[English] 日本語
Yorodumi
- EMDB-4242: Human cap-dependent 48S pre-initiation complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 4242
TitleHuman cap-dependent 48S pre-initiation complex
Map datahuman 48S pre-initiation complex, reconstituted in the presence of capped mRNA, eIF4B and eIF4F, displaying eIF2 ternary complex, eIF3 and eIF4B
Samplehuman cap-dependent 48S translation pre-initiation complex
  • mRNAMessenger RNA
  • (EUKARYOTIC TRANSLATION INITIATION FACTOR ...) x 15
  • (nucleic-acidNucleic acid) x 3
  • (40S ribosomal protein ...) x 31
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
  • ligand
Function / homologyRibosomal protein S17e, conserved site / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S13-like, H2TH / Eukaryotic translation initiation factor 3 subunit K / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation protein, beta-barrel domain superfamily / Ribosomal protein S30 / Ribosomal protein S12/S23 ...Ribosomal protein S17e, conserved site / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S13-like, H2TH / Eukaryotic translation initiation factor 3 subunit K / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation protein, beta-barrel domain superfamily / Ribosomal protein S30 / Ribosomal protein S12/S23 / KOW / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S23, eukaryotic/archaeal / Plectin/S10, N-terminal / Ribosomal protein S25 / Translation elongation factor EFTu-like, domain 2 / K Homology domain, type 2 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / RNA-binding S4 domain / Ribosomal protein S27a / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein S24e / Eukaryotic translation initiation factor 3 subunit E / Ribosomal protein S4 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / Armadillo-type fold / Ribosomal protein S13/S15, N-terminal / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / K homology domain-like, alpha/beta / WD40/YVTN repeat-like-containing domain superfamily / Translation initiation factor 2, gamma subunit, C-terminal / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein S19/S15 / Ribosomal protein S11 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S13 family profile. / Ribosomal protein S28e signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S2 signature 2. / Ribosomal protein S27e signature. / Ribosomal protein S12e signature. / Ribosomal protein S3Ae signature. / Ribosomal protein S8e signature. / Ubiquitin domain profile. / Trp-Asp (WD) repeats profile. / Eukaryotic RNA Recognition Motif (RRM) profile. / PCI domain profile. / Ribosomal protein S17e signature. / Trp-Asp (WD) repeats circular profile. / Type-2 KH domain profile. / S4 RNA-binding domain profile. / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S6e signature. / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / ISG15 antiviral mechanism / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Ribosomal protein S7e signature. / Trp-Asp (WD) repeats signature. / Ribosomal protein S4/S9, N-terminal / Transcription factor, GTP-binding domain / Ribosomal protein S13 / Ribosomal protein S2 / Ribosomal protein S10 / WD40 repeat / Ribosomal protein S3Ae / Ribosomal protein S6e / Ribosomal protein S3, C-terminal / Ribosomal protein S17e / Ribosomal protein S14 / Ribosomal protein S8e / Ribosomal protein S4e / Ribosomal protein S9 / Ribosomal protein S13 signature. / Proteasome component (PCI) domain / Ribosomal protein S8 / Ubiquitin domain / Ribosomal protein S27e
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 6.3 Å resolution
AuthorsSchaffitzel C / Schaffitzel C
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structure of a human cap-dependent 48S translation pre-initiation complex.
Authors: Boris Eliseev / Lahari Yeramala / Alexander Leitner / Manikandan Karuppasamy / Etienne Raimondeau / Karine Huard / Elena Alkalaeva / Ruedi Aebersold / Christiane Schaffitzel
Validation ReportPDB-ID: 6fec

SummaryFull reportAbout validation report
DateDeposition: Dec 31, 2017 / Header (metadata) release: Mar 14, 2018 / Map release: Mar 14, 2018 / Last update: Apr 4, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6fec
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_4242.map.gz (map file in CCP4 format, 35996 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
208 pix
2.5 Å/pix.
= 520. Å
208 pix
2.5 Å/pix.
= 520. Å
208 pix
2.5 Å/pix.
= 520. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density
Contour Level:0.05 (by author), 0.08 (movie #1):
Minimum - Maximum-0.32222414 - 0.5438056
Average (Standard dev.)-0.000108246015 (0.027071523)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions208208208
Origin000
Limit207207207
Spacing208208208
CellA=B=C: 520.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z208208208
origin x/y/z0.0000.0000.000
length x/y/z520.000520.000520.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS208208208
D min/max/mean-0.3220.544-0.000

