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- PDB-5o2r: Cryo-EM structure of the proline-rich antimicrobial peptide Api13... -

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Basic information

Entry
Database: PDB / ID: 5o2r
TitleCryo-EM structure of the proline-rich antimicrobial peptide Api137 bound to the terminating ribosome
DescriptorPeptide chain release factor RF1
Apidaecin/RNA Complex
(50S ribosomal protein ...) x 31
(30S ribosomal protein ...) x 20
KeywordsRIBOSOME / ribosome / termination / release factors / antimicrobial peptides / antibiotic
Specimen sourceEscherichia coli k-12 / bacteria / image: Escherichia coli
Escherichia coli (strain k12) / bacteria /
Staphylococcus aureus / bacteria / スタフィロコッカス・アウレウス, 黄色ブドウ球菌
Apis mellifera / arthropod / Honeybee / セイヨウミツバチ, ヨウシュミツバチ /
MethodElectron microscopy (3.4 Å resolution / Particle / Single particle)
AuthorsGraf, M. / Berninghausen, O. / Beckmann, R. / Wilson, D.N.
CitationNat. Struct. Mol. Biol., 2017

Nat. Struct. Mol. Biol., 2017 StrPapers
An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome.
Tanja Florin / Cristina Maracci / Michael Graf / Prajwal Karki / Dorota Klepacki / Otto Berninghausen / Roland Beckmann / Nora Vázquez-Laslop / Daniel N Wilson / Marina V Rodnina / Alexander S Mankin

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 22, 2017 / Release: Jul 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 26, 2017Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title

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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
I: 50S ribosomal protein L11
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
5: 50S ribosomal protein L10
6: 50S ribosomal protein L31
7: mRNA
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: Peptide chain release factor RF1
x: P-site Ile-tRNA
z: Apidaecin


Theoretical massNumber of molelcules
Total (without water)2,196,43458
Polyers2,196,43458
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)270520
ΔGint (kcal/M)-2264
Surface area (Å2)800110
MethodPISA

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Components

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RNA chain , 5 types, 5 molecules AB7ax

#1: RNA chain23S ribosomal RNA


Mass: 941321.250 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: GenBank: 802133627
#2: RNA chain5S ribosomal RNA


Mass: 38813.133 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: GenBank: 1150448909
#34: RNA chainmRNA


Mass: 2205.379 Da / Num. of mol.: 1 / Source: (synth.) Staphylococcus aureus
#35: RNA chain16S ribosomal RNA


Mass: 498725.406 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: GenBank: 1108591457
#57: RNA chainP-site Ile-tRNA


Mass: 24855.754 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: GenBank: 1162894325

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50S ribosomal protein ... , 31 types, 31 molecules CDEFGHIJKL...

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


Mass: 29663.244 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / 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 (strain K12) / 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 (strain K12) / 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 (strain K12) / 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 (strain K12) / References: UniProt: P0AG55
#8: Polypeptide(L)50S ribosomal protein L9 / Large ribosomal subunit protein bL9


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7R1
#9: Polypeptide(L)50S ribosomal protein L11 / Large ribosomal subunit protein uL11


Mass: 14763.165 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7J7
#10: Polypeptide(L)50S ribosomal protein L13 / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0AA10
#11: Polypeptide(L)50S ribosomal protein L14 / Large ribosomal subunit protein uL14


Mass: 13451.910 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0ADY3
#12: Polypeptide(L)50S ribosomal protein L15 / Large ribosomal subunit protein uL15


Mass: 14877.273 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P02413
#13: Polypeptide(L)50S ribosomal protein L16 / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0ADY7
#14: Polypeptide(L)50S ribosomal protein L17 / Large ribosomal subunit protein bL17


Mass: 13721.938 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0AG44
#15: Polypeptide(L)50S ribosomal protein L18 / Large ribosomal subunit protein uL18


Mass: 12663.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0C018
#16: Polypeptide(L)50S ribosomal protein L19 / Large ribosomal subunit protein bL19


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7K6
#17: Polypeptide(L)50S ribosomal protein L20 / Large ribosomal subunit protein bL20


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7L3
#18: Polypeptide(L)50S ribosomal protein L21 / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0AG48
#19: Polypeptide(L)50S ribosomal protein L22 / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P61175
#20: Polypeptide(L)50S ribosomal protein L23 / Large ribosomal subunit protein uL23


Mass: 10546.472 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0ADZ0
#21: Polypeptide(L)50S ribosomal protein L24 / Large ribosomal subunit protein uL24


Mass: 11078.874 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P60624
#22: Polypeptide(L)50S ribosomal protein L25 / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P68919
#23: Polypeptide(L)50S ribosomal protein L27 / Large ribosomal subunit protein bL27


Mass: 8174.394 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7L8
#24: Polypeptide(L)50S ribosomal protein L28 / Large ribosomal subunit protein bL28


Mass: 8896.354 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7M2
#25: Polypeptide(L)50S ribosomal protein L29 / Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7M6
#26: Polypeptide(L)50S ribosomal protein L30 / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0AG51
#27: Polypeptide(L)50S ribosomal protein L32 / Large ribosomal subunit protein bL32


