplQ b3294 JW3256 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0AG44

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1 / Details: Gene Name(s): rplR b3304 JW3266 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0C018

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)50S ribosomal protein L19


Mass: 13159.278 Da / Num. of mol.: 1 / Details: Gene Name(s): rplS b2606 JW2587 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7K6

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)50S ribosomal protein L20


Mass: 13528.024 Da / Num. of mol.: 1 / Details: Gene Name(s): rplT pdzA b1716 JW1706 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7L3

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Details: Gene Name(s): rplU b3186 JW3153 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0AG48

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 1 / Details: Gene Name(s): rplV eryB b3315 JW3277 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P61175

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1 / Details: Gene Name(s): rplW b3318 JW3280 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0ADZ0

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)50S ribosomal protein L24


Mass: 11339.250 Da / Num. of mol.: 1 / Details: Gene Name(s): rplX b3309 JW3271 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P60624

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 1 / Details: Gene Name(s): rplY b2185 JW2173 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P68919

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)50S ribosomal protein L27


Mass: 9146.540 Da / Num. of mol.: 1 / Details: Gene Name(s): rpmA b3185 JW3152 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7L8

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 1 / Details: Gene Name(s): rpmB b3637 JW3612 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7M2

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 1 / Details: Gene Name(s): rpmC b3312 JW3274 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7M6

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)50S ribosomal protein L30


Mass: 6554.820 Da / Num. of mol.: 1 / Details: Gene Name(s): rpmD b3302 JW3264 / Source: (natural) Escherichia coli / References: UniProt: P0AG51

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 1 / Details: Gene Name(s): rpmF b1089 JW1075 / Source: (natural) Escherichia coli / References: UniProt: P0A7N4

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1 / Details: Gene Name(s): rpmG b3636 JW3611 / Source: (natural) Escherichia coli / References: UniProt: P0A7N9

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Details: Gene Name(s): rpmH rimA ssaF b3703 JW3680 / Source: (natural) Escherichia coli / References: UniProt: P0A7P5

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)50S ribosomal protein L35 / Ribosomal protein A


Mass: 7313.032 Da / Num. of mol.: 1 / Details: Gene Name(s): rpmI b1717 JW1707 / Source: (natural) Escherichia coli / References: UniProt: P0A7Q1

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)50S ribosomal protein L36 / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Details: Gene Name(s): rpmJ b3299 JW3261 / Source: (natural) Escherichia coli / References: UniProt: P0A7Q6

Cellular component

Molecular function

Biological process

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

#33: Polypeptide(L)30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsB b0169 JW0164 / Source: (natural) Escherichia coli / References: UniProt: P0A7V0

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsC b3314 JW3276 / Source: (natural) Escherichia coli / References: UniProt: P0A7V3

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsD ramA b3296 JW3258 / Source: (natural) Escherichia coli / References: UniProt: P0A7V8

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsE spc b3303 JW3265 / Source: (natural) Escherichia coli / References: UniProt: P0A7W1

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)30S ribosomal protein S6


Mass: 15727.512 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsF b4200 JW4158 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P02358

Cellular component

Molecular function

Biological process

#38: Polypeptide(L)30S ribosomal protein S7


Mass: 20055.156 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsG b3341 JW3303 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P02359

Cellular component

Molecular function

Biological process

#39: Polypeptide(L)30S ribosomal protein S8


Mass: 14015.361 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsH b3306 JW3268 / Source: (natural) Escherichia coli / References: UniProt: P0A7W7

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsI b3230 JW3199 / Source: (natural) Escherichia coli / References: UniProt: P0A7X3

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#41: Polypeptide(L)30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsJ nusE b3321 JW3283 / Source: (natural) Escherichia coli / References: UniProt: P0A7R5

Cellular component

Molecular function

Biological process

#42: Polypeptide(L)30S ribosomal protein S11


Mass: 12487.200 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsK b3297 JW3259 / Source: (natural) Escherichia coli / References: UniProt: P0A7R9

