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- EMDB-3770: Human 40S-eIF2D-re-initiation complex -

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Entry
Database: EMDB / ID: 3770
TitleHuman 40S-eIF2D-re-initiation complex
Samplehuman translation re-initiation complex of eIFD, initiator tRNA and the small ribosomal subunit
SourceHomo sapiens / human
Hepatitis C virus / virus
Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map dataThis map was used for refinement (boxed and map origin re-set to 0).
Methodsingle particle reconstruction, at 4.2 Å resolution
AuthorsWeisser M / Schaefer T
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 ReportPDB-ID: 5oa3

SummaryFull reportAbout validation report
DateDeposition: Jun 20, 2017 / Header (metadata) release: Aug 9, 2017 / Map release: Aug 9, 2017 / Last update: Aug 16, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.12
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5oa3
  • Surface level: 0.12
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_3770.map.gz (map file in CCP4 format, 30119 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
196 pix
1.4 Å/pix.
= 274.4 Å
196 pix
1.4 Å/pix.
= 274.4 Å
196 pix
1.4 Å/pix.
= 274.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour Level:0.09 (by author), 0.12 (movie #1):
Minimum - Maximum-0.64837015 - 0.8811471
Average (Standard dev.)0.007678762 (0.047832664)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions196196196
Origin000
Limit195195195
Spacing196196196
CellA=B=C: 274.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z274.400274.400274.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-0.6480.8810.008

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Supplemental data

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Sample components

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Entire human translation re-initiation complex of eIFD, initiator tRNA a...

EntireName: human translation re-initiation complex of eIFD, initiator tRNA and the small ribosomal subunit
Number of components: 44
MassTheoretical: 1.4 MDa

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Component #1: protein, human translation re-initiation complex of eIFD, initiat...

ProteinName: human translation re-initiation complex of eIFD, initiator tRNA and the small ribosomal subunit
Recombinant expression: No
MassTheoretical: 1.4 MDa

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Component #2: protein, eIF2D

ProteinName: eIF2D / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #3: protein, small ribosomal subunit

ProteinName: small ribosomal subunit / Recombinant expression: No
SourceSpecies: Homo sapiens / human

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Component #4: protein, HCV IRES mRNA

ProteinName: HCV IRES mRNA / Recombinant expression: No
SourceSpecies: Hepatitis C virus / virus
Source (engineered)Expression System: Synthetic construct

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Component #5: protein, initiator Met-tRNA-i

ProteinName: initiator Met-tRNA-i / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #6: protein, Eukaryotic translation initiation factor 2D

ProteinName: Eukaryotic translation initiation factor 2D / Recombinant expression: No
MassTheoretical: 64.788301 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #7: nucleic-acid, initiator Met-tRNA-i

Nucleic-acidName: initiator Met-tRNA-i / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGCGCCGUGG CGCAGUGGAA GCGCGCAGGG CUCAUAACCC UGAUGUCCUC GGAUCGAAAC CGAGCGGCGC UACCA
MassTheoretical: 24.2385 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #8: nucleic-acid, 18S ribosomal RNA