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7N4
#28: Polypeptide(L)50S ribosomal protein L33 / Large ribosomal subunit protein bL33


Mass: 5814.842 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7N9
#29: Polypeptide(L)50S ribosomal protein L34 / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7P5
#30: 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 (strain K12) / References: UniProt: P0A7Q1
#31: 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 (strain K12) / References: UniProt: P0A7Q6
#32: Polypeptide(L)50S ribosomal protein L10 / 50S ribosomal protein L8 / Large ribosomal subunit protein uL10


Mass: 14112.345 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7J3
#33: Polypeptide(L)50S ribosomal protein L31 / Large ribosomal subunit protein bL31-A


Mass: 7516.693 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7M9

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

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


Mass: 24253.943 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7V0
#37: Polypeptide(L)30S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 23078.785 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7V3
#38: Polypeptide(L)30S ribosomal protein S4 / Small ribosomal subunit protein uS4


Mass: 23383.002 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7V8
#39: Polypeptide(L)30S ribosomal protein S5 / Small ribosomal subunit protein uS5


Mass: 16532.088 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7W1
#40: Polypeptide(L)30S ribosomal protein S6 / Small ribosomal subunit protein bS6


Mass: 11669.371 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P02358
#41: Polypeptide(L)30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 16861.523 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P02359
#42: Polypeptide(L)30S ribosomal protein S8 / Small ribosomal subunit protein uS8


Mass: 14015.361 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7W7
#43: Polypeptide(L)30S ribosomal protein S9 / Small ribosomal subunit protein uS9


Mass: 14554.882 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7X3
#44: Polypeptide(L)30S ribosomal protein S10 / Small ribosomal subunit protein uS10


Mass: 11196.988 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7R5
#45: Polypeptide(L)30S ribosomal protein S11 / Small ribosomal subunit protein uS11


Mass: 12388.068 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7R9
#46: Polypeptide(L)30S ribosomal protein S12 / Small ribosomal subunit protein uS12


Mass: 13636.961 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7S3
#47: Polypeptide(L)30S ribosomal protein S13 / Small ribosomal subunit protein uS13


Mass: 12625.753 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7S9
#48: Polypeptide(L)30S ribosomal protein S14 / Small ribosomal subunit protein uS14


Mass: 11546.442 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0AG59
#49: Polypeptide(L)30S ribosomal protein S15 / Small ribosomal subunit protein uS15


Mass: 10159.621 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0ADZ4
#50: Polypeptide(L)30S ribosomal protein S16 / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7T3
#51: Polypeptide(L)30S ribosomal protein S17 / Small ribosomal subunit protein uS17


Mass: 9263.946 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0AG63
#52: Polypeptide(L)30S ribosomal protein S18 / Small ribosomal subunit protein bS18


Mass: 7606.768 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7T7
#53: Polypeptide(L)30S ribosomal protein S19 / Small ribosomal subunit protein uS19


Mass: 9057.626 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7U3
#54: Polypeptide(L)30S ribosomal protein S20 / Small ribosomal subunit protein bS20


Mass: 9506.190 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7U7
#55: Polypeptide(L)30S ribosomal protein S21 / Small ribosomal subunit protein bS21


Mass: 7763.073 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P68679

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Polypeptide(L) , 2 types, 2 molecules vz

#56: Polypeptide(L)Peptide chain release factor RF1 / RF-1


Mass: 26822.072 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) / References: UniProt: P0A7I0
#58: Polypeptide(L)Apidaecin


Mass: 1699.052 Da / Num. of mol.: 1 / Source: (synth.) Apis mellifera / References: UniProt: Q8WSY8

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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
IDNameTypeDetailsEntity IDParent IDSource
1Escherichia coli 70S ribosomeRIBOSOME70S ribosome complexed with Ile-tRNA, Api137 and RF11, 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, 580MULTIPLE SOURCES
2Escherichia coli 70S ribosomeRIBOSOME70S ribosome complexed with Ile-tRNA1, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 571NATURAL
3mRNACOMPLEXmRNA341RECOMBINANT
4ApidaecinCOMPLEXApidaecin581RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
1283333Escherichia coli (strain K12)
231280Staphylococcus aureus
347460Apis mellifera
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
1332630synthetic construct
2432630synthetic construct
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 / Cs: 2.7 mm
Image recordingElectron dose: 28 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 1 / Number of real images: 5132
Image scansDimension width: 4096 / Dimension height: 4096

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Processing

EM software
IDNameVersionCategoryImage processing IDFitting ID
1SignaturePARTICLE SELECTION1
4CTFFIND4.1CTF CORRECTION1
7UCSF Chimera1.11.2MODEL FITTING1
8Coot0.8.6MODEL FITTING1
12FREALIGN9.11CLASSIFICATION1
13FREALIGN9.11RECONSTRUCTION1
14PHENIX1.11.1-2575MODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 116212
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 36826 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL

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