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- PDB-5oa3: Human 40S-eIF2D-re-initiation complex -

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Entry
Database: PDB / ID: 5oa3
TitleHuman 40S-eIF2D-re-initiation complex
DescriptorEukaryotic translation initiation factor 2D
X isoform
Ribosomal protein S27a
Receptor of activated protein C kinase 1
RIBOSOMAL PROTEIN EL41/RNA Complex
(40S ribosomal protein ...) x 31
KeywordsTRANSLATION / translation re-initiation complex / small ribosomal subunit / RNA binding protein / eukaryotic translation initiation factor
Specimen sourceHomo sapiens / human
Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Hepatitis C virus / virus
MethodElectron microscopy (4.2 Å resolution / Particle / Single particle)
AuthorsWeisser, M. / Schaefer, T. / Leibundgut, M. / Boehringer, D. / Aylett, C.H.S. / Ban, N.
CitationMol. Cell, 2017, 67, 447-456.e7

Mol. Cell, 2017, 67, 447-456.e7 Yorodumi Papers
Structural and Functional Insights into Human Re-initiation Complexes.
Melanie Weisser / Tanja Schäfer / Marc Leibundgut / Daniel Böhringer / Christopher Herbert Stanley Aylett / Nenad Ban

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 20, 2017 / Release: Aug 9, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 9, 2017Structure modelrepositoryInitial release
1.1Aug 16, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
0: Eukaryotic translation initiation factor 2D
1: initiator Met-tRNA-i
2: 18S ribosomal RNA
3: IRES mRNA
A: 40S ribosomal protein SA
B: 40S ribosomal protein S3a
C: 40S ribosomal protein S2
D: 40S ribosomal protein S3
E: 40S ribosomal protein S4, X isoform
F: 40S ribosomal protein S5
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: 40S ribosomal protein S9
K: 40S ribosomal protein S10
L: 40S ribosomal protein S11
M: 40S ribosomal protein S12
N: 40S ribosomal protein S13
O: 40S ribosomal protein S14
P: 40S ribosomal protein S15
Q: 40S ribosomal protein S16
R: 40S ribosomal protein S17
S: 40S ribosomal protein S18
T: 40S ribosomal protein S19
U: 40S ribosomal protein S20
V: 40S ribosomal protein S21
W: 40S ribosomal protein S15a
X: 40S ribosomal protein S23
Y: 40S ribosomal protein S24
Z: 40S ribosomal protein S25
a: 40S ribosomal protein S26
b: 40S ribosomal protein S27
c: 40S ribosomal protein S28
d: 40S ribosomal protein S29
e: 40S ribosomal protein S30
f: Ribosomal protein S27a
g: Receptor of activated protein C kinase 1
h: RIBOSOMAL PROTEIN EL41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,389,58541
Polyers1,389,38938
Non-polymers1963
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)201360
ΔGint (kcal/M)-1501
Surface area (Å2)464010
MethodPISA

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Components

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Polypeptide(L) , 4 types, 4 molecules 0fgh

#1: Polypeptide(L)Eukaryotic translation initiation factor 2D / eIF2d / Hepatocellular carcinoma-associated antigen 56 / Ligatin


Mass: 64788.301 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / References: UniProt: P41214
#36: Polypeptide(L)Ribosomal protein S27a


Mass: 8453.150 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: Q5RKT7
#37: Polypeptide(L)Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 34857.355 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P63244
#38: Polypeptide(L)RIBOSOMAL PROTEIN EL41


Mass: 3342.255 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens

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RNA chain , 3 types, 3 molecules 123

#2: RNA chaininitiator Met-tRNA-i


Mass: 24238.500 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: 176433
#3: RNA chain18S ribosomal RNA


Mass: 602472.688 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: GenBank: 337376
#4: RNA chainIRES mRNA


Mass: 88648.414 Da / Num. of mol.: 1
Details: HCV IRES mRNA (delta domain II mutant, in which domain II of the IRES is replaced with a small stem loop)
Fragment: (delta domain II mutant, in which domain II of the IRES is replaced with a small stem loop
Source: (synth.) Hepatitis C virus / References: GenBank: 555439351

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40S ribosomal protein ... , 31 types, 31 molecules ABCDEFGHIJ...

#5: Polypeptide(L)40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 32883.938 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P08865
#6: Polypeptide(L)40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P61247
#7: Polypeptide(L)40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 31376.516 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P15880
#8: Polypeptide(L)40S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P23396, EC: 4.2.99.18
#9: Polypeptide(L)40S ribosomal protein S4, X isoform / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62701
#10: Polypeptide(L)40S ribosomal protein S5 / Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P46782
#11: Polypeptide(L)40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62753
#12: Polypeptide(L)40S ribosomal protein S7 / Small ribosomal subunit protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62081
#13: Polypeptide(L)40S ribosomal protein S8 / Small ribosomal subunit protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62241
#14: Polypeptide(L)40S ribosomal protein S9 / Small ribosomal subunit protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P46781
#15: Polypeptide(L)40S ribosomal protein S10 / Small ribosomal subunit protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P46783
#16: Polypeptide(L)40S ribosomal protein S11 / Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62280
#17: Polypeptide(L)40S ribosomal protein S12 / Small ribosomal subunit protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P25398
#18: Polypeptide(L)40S ribosomal protein S13 / Small ribosomal subunit protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62277
#19: Polypeptide(L)40S ribosomal protein S14 / Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62263
#20: Polypeptide(L)40S ribosomal protein S15 / RIG protein / Small ribosomal subunit protein uS19