Nucleic-acidName: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGUUCCUU UGGUCGCUCG CUCCUCUCCU ACUUGGAUAA CUGUGGUAAU UCUAGAGCUA AUACAUGCCG ACGGGCGCUG ACCCCCUUCG CGGGGGGGAU GCGUGCAUUU AUCAGAUCAA AACCAACCCG GUCAGCCCCU CUCCGGCCCC GGCCGGGGGG CGGGCCGCGG CGGCUUUGGU GACUCUAGAU AACCUCGGGC CGAUCGCACG CCCCCCGUGG CGGCGACGAC CCAUUCGAAC GUCUGCCCUA UCAACUUUCG AUGGUAGUCG CCGUGCCUAC CAUGGUGACC ACGGGUGACG GGGAAUCAGG GUUCGAUUCC GGAGAGGGAG CCUGAGAAAC GGCUACCACA UCCAAGGAAG GCAGCAGGCG CGCAAAUUAC CCACUCCCGA CCCGGGGAGG UAGUGACGAA AAAUAACAAU ACAGGACUCU UUCGAGGCCC UGUAAUUGGA AUGAGUCCAC UUUAAAUCCU UUAACGAGGA UCCAUUGGAG GGCAAGUCUG GUGCCAGCAG CCGCGGUAAU UCCAGCUCCA AUAGCGUAUA UUAAAGUUGC UGCAGUUAAA AAGCUCGUAG UUGGAUCUUG GGAGCGGGCG GGCGGUCCGC CGCGAGGCGA GCCACCGCCC GUCCCCGCCC CUUGCCUCUC GGCGCCCCCU CGAUGCUCUU AGCUGAGUGU CCCGCGGGGC CCGAAGCGUU UACUUUGAAA AAAUUAGAGU GUUCAAAGCA GGCCCGAGCC GCCUGGAUAC CGCAGCUAGG AAUAAUGGAA UAGGACCGCG GUUCUAUUUU GUUGGUUUUC GGAACUGAGG CCAUGAUUAA GAGGGACGGC CGGGGGCAUU CGUAUUGCGC CGCUAGAGGU GAAAUUCUUG GACCGGCGCA AGACGGACCA GAGCGAAAGC AUUUGCCAAG AAUGUUUUCA UUAAUCAAGA ACGAAAGUCG GAGGUUCGAA GACGAUCAGA UACCGUCGUA GUUCCGACCA UAAACGAUGC CGACCGGCGA UGCGGCGGCG UUAUUCCCAU GACCCGCCGG GCAGCUUCCG GGAAACCAAA GUCUUUGGGU UCCGGGGGGA GUAUGGUUGC AAAGCUGAAA CUUAAAGGAA UUGACGGAAG GGCACCACCA GGAGUGGAGC CUGCGGCUUA AUUUGACUCA ACACGGGAAA CCUCACCCGG CCCGGACACG GACAGGAUUG ACAGAUUGAU AGCUCUUUCU CGAUUCCGUG GGUGGUGGUG CAUGGCCGUU CUUAGUUGGU GGAGCGAUUU GUCUGGUUAA UUCCGAUAAC GAACGAGACU CUGGCAUGCU AACUAGUUAC GCGACCCCCG AGCGGUCGGC GUCCCCCAAC UUCUUAGAGG GACAAGUGGC GUUCAGCCAC CCGAGAUUGA GCAAUAACAG GUCUGUGAUG CCCUUAGAUG UCCGGGGCUG CACGCGCGCU ACACUGACUG GCUCAGCGUG UGCCUACCCU ACGCCGGCAG GCGCGGGUAA CCCGUUGAAC CCCAUUCGUG AUGGGGAUCG GGGAUUGCAA UUAUUCCCCA UGAACGAGGA AUUCCCAGUA AGUGCGGGUC AUAAGCUUGC GUUGAUUAAG UCCCUGCCCU UUGUACACAC CGCCCGUCGC UACUACCGAU UGGAUGGUUU AGUGAGGCCC UCGGAUCGGC CCCGCCGGGG UCGGCCCACG GCCUGGCGGA GCGCUGAGAA GACGGUCGAA CUUGACUAUC UAGAGGAAGU AAAAGUCGUA ACAAGGUUUC CGUAGGUGAA CCUGCGGAAG GAUCAUUA
MassTheoretical: 602.472688 kDa
SourceSpecies: Homo sapiens / human

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Component #9: nucleic-acid, IRES mRNA

Nucleic-acidName: IRES mRNA / Class: RNA
Details: HCV IRES mRNA (delta domain II mutant, in which domain II of the IRES is replaced with a small stem loop)
Structure: OTHER / Synthetic: No
Sequence:
CUCCCCUGCU UCGGCAGGAC CCCCCCUCCC GGGAGAGCCA UAGUGGUCUG CGGAACCGGU GAGUACACCG GAAUUGCCAG GACGACCGGG UCCUUUCUUG GAUAAACCCG CUCAAUGCCU GGAGAUUUGG GCGUGCCCCC GCAAGACUGC UAGCCGAGUA GUGUUGGGUC GCGAAAGGCC UUGUGGUACU GCCUGAUAGG GUGCUUGCGA GUGCCCCGGG AGGUCUCGUA GACCGUGCAC CAUGAGCACG AAUCCUAAAC CUCAAAGAAA AAGAU
MassTheoretical: 88.648414 kDa

