6YBD Translation date Mar 16, 2020
title Structure Of A Human 48s Translational Initiation Complex -
authors J.Brito Querido, M.Sokabe, S.Kraatz, Y.Gordiyenko, M.Skehel, C.Fr V.Ramakrishnan
compound source
Molecule: Eukaryotic Translation Initiation Factor 3 Subuni
Chain: 6
Synonym: Eif3m,Fetal Lung Protein B5,Hfl-B5,Pci Domain-Cont Protein 1;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Eukaryotic Translation Initiation Factor 3 Subuni
Chain: 4
Synonym: Eif3f,Deubiquitinating Enzyme Eif3f,Eukaryotic Tra Initiation Factor 3 Subunit 5,Eif-3-Epsilon,Eif3 P47;
Ec: 3.4.19.12

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Eukaryotic Translation Initiation Factor 3 Subuni
Chain: u
Synonym: Eif3a,Eukaryotic Translation Initiation Factor 3 S Eif-3-Theta,Eif3 P167,Eif3 P180,Eif3 P185;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Eukaryotic Translation Initiation Factor 3 Subuni
Chain: v
Synonym: Eif3e,Eukaryotic Translation Initiation Factor 3 S Viral Integration Site Protein Int-6 Homolog,Eif-3 P48;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Eukaryotic Translation Initiation Factor 3 Subuni
Chain: y
Synonym: Eif3c,Eukaryotic Translation Initiation Factor 3 S Eif3 P110;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Eukaryotic Translation Initiation Factor 3 Subuni
Chain: 8
Synonym: Eif3h,Eukaryotic Translation Initiation Factor 3 S Eif-3-Gamma,Eif3 P40 Subunit;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S7
Chain: G
Synonym: Small Ribosomal Subunit Protein Es7

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S27
Chain: H
Synonym: Metallopan-Stimulin 1,Mps-1,Small Ribosomal Subuni Es27;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S21
Chain: K
Synonym: Small Ribosomal Subunit Protein Es21

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S17
Chain: M
Synonym: Small Ribosomal Subunit Protein Es17

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S2
Chain: L
Synonym: 40s Ribosomal Protein S4,Protein Llrep3,Small Ribo Subunit Protein Us5;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S3a
Chain: O
Synonym: Small Ribosomal Subunit Protein Es1,V-Fos Transfor Effector Protein,Fte-1;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein Sa
Chain: N
Synonym: 37 Kda Laminin Receptor Precursor,37lrp,3767 Kda Receptor,Lrplr,67 Kda Laminin Receptor,67lr,Colon Carcinom Binding Protein,Laminin Receptor 1,Lamr,Laminin-Binding Pro Precursor P40,Lbpp40,Multidrug Resistance-Associated Prote Ag,Nem1chd4,Small Ribosomal Subunit Protein Us2;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S26
Chain: Q
Synonym: Small Ribosomal Subunit Protein Es26

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S14
Chain: P
Synonym: Small Ribosomal Subunit Protein Us11

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S13
Chain: I
Synonym: Small Ribosomal Subunit Protein Us15

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Eukaryotic Translation Initiation Factor 3 Subuni
Chain: x
Synonym: Eif3d,Eukaryotic Translation Initiation Factor 3 S Eif-3-Zeta,Eif3 P66;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Eukaryotic Translation Initiation Factor 3 Subuni
Chain: 3
Synonym: Eif3k,Eukaryotic Translation Initiation Factor 3 S Muscle-Specific Gene M9 Protein,Plac-24,Eif-3 P25,Eif-3 P28

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Eukaryotic Translation Initiation Factor 3 Subuni
Chain: 5
Synonym: Eif3l,Eukaryotic Translation Initiation Factor 3 S Interacting Protein,Eukaryotic Translation Initiation Facto Subunit E-Interacting Protein

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.30 Å
ligand
enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
3

  • eukaryotic translation initi...
  • 4

  • eukaryotic translation initi...
  • 5

  • eukaryotic translation initi...
  • 6

  • eukaryotic translation initi...
  • 8
  • metallopeptidase activity
  • isopeptidase activity

  • eukaryotic translation initi...
  • G

  • cytosolic small ribosomal su...
  • H

  • cytosolic small ribosomal su...
  • I

  • cytosolic small ribosomal su...
  • K

  • cytosolic small ribosomal su...
  • L

  • cytosolic small ribosomal su...
  • M

  • cytosolic small ribosomal su...
  • N
  • virus receptor activity

  • cytosolic small ribosomal su...
  • O

  • cytosolic small ribosomal su...
  • P
  • translation regulator activi...

  • cytosolic small ribosomal su...
  • Q

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • u

  • eukaryotic translation initi...
  • v

  • eukaryotic translation initi...
  • x

  • eukaryotic translation initi...
  • y

  • eukaryotic translation initi...
  • Primary referenceStructure of a human 48S translational initiation complex., Brito Querido J, Sokabe M, Kraatz S, Gordiyenko Y, Skehel JM, Fraser CS, Ramakrishnan V, Science. 2020 Sep 4;369(6508):1220-1227. doi: 10.1126/science.aba4904. PMID:32883864
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (588 Kb) [Save to disk]
  • Biological Unit Coordinates (6ybd.pdb1.gz) 555 Kb
  • CSU: Contacts of Structural Units for 6YBD
  • Retrieve 6YBD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6YBD from S2C, [Save to disk]
  • View 6YBD in 3D
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  • Visual 3D analysis of 6YBD
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  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6ybd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ybd_M] [6ybd_I] [6ybd_5] [6ybd_v] [6ybd_H] [6ybd_3] [6ybd_G] [6ybd_L] [6ybd_Q] [6ybd_K] [6ybd_4] [6ybd_N] [6ybd_P] [6ybd_u] [6ybd_O] [6ybd_y] [6ybd_x] [6ybd_8] [6ybd_6]
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  • Domain organization of by SWISSPFAM
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  • Community annotation for 6YBD at PDBWiki (http://pdbwiki.org)

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