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • ribosomal small subunit assembly (GO: 0000028)
  • translation (GO: 0006412)
#43: Polypeptide(L)30S ribosomal protein S12


Mass: 13636.961 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsL strA b3342 JW3304 / Source: (natural) Escherichia coli / References: UniProt: P0A7S3

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsM b3298 JW3260 / Source: (natural) Escherichia coli / References: UniProt: P0A7S9

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)30S ribosomal protein S14


Mass: 11475.364 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsN b3307 JW3269 / Source: (natural) Escherichia coli / References: UniProt: P0AG59

Cellular component

Molecular function

Biological process

#46: Polypeptide(L)30S ribosomal protein S15


Mass: 10159.621 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsO secC b3165 JW3134 / Source: (natural) Escherichia coli / References: UniProt: P0ADZ4

Cellular component

Molecular function

Biological process

#47: Polypeptide(L)30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsP b2609 JW2590 / Source: (natural) Escherichia coli / References: UniProt: P0A7T3

Cellular component

Molecular function

Biological process

#48: Polypeptide(L)30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsQ neaA b3311 JW3273 / Source: (natural) Escherichia coli / References: UniProt: P0AG63

Cellular component

Molecular function

Biological process

#49: Polypeptide(L)30S ribosomal protein S18


Mass: 9063.508 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsR b4202 JW4160 / Source: (natural) Escherichia coli / References: UniProt: P0A7T7

Cellular component

Molecular function

Biological process

#50: Polypeptide(L)30S ribosomal protein S19


Mass: 9349.939 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsS b3316 JW3278 / Source: (natural) Escherichia coli / References: UniProt: P0A7U3

Cellular component

Molecular function

Biological process

#51: Polypeptide(L)30S ribosomal protein S20


Mass: 9577.268 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsT b0023 JW0022 / Source: (natural) Escherichia coli / References: UniProt: P0A7U7

Cellular component

Molecular function

Biological process

#52: Polypeptide(L)30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsU b3065 JW3037 / Source: (natural) Escherichia coli / References: UniProt: P68679

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 2 types, 2 molecules vw

#53: Polypeptide(L)Peptide chain release factor 2 / RF-2


Mass: 43313.871 Da / Num. of mol.: 1 / Details: Gene Name(s): prfB ECK2886 JW5847 supK / Mutation: Q252MEQ / Source: (gene. exp.) Escherichia coli (strain K12) / References: UniProt: P07012

Cellular component

Molecular function

  • translation release factor activity, codon specific (GO: 0016149)

Biological process

#54: Polypeptide(L)Alternative ribosome-rescue factor A


Mass: 6513.396 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (strain K12) / References: UniProt: P36675

Molecular function

Biological process

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Non-polymers , 2 types, 125 molecules

#57: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 124 / Formula: Mg
#58: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