Mass: 17076.207 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62841
#21: Polypeptide(L)40S ribosomal protein S16 / Small ribosomal subunit protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62249
#22: Polypeptide(L)40S ribosomal protein S17 / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P08708
#23: Polypeptide(L)40S ribosomal protein S18 / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62269
#24: Polypeptide(L)40S ribosomal protein S19 / Small ribosomal subunit protein eS19


Mass: 16091.562 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P39019
#25: Polypeptide(L)40S ribosomal protein S20 / Small ribosomal subunit protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P60866
#26: Polypeptide(L)40S ribosomal protein S21 / Small ribosomal subunit protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P63220
#27: Polypeptide(L)40S ribosomal protein S15a / Small ribosomal subunit protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62244
#28: Polypeptide(L)40S ribosomal protein S23 / Small ribosomal subunit protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62266
#29: Polypeptide(L)40S ribosomal protein S24 / Small ribosomal subunit protein eS24


Mass: 15107.924 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62847
#30: Polypeptide(L)40S ribosomal protein S25 / Small ribosomal subunit protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62851
#31: Polypeptide(L)40S ribosomal protein S26 / Small ribosomal subunit protein eS26


Mass: 11645.794 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62854
#32: Polypeptide(L)40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9210.843 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P42677
#33: Polypeptide(L)40S ribosomal protein S28 / Small ribosomal subunit protein eS28


Mass: 6878.940 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62857
#34: Polypeptide(L)40S ribosomal protein S29 / Small ribosomal subunit protein uS14


Mass: 6559.625 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62273
#35: Polypeptide(L)40S ribosomal protein S30 / Small ribosomal subunit protein eS30


Mass: 6302.480 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P62861

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Non-polymers , 1 types, 3 molecules

#39: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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 IDSource
1human translation re-initiation complex of eIFD, initiator tRNA and the small ribosomal subunitCOMPLEX1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,380MULTIPLE SOURCES
2eIF2DCOMPLEX11RECOMBINANT
3small ribosomal subunitCOMPLEX3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,381NATURAL
4HCV IRES mRNACOMPLEX41RECOMBINANT
5initiator Met-tRNA-iCOMPLEX21NATURAL
Molecular weightValue: 1.4 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens
239606Homo sapiens
3411103Hepatitis C virus
454932Saccharomyces cerevisiae
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
12562Escherichia coli
2432630Synthetic construct
Buffer solutionpH: 7.6
Buffer component
IDConc.UnitsNameFormulaBuffer ID
125mMHEPES-KOH1
275mMPotassium chlorideKCl1
32.5mMMagnesium acetate1
42mMDTT1
SpecimenConc.: 0.11 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE-PROPANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDDetails
1EMAN1PARTICLE SELECTION1
4RELION1.4CTF CORRECTION1CTFFIND4
10RELIONINITIAL EULER ASSIGNMENT1
11RELIONFINAL EULER ASSIGNMENT1
12RELIONCLASSIFICATION1
13RELIONRECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 62177 / Symmetry type: POINT
Refine
Refine IDR factor R freeR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection R freeNumber reflection obsPercent reflection R freePercent reflection obsOverall SU MLSigma FOverall phase errorSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
10.32520.30180.30244.30048.508136075435652.5099.920.741.1833.960.901.11MLHLFLAT BULK SOLVENT MODEL
ELECTRON MICROSCOPY
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00589370
ELECTRON MICROSCOPYf_angle_d0.923129914
ELECTRON MICROSCOPYf_dihedral_angle_d18.78140002
ELECTRON MICROSCOPYf_chiral_restr0.03916099
ELECTRON MICROSCOPYf_plane_restr0.0059328
Refine LS shell

Refine ID: ELECTRON MICROSCOPY

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
4.30010.44820.44184.348942217665100.00
4.34890.42210.41704.400144518049100.00
4.40010.43700.40434.453743617528100.00
4.45370.43740.39114.510043917718100.00
4.51000.43880.38424.569345117631100.00
4.56930.38810.37214.631943917522100.00
4.63190.38450.36854.698046717696100.00
4.69800.35800.35564.768146817841100.00
4.76810.34610.34304.842543017649100.00
4.84250.38180.33644.921842817677100.00
4.92180.36630.33035.006643317735100.00
5.00660.34450.32355.097648117702100.00
5.09760.35560.32195.195546417393100.00
5.19550.33910.31855.301443917826100.00
5.30140.32090.30815.416544617587100.00
5.41650.32040.30025.542446817707100.00
5.54240.32770.29585.680845217693100.00
5.68080.31880.29075.834149617789100.00
5.83410.32870.28466.005543917732100.00
6.00550.31100.27796.199044717578100.00
6.19900.31110.27476.420046217626100.00
6.42000.29460.26836.676546917700100.00
6.67650.29010.26006.979545417736100.00
6.97950.27460.24967.346346317481100.00
7.34630.25310.23217.804848917725100.00
7.80480.26720.23198.404549417757100.00
8.40450.26560.22329.245043817797100.00
9.24500.22770.207810.570745017579100.00
10.57070.20810.188013.27274511727699.00
13.27270.21210.198348.51064471756399.00

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