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

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Basic information

Entry
Database: PDB / ID: 5oa3
TitleHuman 40S-eIF2D-re-initiation complex
Components
  • (40S ribosomal protein ...) x 31
  • 18S ribosomal RNA
  • Eukaryotic translation initiation factor 2D
  • IRES mRNA
  • RIBOSOMAL PROTEIN EL41
  • Receptor of activated protein C kinase 1
  • Ribosomal protein S27aRibosome
  • initiator Met-tRNA-i
KeywordsTRANSLATION / translation re-initiation complex / small ribosomal subunit / RNA binding protein / eukaryotic translation initiation factor
Function / homologyRibosomal protein S4/S9, N-terminal / Ubiquitin / 30s ribosomal protein S13, C-terminal / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S15P / Ribosomal protein S4/S9 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S19 conserved site ...Ribosomal protein S4/S9, N-terminal / Ubiquitin / 30s ribosomal protein S13, C-terminal / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S15P / Ribosomal protein S4/S9 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S19 conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / Ubiquitin conserved site / Ribosomal protein S2, eukaryotic / WD40 repeat, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S5/S7 / Ribosomal protein S17/S11 / Ribosomal protein S28e / Ribosomal protein S12e / Ribosomal protein S7e / Ribosomal protein S15 / Ribosomal protein S27e / Ubiquitin domain / Ribosomal protein S8 / Ribosomal protein S10 domain / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S5 / SUI1 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / S27a-like superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S26e superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S19e domain superfamily / 40S Ribosomal protein S10 / RNA-binding S4 domain superfamily / PUA domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S19e, conserved site / Ribosomal protein S10 domain superfamily / 40S ribosomal protein SA / Ribosomal protein S7 domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein S8 superfamily / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein S4, C-terminal domain / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S9 / Ribosomal protein S4e / Ribosomal protein S19 / Ribosomal protein S6, eukaryotic / Ribosomal protein S12/S23 / Ribosomal protein S30 / Ribosomal protein L41 / K homology domain superfamily, prokaryotic type / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L2, domain 2 / WD40/YVTN repeat-like-containing domain superfamily / K homology domain-like, alpha/beta / PUA-like superfamily / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / KOW / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S26e
Function and homology information
Specimen sourceHomo sapiens (human)
Saccharomyces cerevisiae (baker's yeast)
Hepatitis C virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsWeisser, M. / Schaefer, T. / Leibundgut, M. / Boehringer, D. / Aylett, C.H.S. / Ban, N.
CitationJournal: Mol. Cell / Year: 2017
Title: Structural and Functional Insights into Human Re-initiation Complexes.
Authors: Melanie Weisser / Tanja Schäfer / Marc Leibundgut / Daniel Böhringer / Christopher Herbert Stanley Aylett / Nenad Ban
Abstract: After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large ...After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large fraction of mammalian cellular mRNAs, many of which are important in cancer. Key ribosomal binding proteins involved in re-initiation are the eukaryotic translation initiation factor 2D (eIF2D) or the homologous complex of MCT-1/DENR. We determined the structures of these factors bound to the human 40S ribosomal subunit in complex with initiator tRNA positioned on an mRNA start codon in the P-site using a combination of cryoelectron microscopy and X-ray crystallography. The structures, supported by biochemical experiments, reveal how eIF2D emulates the function of several canonical translation initiation factors by using three independent, flexibly connected RNA binding domains to simultaneously monitor codon-anticodon interactions in the ribosomal P-site and position the initiator tRNA.
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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Structure visualization

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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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Protein/peptide , 4 types, 4 molecules 0fgh

#1: Protein/peptide 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 (human) / Gene: EIF2D, HCA56, LGTN / Production host: Escherichia coli (E. coli) / References: UniProt: P41214
#36: Protein/peptide Ribosomal protein S27a / Ribosome


Mass: 8453.150 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q5RKT7
#37: Protein/peptide 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 (human) / References: UniProt: P63244
#38: Protein/peptide RIBOSOMAL PROTEIN EL41 /


Mass: 3342.255 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P62945*PLUS

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RNA chain , 3 types, 3 molecules 123

#2: RNA chain initiator Met-tRNA-i


Mass: 24238.500 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 176433
#3: RNA chain 18S ribosomal RNA /


Mass: 602472.688 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: GenBank: 337376
#4: RNA chain IRES 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 ABCDEFGHIJKLMNOPQRSTUVWXYZabcde

#5: Protein/peptide 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 (human) / References: UniProt: P08865
#6: Protein/peptide 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 (human) / References: UniProt: P61247
#7: Protein/peptide 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 (human) / References: UniProt: P15880
#8: Protein/peptide 40S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#9: Protein/peptide 40S ribosomal protein S4, X isoform / Ribosome / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 11645.794 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#32: Protein/peptide 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 (human) / References: UniProt: P42677
#33: Protein/peptide 40S ribosomal protein S28 / / Small ribosomal subunit protein eS28


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


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


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

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Non-polymers , 1 types, 3 molecules

#39: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Formula: Zn / Zinc

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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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 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens (human)
239606Homo sapiens (human)
3411103Hepatitis C virus
454932Saccharomyces cerevisiae (baker's yeast)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
12562Escherichia coli (E. coli)
2432630Synthetic construct (others)
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer ID
125 mMHEPES-KOH1
275 mMPotassium chlorideKCl1
32.5 mMMagnesium acetate1
42 mMDTT1
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 FIELDBright-field microscopy
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
IDNameVersionCategoryDetails
1EMAN1particle selection
4RELION1.4CTF correctionCTFFIND4
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
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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