Assembly of specimen
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
56
57
58
59
Component
IDNameDetailsTypeAssembly id
1Non-stop ribosomal complex with ArfA and RF2COMPLEX1
230S subunitCOMPLEX2
350S subunitCOMPLEX3
4Alternative ribosome-rescue factor AORGANELLE OR CELLULAR COMPONENT4
5Peptide chain release factor 2ORGANELLE OR CELLULAR COMPONENT5
6P-site or E-site fMet-tRNA(fMet)fMet tRNA was in vitro transcribedORGANELLE OR CELLULAR COMPONENT6
7mRNAORGANELLE OR CELLULAR COMPONENT7
823S rRNAORGANELLE OR CELLULAR COMPONENT8
950S ribosomal protein L2ORGANELLE OR CELLULAR COMPONENT9
1016S rRNAORGANELLE OR CELLULAR COMPONENT10
1130S ribosomal protein S2COMPLEX11
1230S ribosomal protein S3ORGANELLE OR CELLULAR COMPONENT12
1330S ribosomal protein S4ORGANELLE OR CELLULAR COMPONENT13
1430S ribosomal protein S5ORGANELLE OR CELLULAR COMPONENT14
1530S ribosomal protein S6ORGANELLE OR CELLULAR COMPONENT15
1630S ribosomal protein S7ORGANELLE OR CELLULAR COMPONENT16
1730S ribosomal protein S8ORGANELLE OR CELLULAR COMPONENT17
1830S ribosomal protein S9ORGANELLE OR CELLULAR COMPONENT18
1930S ribosomal protein S10ORGANELLE OR CELLULAR COMPONENT19
2030S ribosomal protein S11ORGANELLE OR CELLULAR COMPONENT20
2130S ribosomal protein S12ORGANELLE OR CELLULAR COMPONENT21
2230S ribosomal protein S13ORGANELLE OR CELLULAR COMPONENT22
2330S ribosomal protein S14ORGANELLE OR CELLULAR COMPONENT23
2430S ribosomal protein S15ORGANELLE OR CELLULAR COMPONENT24
2530S ribosomal protein S16ORGANELLE OR CELLULAR COMPONENT25
2630S ribosomal protein S17ORGANELLE OR CELLULAR COMPONENT26
2730S ribosomal protein S18ORGANELLE OR CELLULAR COMPONENT27
2830S ribosomal protein S19ORGANELLE OR CELLULAR COMPONENT28
2930S ribosomal protein S20ORGANELLE OR CELLULAR COMPONENT29
3030S ribosomal protein S21ORGANELLE OR CELLULAR COMPONENT30
3150S ribosomal protein L3ORGANELLE OR CELLULAR COMPONENT31
3250S ribosomal protein L4ORGANELLE OR CELLULAR COMPONENT32
3350S ribosomal protein L5ORGANELLE OR CELLULAR COMPONENT33
3450S ribosomal protein L6ORGANELLE OR CELLULAR COMPONENT34
3550S ribosomal protein L9ORGANELLE OR CELLULAR COMPONENT35
3650S ribosomal protein L11ORGANELLE OR CELLULAR COMPONENT36
3750S ribosomal protein L13ORGANELLE OR CELLULAR COMPONENT37
3850S ribosomal protein L14ORGANELLE OR CELLULAR COMPONENT38
3950S ribosomal protein L15ORGANELLE OR CELLULAR COMPONENT39
4050S ribosomal protein L16ORGANELLE OR CELLULAR COMPONENT40
4150S ribosomal protein L17ORGANELLE OR CELLULAR COMPONENT41
4250S ribosomal protein L18ORGANELLE OR CELLULAR COMPONENT42
4350S ribosomal protein L19ORGANELLE OR CELLULAR COMPONENT43
4450S ribosomal protein L20ORGANELLE OR CELLULAR COMPONENT44
4550S ribosomal protein L21ORGANELLE OR CELLULAR COMPONENT45
4650S ribosomal protein L22ORGANELLE OR CELLULAR COMPONENT46
4750S ribosomal protein L23ORGANELLE OR CELLULAR COMPONENT47
4850S ribosomal protein L24ORGANELLE OR CELLULAR COMPONENT48
4950S ribosomal protein L25COMPLEX49
5050S ribosomal protein L27ORGANELLE OR CELLULAR COMPONENT50
5150S ribosomal protein L28ORGANELLE OR CELLULAR COMPONENT51
5250S ribosomal protein L29ORGANELLE OR CELLULAR COMPONENT52
5350S ribosomal protein L30ORGANELLE OR CELLULAR COMPONENT53
5450S ribosomal protein L32ORGANELLE OR CELLULAR COMPONENT54
5550S ribosomal protein L33ORGANELLE OR CELLULAR COMPONENT55
5650S ribosomal protein L34ORGANELLE OR CELLULAR COMPONENT56
5750S ribosomal protein L35ORGANELLE OR CELLULAR COMPONENT57
5850S ribosomal protein L36ORGANELLE OR CELLULAR COMPONENT58
595S rRNAORGANELLE OR CELLULAR COMPONENT59
Specimen supportGrid material: COPPER / Grid mesh size: 400 /inch. / Grid type: C-Flat TM Holey Carbon Grid CF-2/0.5-4C
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 83822 X / Nominal defocus max: 3000 nm / Nominal defocus min: 700 nm

