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- PDB-5mgp: Structural basis for ArfA-RF2 mediated translation termination on... -

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Entry
Database: PDB / ID: 5mgp
TitleStructural basis for ArfA-RF2 mediated translation termination on stop-codon lacking mRNAs
DescriptorAlternative ribosome-rescue factor A
Peptide chain release factor 2/RNA Complex
(50S ribosomal protein ...) x 29
(30S ribosomal protein ...) x 20
KeywordsRIBOSOME / Cryo-Em / Ribosome / Termination / alternative rescue factor A
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (3.1 Å resolution / Particle / Single particle)
AuthorsHuter, P. / Mueller, C. / Beckert, B. / Arenz, S. / Berninghausen, O. / Beckmann, R. / Wilson, N.D.
CitationNature, 2017, 541, 546-549

Nature, 2017, 541, 546-549 Yorodumi Papers
Structural basis for ArfA-RF2-mediated translation termination on mRNAs lacking stop codons.
Paul Huter / Claudia Müller / Bertrand Beckert / Stefan Arenz / Otto Berninghausen / Roland Beckmann / Daniel N Wilson

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 21, 2016 / Release: Dec 14, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 14, 2016Structure modelrepositoryInitial release
1.1Feb 8, 2017Structure modelDatabase references
1.2Aug 30, 2017Structure modelAuthor supporting evidence / Data collection / Derived calculationsem_image_scans / em_software / pdbx_audit_support / struct_conn_em_software.name / _pdbx_audit_support.funding_organization

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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
H: 50S ribosomal protein L9
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
v: mRNA
w: Alternative ribosome-rescue factor A
x: P-site tRNA
z: Peptide chain release factor 2


Theoretical massNumber of molelcules
Total (without water)2,184,50556
Polyers2,184,50556
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)267710
ΔGint (kcal/M)-2270
Surface area (Å2)794370
MethodPISA

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Components

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RNA chain , 5 types, 5 molecules ABavx

#1: RNA chain23S ribosomal RNA


Mass: 941305.250 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: 1028480521
#32: RNA chain16S ribosomal RNA


Mass: 498725.406 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 802133627
#53: RNA chainmRNA


Mass: 1866.181 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli
#55: RNA chainP-site tRNA


Mass: 24846.746 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 1052521625

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

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


Mass: 29663.244 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60422

Cellular component

Molecular function

Biological process

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


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60438

Cellular component

Molecular function

Biological process

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


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60723

Cellular component

Molecular function

Biological process

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


Mass: 20073.234 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P62399

Cellular component

Molecular function

Biological process

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


Mass: 18801.598 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG55

Cellular component

Molecular function

Biological process

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


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7R1

Cellular component

Molecular function

Biological process

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


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AA10

Cellular component

Molecular function

Biological process

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


Mass: 13451.910 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0ADY3

Cellular component

Molecular function

Biological process

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


Mass: 14877.273 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P02413

Cellular component

Molecular function

Biological process

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


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0ADY7

Cellular component

Molecular function

Biological process

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


Mass: 13721.938 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG44

Cellular component

Molecular function

Biological process

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


Mass: 12663.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0C018

Cellular component

Molecular function

Biological process

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


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7K6

Cellular component

Molecular function

Biological process

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


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7L3

Cellular component

Molecular function

Biological process

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


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG48

Cellular component

Molecular function

Biological process

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


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P61175

Cellular component

Molecular function

Biological process

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


Mass: 10546.472 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0ADZ0

Cellular component

Molecular function

Biological process

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


Mass: 11078.874 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60624

Cellular component

Molecular function

Biological process

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


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P68919

Cellular component

Molecular function

Biological process

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


Mass: 8174.394 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7L8

Cellular component

Molecular function

Biological process

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


Mass: 8896.354 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7M2

Cellular component

Molecular function

Biological process

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


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7M6

Cellular component

Molecular function

Biological process

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


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG51

Cellular component

Molecular function

Biological process

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


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7N4

Cellular component

Molecular function

Biological process

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


Mass: 5814.842 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7N9

Cellular component

Molecular function

Biological process

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


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7P5

Cellular component

Molecular function

Biological process

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


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7Q1

Cellular component

Molecular function

Biological process

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


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7Q6

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)50S ribosomal protein L31


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

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: 24253.943 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7V0

Cellular component

Molecular function

Biological process

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


Mass: 23078.785 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7V3

Cellular component

Molecular function

Biological process

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


Mass: 23383.002 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7V8

Cellular component

Molecular function

Biological process

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


Mass: 16532.088 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7W1

Cellular component

Molecular function

Biological process

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


Mass: 11669.371 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P02358

Cellular component

Molecular function

Biological process

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


Mass: 16861.523 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P02359

Cellular component

Molecular function

Biological process

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


Mass: 14015.361 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7W7

Cellular component

Molecular function

Biological process

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


Mass: 14554.882 Da / Num. of mol.: 1 / 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: 11196.988 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7R5

Cellular component

Molecular function

Biological process

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


Mass: 12388.068 Da / Num. of mol.: 1 / 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 / Source: (natural) Escherichia coli / References: UniProt: P0A7S3

Cellular component

Molecular function

Biological process

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


Mass: 12625.753 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7S9

Cellular component

Molecular function

Biological process

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


Mass: 11546.442 Da / Num. of mol.: 1 / 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 / 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 / Source: (natural) Escherichia coli / References: UniProt: P0A7T3

Cellular component

Molecular function

Biological process

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


Mass: 9263.946 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG63

Cellular component

Molecular function

Biological process

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


Mass: 7606.768 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7T7

Cellular component

Molecular function

Biological process

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


Mass: 9057.626 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7U3

Cellular component

Molecular function

Biological process

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


Mass: 9506.190 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7U7

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 2 types, 2 molecules wz

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


Mass: 5265.089 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P36675

Molecular function

Biological process

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


Mass: 40566.781 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P07012

Cellular component

Molecular function

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

Biological process

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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 IDSource
1Structural basis for ArfA-RF2 mediated translation termination 1 on stop-codon lacking mRNAsRIBOSOME1, 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
2ribosomeRIBOSOME1, 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, 551NATURAL
3mRNA, tRNA, Peptide chain release factor 2RIBOSOME53, 54, 561RECOMBINANT
Molecular weightValue: 2.5 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
11562Escherichia coli
22562Escherichia coli
33562Escherichia coli
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.2
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: 302 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 2.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: FREALIGN / Version: 9.11 / Category: RECONSTRUCTION
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 69089 / Symmetry type: POINT

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