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Component #10: protein, 40S ribosomal protein SA

ProteinName: 40S ribosomal protein SA / Recombinant expression: No
MassTheoretical: 32.883938 kDa
SourceSpecies: Homo sapiens / human

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Component #11: protein, 40S ribosomal protein S3a

ProteinName: 40S ribosomal protein S3a / Recombinant expression: No
MassTheoretical: 30.002061 kDa
SourceSpecies: Homo sapiens / human

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Component #12: protein, 40S ribosomal protein S2

ProteinName: 40S ribosomal protein S2 / Recombinant expression: No
MassTheoretical: 31.376516 kDa
SourceSpecies: Homo sapiens / human

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Component #13: protein, 40S ribosomal protein S3

ProteinName: 40S ribosomal protein S3 / Recombinant expression: No
MassTheoretical: 26.729369 kDa
SourceSpecies: Homo sapiens / human

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Component #14: protein, 40S ribosomal protein S4, X isoform

ProteinName: 40S ribosomal protein S4, X isoform / Recombinant expression: No
MassTheoretical: 29.654869 kDa
SourceSpecies: Homo sapiens / human

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Component #15: protein, 40S ribosomal protein S5

ProteinName: 40S ribosomal protein S5 / Recombinant expression: No
MassTheoretical: 22.913453 kDa
SourceSpecies: Homo sapiens / human

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Component #16: protein, 40S ribosomal protein S6

ProteinName: 40S ribosomal protein S6 / Recombinant expression: No
MassTheoretical: 28.751906 kDa
SourceSpecies: Homo sapiens / human

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Component #17: protein, 40S ribosomal protein S7

ProteinName: 40S ribosomal protein S7 / Recombinant expression: No
MassTheoretical: 22.168914 kDa
SourceSpecies: Homo sapiens / human

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Component #18: protein, 40S ribosomal protein S8

ProteinName: 40S ribosomal protein S8 / Recombinant expression: No
MassTheoretical: 24.263387 kDa
SourceSpecies: Homo sapiens / human

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Component #19: protein, 40S ribosomal protein S9

ProteinName: 40S ribosomal protein S9 / Recombinant expression: No
MassTheoretical: 22.641564 kDa
SourceSpecies: Homo sapiens / human

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Component #20: protein, 40S ribosomal protein S10

ProteinName: 40S ribosomal protein S10 / Recombinant expression: No
MassTheoretical: 18.933846 kDa
SourceSpecies: Homo sapiens / human

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Component #21: protein, 40S ribosomal protein S11

ProteinName: 40S ribosomal protein S11 / Recombinant expression: No
MassTheoretical: 18.468826 kDa
SourceSpecies: Homo sapiens / human

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Component #22: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Recombinant expression: No
MassTheoretical: 14.538987 kDa
SourceSpecies: Homo sapiens / human

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Component #23: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Recombinant expression: No
MassTheoretical: 17.259389 kDa
SourceSpecies: Homo sapiens / human

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Component #24: protein, 40S ribosomal protein S14

ProteinName: 40S ribosomal protein S14 / Recombinant expression: No
MassTheoretical: 16.302772 kDa
SourceSpecies: Homo sapiens / human

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Component #25: protein, 40S ribosomal protein S15

ProteinName: 40S ribosomal protein S15 / Recombinant expression: No
MassTheoretical: 17.076207 kDa
SourceSpecies: Homo sapiens / human

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Component #26: protein, 40S ribosomal protein S16

ProteinName: 40S ribosomal protein S16 / Recombinant expression: No
MassTheoretical: 16.477377 kDa
SourceSpecies: Homo sapiens / human

