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

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Basic information

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 Å resolution / Particle / 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 Yorodumi Papers
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 4, 2016 / Release: Jan 11, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 11, 2017Structure modelrepositoryInitial release
1.1Jan 25, 2017Structure modelDatabase references
1.2Feb 8, 2017Structure modelDatabase references
1.3Sep 27, 2017Structure modelAuthor supporting evidence / Data collectionem_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization

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Structure visualization

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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 (Å2)325460
ΔGint (kcal/M)-3695
Surface area (Å2)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 experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

Component
IDNameTypeEntity IDParent IDSourceDetails
1Non-stop ribosomal complex with ArfA and RF2COMPLEX1, 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, 560MULTIPLE SOURCES
230S subunitCOMPLEX32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 521MULTIPLE SOURCES
350S subunitCOMPLEX1, 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, 311MULTIPLE SOURCES
4Alternative ribosome-rescue factor AORGANELLE OR CELLULAR COMPONENT541RECOMBINANT
5Peptide chain release factor 2ORGANELLE OR CELLULAR COMPONENT531RECOMBINANT
6P-site or E-site fMet-tRNA(fMet)ORGANELLE OR CELLULAR COMPONENT551MULTIPLE SOURCESfMet tRNA was in vitro transcribed
7mRNAORGANELLE OR CELLULAR COMPONENT561MULTIPLE SOURCES
823S rRNAORGANELLE OR CELLULAR COMPONENT13NATURAL
950S ribosomal protein L2ORGANELLE OR CELLULAR COMPONENT33NATURAL
1016S rRNAORGANELLE OR CELLULAR COMPONENT322NATURAL
1130S ribosomal protein S2COMPLEX332MULTIPLE SOURCES
1230S ribosomal protein S3ORGANELLE OR CELLULAR COMPONENT342NATURAL
1330S ribosomal protein S4ORGANELLE OR CELLULAR COMPONENT352NATURAL
1430S ribosomal protein S5ORGANELLE OR CELLULAR COMPONENT362NATURAL
1530S ribosomal protein S6ORGANELLE OR CELLULAR COMPONENT372NATURAL
1630S ribosomal protein S7ORGANELLE OR CELLULAR COMPONENT382NATURAL
1730S ribosomal protein S8ORGANELLE OR CELLULAR COMPONENT392NATURAL
1830S ribosomal protein S9ORGANELLE OR CELLULAR COMPONENT402NATURAL
1930S ribosomal protein S10ORGANELLE OR CELLULAR COMPONENT412NATURAL
2030S ribosomal protein S11ORGANELLE OR CELLULAR COMPONENT422NATURAL
2130S ribosomal protein S12ORGANELLE OR CELLULAR COMPONENT432NATURAL
2230S ribosomal protein S13ORGANELLE OR CELLULAR COMPONENT442NATURAL
2330S ribosomal protein S14ORGANELLE OR CELLULAR COMPONENT452NATURAL
2430S ribosomal protein S15ORGANELLE OR CELLULAR COMPONENT462NATURAL
2530S ribosomal protein S16ORGANELLE OR CELLULAR COMPONENT472NATURAL
2630S ribosomal protein S17ORGANELLE OR CELLULAR COMPONENT482NATURAL
2730S ribosomal protein S18ORGANELLE OR CELLULAR COMPONENT492NATURAL
2830S ribosomal protein S19ORGANELLE OR CELLULAR COMPONENT502NATURAL
2930S ribosomal protein S20ORGANELLE OR CELLULAR COMPONENT512NATURAL
3030S ribosomal protein S21ORGANELLE OR CELLULAR COMPONENT522NATURAL
3150S ribosomal protein L3ORGANELLE OR CELLULAR COMPONENT43NATURAL
3250S ribosomal protein L4ORGANELLE OR CELLULAR COMPONENT53NATURAL
3350S ribosomal protein L5ORGANELLE OR CELLULAR COMPONENT63NATURAL
3450S ribosomal protein L6ORGANELLE OR CELLULAR COMPONENT73NATURAL
3550S ribosomal protein L9ORGANELLE OR CELLULAR COMPONENT83NATURAL
3650S ribosomal protein L11ORGANELLE OR CELLULAR COMPONENT93NATURAL
3750S ribosomal protein L13ORGANELLE OR CELLULAR COMPONENT103NATURAL
3850S ribosomal protein L14ORGANELLE OR CELLULAR COMPONENT113NATURAL
3950S ribosomal protein L15ORGANELLE OR CELLULAR COMPONENT123NATURAL
4050S ribosomal protein L16ORGANELLE OR CELLULAR COMPONENT133NATURAL
4150S ribosomal protein L17ORGANELLE OR CELLULAR COMPONENT143NATURAL
4250S ribosomal protein L18ORGANELLE OR CELLULAR COMPONENT153NATURAL
4350S ribosomal protein L19ORGANELLE OR CELLULAR COMPONENT163NATURAL
4450S ribosomal protein L20ORGANELLE OR CELLULAR COMPONENT3NATURAL