-
Supplemental data

-
Sample components

+
Entire human cap-dependent 48S translation pre-initiation complex

EntireName: human cap-dependent 48S translation pre-initiation complex
Number of components: 55
MassTheoretical: 2.0 MDa

+
Component #1: protein, human cap-dependent 48S translation pre-initiation complex

ProteinName: human cap-dependent 48S translation pre-initiation complex
Recombinant expression: No
MassTheoretical: 2.0 MDa

+
Component #2: protein, human cap-dependent 48S translation pre-initiation complex

ProteinName: human cap-dependent 48S translation pre-initiation complex
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

+
Component #3: protein, mRNA

ProteinName: mRNAMessenger RNA / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #4: protein, Eukaryotic translation initiation factor 4B

ProteinName: Eukaryotic translation initiation factor 4B / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

+
Component #5: protein, Eukaryotic translation initiation factor 3 subunit A

ProteinName: Eukaryotic translation initiation factor 3 subunit A / Recombinant expression: No
MassTheoretical: 164.902656 kDa
SourceSpecies: Homo sapiens (human)

+
Component #6: protein, Eukaryotic translation initiation factor 3 subunit C

ProteinName: Eukaryotic translation initiation factor 3 subunit C / Recombinant expression: No
MassTheoretical: 97.923547 kDa
SourceSpecies: Homo sapiens (human)

+
Component #7: protein, Eukaryotic translation initiation factor 3 subunit E

ProteinName: Eukaryotic translation initiation factor 3 subunit E / Recombinant expression: No
MassTheoretical: 52.281633 kDa
SourceSpecies: Homo sapiens (human)

+
Component #8: protein, Eukaryotic translation initiation factor 3 subunit F

ProteinName: Eukaryotic translation initiation factor 3 subunit F / Recombinant expression: No
MassTheoretical: 37.84673 kDa
SourceSpecies: Homo sapiens (human)

+
Component #9: protein, Eukaryotic translation initiation factor 3 subunit H

ProteinName: Eukaryotic translation initiation factor 3 subunit H / Recombinant expression: No
MassTheoretical: 39.952281 kDa
SourceSpecies: Homo sapiens (human)

+
Component #10: protein, Eukaryotic translation initiation factor 3 subunit K

ProteinName: Eukaryotic translation initiation factor 3 subunit K / Recombinant expression: No
MassTheoretical: 25.129709 kDa
SourceSpecies: Homo sapiens (human)

+
Component #11: protein, Eukaryotic translation initiation factor 3 subunit L

ProteinName: Eukaryotic translation initiation factor 3 subunit L / Recombinant expression: No
MassTheoretical: 66.804766 kDa
SourceSpecies: Homo sapiens (human)

+
Component #12: protein, Eukaryotic translation initiation factor 3 subunit M

ProteinName: Eukaryotic translation initiation factor 3 subunit M / Recombinant expression: No
MassTheoretical: 42.555832 kDa
SourceSpecies: Homo sapiens (human)

+
Component #13: protein, EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT D

ProteinName: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT D / Recombinant expression: No
MassTheoretical: 42.203555 kDa
SourceSpecies: Homo sapiens (human)