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Component #27: protein, 40S ribosomal protein S17

ProteinName: 40S ribosomal protein S17 / Recombinant expression: No
MassTheoretical: 15.578156 kDa
SourceSpecies: Homo sapiens / human

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Component #28: protein, 40S ribosomal protein S18

ProteinName: 40S ribosomal protein S18 / Recombinant expression: No
MassTheoretical: 17.759777 kDa
SourceSpecies: Homo sapiens / human

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Component #29: protein, 40S ribosomal protein S19

ProteinName: 40S ribosomal protein S19 / Recombinant expression: No
MassTheoretical: 16.091562 kDa
SourceSpecies: Homo sapiens / human

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Component #30: protein, 40S ribosomal protein S20

ProteinName: 40S ribosomal protein S20 / Recombinant expression: No
MassTheoretical: 13.398763 kDa
SourceSpecies: Homo sapiens / human

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Component #31: protein, 40S ribosomal protein S21

ProteinName: 40S ribosomal protein S21 / Recombinant expression: No
MassTheoretical: 9.124389 kDa
SourceSpecies: Homo sapiens / human

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Component #32: protein, 40S ribosomal protein S15a

ProteinName: 40S ribosomal protein S15a / Recombinant expression: No
MassTheoretical: 14.865555 kDa
SourceSpecies: Homo sapiens / human

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Component #33: protein, 40S ribosomal protein S23

ProteinName: 40S ribosomal protein S23 / Recombinant expression: No
MassTheoretical: 15.844666 kDa
SourceSpecies: Homo sapiens / human

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Component #34: protein, 40S ribosomal protein S24

ProteinName: 40S ribosomal protein S24 / Recombinant expression: No
MassTheoretical: 15.107924 kDa
SourceSpecies: Homo sapiens / human

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Component #35: protein, 40S ribosomal protein S25

ProteinName: 40S ribosomal protein S25 / Recombinant expression: No
MassTheoretical: 13.776224 kDa
SourceSpecies: Homo sapiens / human

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Component #36: protein, 40S ribosomal protein S26

ProteinName: 40S ribosomal protein S26 / Recombinant expression: No
MassTheoretical: 11.645794 kDa
SourceSpecies: Homo sapiens / human

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Component #37: protein, 40S ribosomal protein S27

ProteinName: 40S ribosomal protein S27 / Recombinant expression: No
MassTheoretical: 9.210843 kDa
SourceSpecies: Homo sapiens / human

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Component #38: protein, 40S ribosomal protein S28

ProteinName: 40S ribosomal protein S28 / Recombinant expression: No
MassTheoretical: 6.87894 kDa
SourceSpecies: Homo sapiens / human

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Component #39: protein, 40S ribosomal protein S29

ProteinName: 40S ribosomal protein S29 / Recombinant expression: No
MassTheoretical: 6.559625 kDa
SourceSpecies: Homo sapiens / human

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Component #40: protein, 40S ribosomal protein S30

ProteinName: 40S ribosomal protein S30 / Recombinant expression: No
MassTheoretical: 6.30248 kDa
SourceSpecies: Homo sapiens / human

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Component #41: protein, Ribosomal protein S27a

ProteinName: Ribosomal protein S27a / Recombinant expression: No
MassTheoretical: 8.45315 kDa
SourceSpecies: Homo sapiens / human

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Component #42: protein, Receptor of activated protein C kinase 1

ProteinName: Receptor of activated protein C kinase 1 / Recombinant expression: No
MassTheoretical: 34.857355 kDa
SourceSpecies: Homo sapiens / human

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Component #43: protein, RIBOSOMAL PROTEIN EL41

ProteinName: RIBOSOMAL PROTEIN EL41 / Recombinant expression: No
MassTheoretical: 3.342255 kDa
SourceSpecies: Homo sapiens / human

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Component #44: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.11 mg/ml / pH: 7.6
VitrificationCryogen name: ETHANE-PROPANE MIXTURE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 62177
3D reconstructionSoftware: RELION / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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