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Processing

SoftwareName: REFMAC / Version: 5.8.0155 / Classification: refinement
ComputingStructure refinement: REFMAC 5.8.0155
3D reconstructionResolution: 3.5 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 155440
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: RECIPROCAL / Target criteria: Average FSC
RefineCorrelation coeff Fo to Fc: 0.768
Details: Hydrogens have been added in their riding positions
Overall SU B: 29.504 / Overall SU ML: 0.382 / Overall ESU R: 0.257
Solvent computationSolvent model details: BABINET MODEL
Displacement parametersB iso mean: 303.637 A2 / Aniso B11: -0.453 A2 / Aniso B12: 1.509 A2 / Aniso B13: -1.254 A2 / Aniso B22: 3.23 A2 / Aniso B23: 2.7 A2 / Aniso B33: -2.778 A2
Least-squares processR factor R work: 0.3838 / R factor all: 0.384 / Highest resolution: 3.5 A / Lowest resolution: 458.112 A / Number reflection R work: 4696443 / Percent reflection obs: 1 / WR factor R work: 0.384
Refine LS restraints
Refine idTypeDev idealDev ideal targetNumber
FIT TO EM MODELr_bond_refined_d0.0050.014165101
FIT TO EM MODELr_ext_dist_refined_d0.1060.02029707
FIT TO EM MODELr_angle_refined_deg0.9471.469242315
FIT TO EM MODELr_dihedral_angle_1_deg20.8439.79833567
FIT TO EM MODELr_dihedral_angle_2_deg43.40522.5031742
FIT TO EM MODELr_dihedral_angle_3_deg17.72815.0007469
FIT TO EM MODELr_dihedral_angle_4_deg12.77315.000454
FIT TO EM MODELr_chiral_restr0.1290.21727721
FIT TO EM MODELr_gen_planes_refined0.0050.02085395
FIT TO EM MODELr_nbd_refined0.1560.200139524
FIT TO EM MODELr_nbtor_refined0.2730.200197596
FIT TO EM MODELr_xyhbond_nbd_refined0.1280.2006720
FIT TO EM MODELr_metal_ion_refined0.0990.20070
FIT TO EM MODELr_paralell_plane_angle_deg4.1081.2003447
FIT TO EM MODELr_mcbond_it4.70833.95624596
FIT TO EM MODELr_mcangle_it8.66050.91530654
FIT TO EM MODELr_scbond_it4.08829.510140505
FIT TO EM MODELr_scangle_it7.07544.245211661
FIT TO EM MODELr_lrange_it23.169816.292683576
Refine LS shell

Refine id: FIT TO EM MODEL / Number reflection R free: 0 / Total number of bins used: 20 / Percent reflection obs: 1

Highest resolutionR factor R workLowest resolutionNumber reflection R workNumber reflection allWR factor R work
3.5000.5893.5913475943475940.589
3.5910.5743.6893391313391310.574
3.6890.5523.7963293003293000.552
3.7960.5383.9133200993200990.538
3.9130.5104.0413098003098000.510
4.0410.4784.1832998222998220.478
4.1830.4504.3412895302895300.450
4.3410.4254.5182784382784380.425
4.5180.4034.7192671462671460.403
4.7190.3884.9502548292548290.388
4.9500.3645.2172429492429490.364
5.2170.3575.5342294072294070.357
5.5340.3425.9162157752157750.342
5.9160.3356.3902007062007060.335
6.3900.3346.9991846541846540.334
6.9990.3147.8251670471670470.314
7.8250.3139.0351472081472080.313
9.0350.29111.0651242871242870.291
11.0650.29215.64496022960220.292
15.6440.416458.11252699526990.416

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