+
Component #14: 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 ACGGCGCUGA CUCCCUUUGU GUGGGAUGCG UGCAUUUAUC AGAUCAAAAC CAACCCGGUC AGCGGCGGCG GCUUUGGUGA CUCUAGAUAA CCUCGGGCCG AUCGCAGCCC UCCGUGGCGG CGACGACCCA UUCGAACGUC UGCCCUAUCA ACUUUCGAUG GUAGUCGCCG UGCCUACCAU GGUGACCACG GGUGACGGGG AAUCAGGGUU CGAUUCCGGA GAGGGAGCCU GAGAAACGGC UACCACAUCC AAGGAAGGCA GCAGGCGCGC AAAUUACCCA CUCCCGACCC GGGGAGGUAG UGACGAAAAA UAACAAUACA GGACUCUUUC GAGGCCCUGU AAUUGGAAUG AGUCCACUUU AAAUCCUUUA ACGAGGAUCC AUUGGAGGGC AAGUCUGGUC GCAGCAGCCG CGGUAAUUCC AGCUCCAAUA GCGUAUAUUA AAGUUGCUGC AGUUAAAAAG CUCGUAGUUG GAUCUUGAGG GCCCGCCCCU CGGCGCCCCC UCGAUGUGUC CCGCGGGGCC CGAAGCGUUU ACUUUGAAAA AAUUAGAGUG UUCAAAGCAG GCCCGAGCCG CCUGGAUACC GCAGCUAGGA AUAAUGGAAU AGGACCGCGG UUCUAUUUUG UUGGUUUUCG GAACUGAGGC CAUGAUUAAG AGGGACGGCC GGGGGCAUUC GUAUUGCGCC GCUAGAGGUG AAAUUCUUGG ACCGGCGCAA GACGGACCAG AGCGAAAGCA UUUGCCAAGA AUGUUUUCAU UAAUCAAGAA CGAAAGUCGG AGGUUCGAAG ACGAUCAGAU ACCGUCGUAG UUCCGACCAU AAACGAUGCC GACUGGCGAU GCGGCGGCGU UAUUCCCAUG ACCCGCCGGG CAGCUUCCGG GAAACCAAAG UCUUUGGGUU CCGGGGGGAG UAUGGUUGCA AAGCUGAAAC UUAAAGGAAU UGACGGAAGG GCACCACCAG GAGUGGAGCC UGCGGCUUAA UUUGACUCAA CACGGGAAAC CUCACCCGGC CCGGACACGG ACAGGAUUGA CAGAUUGAUA GCUCUUUCUC GAUUCUGUGG GUGGUGGUGC AUGGCCGUUC UUAGUUGGUG GAGCGAUUUG UCUGGUUAAU UCCGAUAACG AACGAGACUC UGGCAUGCUA ACUAGUUACG CGACCCCCGA GCGGUCGGCG UCCCCCAACU UCUUAGAGGG ACAAGUGGCG UUCAGCCACC CGAGAUUGAG CAAUAACAGG UCUGUGAUGC CCUUAGAUGU CGGGGCUGCA CGCGCGCUAC ACUGACUGGC UCAGCGUGUG CCUACCCUAC GCCGGCAGGC GCGGGUAACC CGUUGAACCC CAUUCGUGAU GGGGAUCGGG GAUUGCAAUU AUUCCCCAUG AACGAGGAAU UCCCAGUAAG UGCGGGUCAU AAGCUUGCGU UGAUUAAGUC CCUGCCCUUU GUACACACCG CCCGUCGCUA CUACCGAUUG GAUGGUUUAG UGAGGCCCUC GGAUCGGCCC GCCGGGGUCG GCCCACGGCC CUGGCGGAGC GCUGAGAAGA CGGUCGAACU UGACUAUCUA GAGGAAGUAA AAGUCGUAAC AAGGUUUCCG UAGGUGAACC UGCGGAAGGA UCAUUA
MassTheoretical: 572.789812 kDa
SourceSpecies: Homo sapiens (human)

+
Component #15: nucleic-acid, Messenger RNA (26-MER)

Nucleic-acidName: Messenger RNA (26-MER) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CAGACACCAU GGUGCACCUG ACUCCU
MassTheoretical: 8.238953 kDa

+
Component #16: protein, 40S ribosomal protein S11

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

+
Component #17: protein, 40S ribosomal protein S16

ProteinName: 40S ribosomal protein S16 / Recombinant expression: No
MassTheoretical: 15.975753 kDa
SourceSpecies: Homo sapiens (human)

+
Component #18: protein, 40S ribosomal protein S4, X isoform

ProteinName: 40S ribosomal protein S4, X isoformRibosome / Recombinant expression: No
MassTheoretical: 29.65892 kDa
SourceSpecies: Homo sapiens (human)

+
Component #19: protein, 40S ribosomal protein S29

ProteinName: 40S ribosomal protein S29 / Recombinant expression: No
MassTheoretical: 6.364426 kDa
SourceSpecies: Homo sapiens (human)

