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- PDB-5lmp: Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiatio... -

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Basic information

Entry
Database: PDB / ID: 5lmp
TitleStructure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1C)
Descriptor(30S ribosomal protein ...) x 20
(Translation initiation factor IF- ...) x 2
KeywordsRIBOSOME / ribosome / translation / initiation factors / 30S / IF1 / IF3 / PIC / Thermus thermophilus
Specimen sourceThermus thermophilus (strain hb8 / atcc 27634 / dsm 579) / bacteria / thermophilic
Thermus thermophilus hb8 / bacteria / thermophilic
Thermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス
MethodElectron microscopy (5.35 Å resolution / Particle / Single particle)
AuthorsHussain, T. / Llacer, J.L. / Wimberly, B.T. / Ramakrishnan, V.
CitationCell, 2016, 167, 133-144.e13

Cell, 2016, 167, 133-144.e13 Yorodumi Papers
Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation.
Tanweer Hussain / Jose L Llácer / Brian T Wimberly / Jeffrey S Kieft / V Ramakrishnan

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 1, 2016 / Release: Oct 5, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 5, 2016Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collection / Derived calculationsem_image_scans / em_software / pdbx_struct_conn_angle / struct_conn_em_software.name / _em_software.version

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Assembly

Deposited unit
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 type Z
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
V: 30S ribosomal protein Thx
W: Translation initiation factor IF-1
X: Translation initiation factor IF-3
Y: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)826,828134
Polyers824,07224
Non-polymers2,756110
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)121370
ΔGint (kcal/M)-1756
Surface area (Å2)274890
MethodPISA

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Components

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RNA chain , 2 types, 2 molecules AY

#1: RNA chain16S rRNA


Mass: 493958.281 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus HB8 / References: GenBank: 55771382
#24: RNA chainmRNA


Mass: 12525.466 Da / Num. of mol.: 1 / Source: (synth.) Thermus thermophilus

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

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


Mass: 29317.703 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: P80371

Cellular component

Molecular function

Biological process

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


Mass: 26751.076 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: P80372

Cellular component

Molecular function

Biological process

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


Mass: 24373.447 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: P80373

Cellular component

Molecular function

Biological process

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


Mass: 17583.416 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SHQ5

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)30S ribosomal protein S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SLP8

Cellular component

Molecular function

Biological process

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


Mass: 18050.973 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: P17291

Cellular component

Molecular function

Biological process

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


Mass: 15868.570 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SHQ2

Cellular component

Molecular function

Biological process

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


Mass: 14410.614 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: P80374

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)30S ribosomal protein S10


Mass: 11954.968 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SHN7

Cellular component

Molecular function

Biological process

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


Mass: 13737.868 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: P80376

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)30S ribosomal protein S12


Mass: 14637.384 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SHN3

Cellular component

Molecular function

Biological process

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


Mass: 14338.861 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: P80377

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)30S ribosomal protein S14 type Z


Mass: 7158.725 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SHQ1

Cellular component

Molecular function

Biological process

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


Mass: 10578.407 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SJ76

Cellular component

Molecular function

Biological process

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


Mass: 10409.983 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SJH3

Cellular component

Molecular function

Biological process

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


Mass: 12325.655 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SHP7

Cellular component

Molecular function

Biological process

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


Mass: 10258.299 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SLQ0

Cellular component

Molecular function

Biological process

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


Mass: 10605.464 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SHP2

Cellular component

Molecular function

Biological process

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


Mass: 11736.143 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: P80380

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)30S ribosomal protein Thx / S31


Mass: 3350.030 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SIH3

Cellular component

Molecular function

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Translation initiation factor IF- ... , 2 types, 2 molecules WX

#22: Polypeptide(L)Translation initiation factor IF-1


Mass: 8247.664 Da / Num. of mol.: 1
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SHR1

Cellular component

Molecular function

#23: Polypeptide(L)Translation initiation factor IF-3


Mass: 19904.377 Da / Num. of mol.: 1
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SKU2

Cellular component

Molecular function

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Non-polymers , 2 types, 110 molecules

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


Mass: 24.305 Da / Num. of mol.: 108 / Formula: Mg
#26: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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

ComponentName: 30S-IF1-IF3-mRNA pre-initiation complex (state-1C) / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24
Source: MULTIPLE SOURCES
Molecular weightValue: 0.8261 deg. / Units: MEGADALTONS / Experimental value: NO
Buffer solutionpH: 7.5
Buffer component
IDConc.UnitsNameBuffer ID
15mMHepes-K1
210mMMagnessium acetate1
350mMPotassium chloride1
410mMAmmonium chloride1
56mMBeta mercaptoethanol1
SpecimenConc.: 0.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 78000 / Calibrated magnification: 104478 / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / C2 aperture diameter: 50 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Temperature (max): 100 kelvins / Temperature (min): 90 kelvins
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 30 e/Å2
Details: Recorded in a FEI Falcon III direct electron detector. Images were collected in movie-mode at 32 frames per second
Film or detector model: OTHER / Number of grids imaged: 5 / Number of real images: 4400

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1RELION1.4PARTICLE SELECTION1
2EMANPARTICLE SELECTION1
3EPUIMAGE ACQUISITION1
5CTFFIND3CTF CORRECTION1
8UCSF Chimera1.1MODEL FITTING1
9Coot0.8MODEL FITTING1
11RELION1.4INITIAL EULER ASSIGNMENT1
12RELION1.4FINAL EULER ASSIGNMENT1
13RELION1.4CLASSIFICATION1
14RELION1.4RECONSTRUCTION1
15REFMAC5.8MODEL REFINEMENT1
Image processingDetails: FEI Falcon III
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 666610
3D reconstructionResolution: 5.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 18830 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: RECIPROCAL / Target criteria: FSC

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