4550S ribosomal protein L21ORGANELLE OR CELLULAR COMPONENT183NATURAL
4650S ribosomal protein L22ORGANELLE OR CELLULAR COMPONENT193NATURAL
4750S ribosomal protein L23ORGANELLE OR CELLULAR COMPONENT203NATURAL
4850S ribosomal protein L24ORGANELLE OR CELLULAR COMPONENT213NATURAL
4950S ribosomal protein L25COMPLEX223NATURAL
5050S ribosomal protein L27ORGANELLE OR CELLULAR COMPONENT233NATURAL
5150S ribosomal protein L28ORGANELLE OR CELLULAR COMPONENT243NATURAL
5250S ribosomal protein L29ORGANELLE OR CELLULAR COMPONENT253NATURAL
5350S ribosomal protein L30ORGANELLE OR CELLULAR COMPONENT263NATURAL
5450S ribosomal protein L32ORGANELLE OR CELLULAR COMPONENT273NATURAL
5550S ribosomal protein L33ORGANELLE OR CELLULAR COMPONENT283NATURAL
5650S ribosomal protein L34ORGANELLE OR CELLULAR COMPONENT293NATURAL
5750S ribosomal protein L35ORGANELLE OR CELLULAR COMPONENT303NATURAL
5850S ribosomal protein L36ORGANELLE OR CELLULAR COMPONENT313NATURAL
595S rRNAORGANELLE OR CELLULAR COMPONENT23NATURAL
Molecular weight
IDValueUnitsEntity assembly IDExperimental value
11
12
13
26.35KILODALTONS/NANOMETER4NO
340.13KILODALTONS/NANOMETER5NO
16
17
18
19
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
24562Escherichia coli
35562Escherichia coli
28562Escherichia coli
39562Escherichia coli
410562Escherichia coli
511562Escherichia coli
612562Escherichia coli
713562Escherichia coli
814562Escherichia coli
915562Escherichia coli
1016562Escherichia coli
1117562Escherichia coli
1218562Escherichia coli
1319562Escherichia coli
1420562Escherichia coli
1521562Escherichia coli
1622562Escherichia coli
1723562Escherichia coli
1824562Escherichia coli
1925562Escherichia coli
2026562Escherichia coli
2127562Escherichia coli
2228562Escherichia coli
2329562Escherichia coli
2430562Escherichia coli
2531562Escherichia coli
2632562Escherichia coli
2733562Escherichia coli
2834562Escherichia coli
2935562Escherichia coli
3036562Escherichia coli
3137562Escherichia coli
3238562Escherichia coli
3339562Escherichia coli
3440562Escherichia coli
3541562Escherichia coli
3642562Escherichia coli
3743562Escherichia coli
3844562Escherichia coli
3945562Escherichia coli
4046562Escherichia coli
4147562Escherichia coli
4248562Escherichia coli
4349562Escherichia coli
4450562Escherichia coli
4551562Escherichia coli
4652562Escherichia coli
4753562Escherichia coli
4854562Escherichia coli
4955562Escherichia coli
5056562Escherichia coli
5157562Escherichia coli
5258562Escherichia coli
5359562Escherichia coli
11562Escherichia coli
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganismPlasmidStrain
24562Escherichia colipET28BL21
35562Escherichia colipETNKI-his3C-LIC-KanBL21
Buffer solutionpH: 7.5
Buffer component
IDConc.UnitsNameFormulaBuffer ID
120mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidC8H18N2O4S1
215mMmagnesium acetateMg(CH3COO)21
3150mMpotassium acetateCH3CO2K1
44mM2-mercapthoethanolHOCH2CH2SH1
52mMspermidineC7H19N31
60.05mMsperminC10H26N41
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-Flat TM Holey Carbon Grid CF-2/0.5-4C
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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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 / Nominal defocus max: 3000 nm / Nominal defocus min: 700 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 6 sec. / Electron dose: 20 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 30 / Used frames/image: 4-25

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Processing

SoftwareName: REFMAC / Version: 5.8.0155 / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDFitting ID
1RELION1.4PARTICLE SELECTION1
4CTFFIND4CTF CORRECTION1
7ChimeraMODEL FITTING1
9RELION2.0INITIAL EULER ASSIGNMENT1
10RELION2.0FINAL EULER ASSIGNMENT1
12RELION2.0RECONSTRUCTION1
13REFMAC5.8MODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 155440 / Symmetry type: POINT
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 Å2 / Aniso B11: -0.453 Å2 / Aniso B12: 1.509 Å2 / Aniso B13: -1.254 Å2 / Aniso B22: 3.23 Å2 / Aniso B23: 2.7 Å2 / Aniso B33: -2.778 Å2
Least-squares processR factor R work: 0.3838 / R factor all: 0.384 / Highest resolution: 3.5 Å / Lowest resolution: 458.112 Å / 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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