+
Component #20: protein, 40S ribosomal protein S9

ProteinName: 40S ribosomal protein S9 / Recombinant expression: No
MassTheoretical: 21.266166 kDa
SourceSpecies: Homo sapiens (human)

+
Component #21: protein, 40S ribosomal protein S18

ProteinName: 40S ribosomal protein S18 / Recombinant expression: No
MassTheoretical: 16.170774 kDa
SourceSpecies: Homo sapiens (human)

+
Component #22: nucleic-acid, Transfer RNA (75-MER)

Nucleic-acidName: Transfer RNA (75-MER) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGCAGAGUGG CGCAGCGGAA GCGUGCUGGG CCCAUAACCC AGAGGUCGAU GGAUCGAAAC CAUCCUCUGC UACCA
MassTheoretical: 24.23151 kDa
SourceSpecies: Homo sapiens (human)

+
Component #23: protein, Eukaryotic translation initiation factor 2 subunit 1

ProteinName: Eukaryotic translation initiation factor 2 subunit 1 / Recombinant expression: No
MassTheoretical: 30.633297 kDa
SourceSpecies: Homo sapiens (human)

+
Component #24: protein, 40S ribosomal protein S23

ProteinName: 40S ribosomal protein S23 / Recombinant expression: No
MassTheoretical: 15.757587 kDa
SourceSpecies: Homo sapiens (human)

+
Component #25: protein, 40S ribosomal protein S19

ProteinName: 40S ribosomal protein S19 / Recombinant expression: No
MassTheoretical: 15.812286 kDa
SourceSpecies: Homo sapiens (human)

+
Component #26: protein, Eukaryotic translation initiation factor 2 subunit 3

ProteinName: Eukaryotic translation initiation factor 2 subunit 3 / Recombinant expression: No
MassTheoretical: 45.862441 kDa
SourceSpecies: Homo sapiens (human)

+
Component #27: protein, 40S ribosomal protein S5

ProteinName: 40S ribosomal protein S5 / Recombinant expression: No
MassTheoretical: 21.525941 kDa
SourceSpecies: Homo sapiens (human)

+
Component #28: protein, 40S ribosomal protein S30

ProteinName: 40S ribosomal protein S30 / Recombinant expression: No
MassTheoretical: 6.741048 kDa
SourceSpecies: Homo sapiens (human)

+
Component #29: protein, 40S ribosomal protein S25

ProteinName: 40S ribosomal protein S25 / Recombinant expression: No
MassTheoretical: 8.526119 kDa
SourceSpecies: Homo sapiens (human)

+
Component #30: protein, 40S ribosomal protein S7

ProteinName: 40S ribosomal protein S7 / Recombinant expression: No
MassTheoretical: 21.716387 kDa
SourceSpecies: Homo sapiens (human)

+
Component #31: protein, 40S ribosomal protein S27

ProteinName: 40S ribosomal protein S27 / Recombinant expression: No
MassTheoretical: 9.480186 kDa
SourceSpecies: Homo sapiens (human)

+
Component #32: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Recombinant expression: No
MassTheoretical: 17.128191 kDa
SourceSpecies: Homo sapiens (human)

+
Component #33: protein, 40S ribosomal protein S15a

ProteinName: 40S ribosomal protein S15a / Recombinant expression: No
MassTheoretical: 14.734357 kDa
SourceSpecies: Homo sapiens (human)

+
Component #34: protein, 40S ribosomal protein S21

ProteinName: 40S ribosomal protein S21 / Recombinant expression: No
MassTheoretical: 8.896102 kDa
SourceSpecies: Homo sapiens (human)

+
Component #35: protein, 40S ribosomal protein S2

ProteinName: 40S ribosomal protein S2 / Recombinant expression: No
MassTheoretical: 24.814285 kDa
SourceSpecies: Homo sapiens (human)

+
Component #36: protein, EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT ...

ProteinName: EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT (eIF2-Beta)
Recombinant expression: No
MassTheoretical: 2.103416 kDa
SourceSpecies: Homo sapiens (human)

+
Component #37: protein, 40S ribosomal protein S17

ProteinName: 40S ribosomal protein S17 / Recombinant expression: No
MassTheoretical: 14.578988 kDa
SourceSpecies: Homo sapiens (human)

+
Component #38: protein, 40S ribosomal protein SA

ProteinName: 40S ribosomal protein SA / Recombinant expression: No
MassTheoretical: 23.360791 kDa
SourceSpecies: Homo sapiens (human)

+
Component #39: protein, 40S ribosomal protein S3

ProteinName: 40S ribosomal protein S3 / Recombinant expression: No
MassTheoretical: 25.158535 kDa
SourceSpecies: Homo sapiens (human)

+
Component #40: protein, 40S ribosomal protein S20

ProteinName: 40S ribosomal protein S20 / Recombinant expression: No
MassTheoretical: 11.76589 kDa
SourceSpecies: Homo sapiens (human)

+
Component #41: protein, 40S ribosomal protein S3a

ProteinName: 40S ribosomal protein S3a / Recombinant expression: No
MassTheoretical: 24.944408 kDa
SourceSpecies: Homo sapiens (human)

+
Component #42: protein, 40S ribosomal protein S14

ProteinName: 40S ribosomal protein S14 / Recombinant expression: No
MassTheoretical: 14.544659 kDa
SourceSpecies: Homo sapiens (human)

+
Component #43: protein, 40S ribosomal protein S26

ProteinName: 40S ribosomal protein S26 / Recombinant expression: No
MassTheoretical: 11.315428 kDa
SourceSpecies: Homo sapiens (human)

+
Component #44: protein, 40S ribosomal protein S28

ProteinName: 40S ribosomal protein S28 / Recombinant expression: No
MassTheoretical: 7.263394 kDa
SourceSpecies: Homo sapiens (human)

+
Component #45: protein, Receptor of activated protein C kinase 1

ProteinName: Receptor of activated protein C kinase 1 / Recombinant expression: No
MassTheoretical: 34.669113 kDa
SourceSpecies: Homo sapiens (human)

+
Component #46: protein, 40S ribosomal protein S15

ProteinName: 40S ribosomal protein S15 / Recombinant expression: No
MassTheoretical: 15.151948 kDa
SourceSpecies: Homo sapiens (human)

+
Component #47: protein, 40S ribosomal protein S8

ProteinName: 40S ribosomal protein S8 / Recombinant expression: No
MassTheoretical: 23.902871 kDa
SourceSpecies: Homo sapiens (human)

+
Component #48: protein, Ubiquitin-40S ribosomal protein S27a

ProteinName: Ubiquitin-40S ribosomal protein S27a / Recombinant expression: No
MassTheoretical: 8.358903 kDa
SourceSpecies: Homo sapiens (human)

+
Component #49: protein, 40S ribosomal protein S6

ProteinName: 40S ribosomal protein S6 / Recombinant expression: No
MassTheoretical: 27.471535 kDa
SourceSpecies: Homo sapiens (human)

+
Component #50: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Recombinant expression: No
MassTheoretical: 13.766122 kDa
SourceSpecies: Homo sapiens (human)

+
Component #51: protein, 40S ribosomal protein S24

ProteinName: 40S ribosomal protein S24 / Recombinant expression: No
MassTheoretical: 15.18897 kDa
SourceSpecies: Homo sapiens (human)

+
Component #52: protein, 40S ribosomal protein S10

ProteinName: 40S ribosomal protein S10 / Recombinant expression: No
MassTheoretical: 11.773953 kDa
SourceSpecies: Homo sapiens (human)

+
Component #53: protein, Eukaryotic translation initiation factor 4B

ProteinName: Eukaryotic translation initiation factor 4B / Recombinant expression: No
MassTheoretical: 72.32482 kDa
Source (engineered)Expression System: Homo sapiens (human) / Vector: pFastBac_eIF4B

+
Component #54: protein, Eukaryotic translation initiation factor 3 subunit B

ProteinName: Eukaryotic translation initiation factor 3 subunit B / Recombinant expression: No
MassTheoretical: 124.402336 kDa
SourceSpecies: Homo sapiens (human)

+
Component #55: ligand, water

LigandName: water / Number of Copies: 415 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 20 mM Tris HCl, 50 mM KOAc, 2.5 mM MgCl2, 2 mM DTT, 0.25 mM spermidine 0.25 mM GMPPNP
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 1 %

-
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: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 112000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 4000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 50604
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more