3J3A Ribosome date Feb 27, 2013
title Structure Of The Human 40s Ribosomal Proteins
authors A.M.Anger, J.P.Armache, O.Berninghausen, M.Habeck, M.Subklewe, D.N.Wilson, R.Beckmann
compound source
Molecule: Elongation Factor 2
Chain: z
Synonym: Ef-2
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Guanine Nucleotide-Binding Protein Subunit Beta-2
Chain: g
Synonym: Cell Proliferation-Inducing Gene 21 Protein, Guani Nucleotide-Binding Protein Subunit Beta-Like Protein 12.3, Cancer Oncogene 7 Protein, Hlc-7, Receptor For Activated C Receptor Of Activated Protein Kinase C 1, Rack1;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S20
Chain: U

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S10
Chain: K

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S14
Chain: O

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S23
Chain: X

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S12
Chain: M

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S18
Chain: S
Synonym: Ke-3, Ke3

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S29
Chain: d

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S13
Chain: N

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S11
Chain: L

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S17
Chain: R

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S15
Chain: P
Synonym: Rig Protein

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S19
Chain: T

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S3a
Chain: B
Synonym: V-Fos Transformation Effector Protein, Fte-1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein Sa
Chain: A
Synonym: 37 Kda Laminin Receptor Precursor, 37lrp, 3767 Kd Receptor, Lrplr, 67 Kda Laminin Receptor, 67lr, Colon Carc Laminin-Binding Protein, Laminin Receptor 1, Lamr, Laminin- Protein Precursor P40, Lbpp40, Multidrug Resistance-Associ Protein Mgr1-Ag, Nem1chd4;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S21
Chain: V

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S24
Chain: Y

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S25
Chain: Z

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S26
Chain: a

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S27
Chain: b
Synonym: Metallopan-Stimulin 1, Mps-1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S28
Chain: c

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S3
Chain: D

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S30
Chain: e

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S27a
Chain: f

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S9
Chain: J

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S4, X Isoform
Chain: E
Synonym: Scr10, Single Copy Abundant Mrna Protein

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S2
Chain: C
Synonym: 40s Ribosomal Protein S4, Protein Llrep3

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S6
Chain: G
Synonym: Phosphoprotein Np33

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S5
Chain: F
Synonym: 40s Ribosomal Protein S5, N-Terminally Processed

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S7
Chain: H

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S15a
Chain: W

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S8
Chain: I

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 40s Ribosomal Protein S16
Chain: Q

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Plasminogen Activator Inhibitor 1 Rna-Binding Pro
Chain: h
Synonym: Pai1 Rna-Binding Protein 1, Pai-Rbp1, Serpine1 Mrn Protein 1

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 5.00 Å
Gene
Ontology
ChainFunctionProcessComponent
A

  • cytosolic small ribosomal su...
  • B

  • cytosolic small ribosomal su...
  • C

  • cytosolic small ribosomal su...
  • D

  • cytosolic small ribosomal su...
  • E

  • ribosome
  • cytosolic small ribosomal su...
  • F

  • cytosolic small ribosomal su...
  • G

  • cytosolic small ribosomal su...
  • H

  • cytosolic small ribosomal su...
  • I

  • cytosolic small ribosomal su...
  • J

  • cytosolic small ribosomal su...
  • K

  • cytosolic small ribosomal su...
  • L

  • cytosolic small ribosomal su...
  • M

  • cytosolic small ribosomal su...
  • N

  • cytosolic small ribosomal su...
  • O

  • cytosolic small ribosomal su...
  • P

  • cytosolic small ribosomal su...
  • Q

  • cytosolic small ribosomal su...
  • R

  • cytosolic small ribosomal su...
  • S

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • T

  • cytosolic small ribosomal su...
  • U

  • cytosolic small ribosomal su...
  • V

  • cytosolic small ribosomal su...
  • W

  • cytosolic small ribosomal su...
  • X

  • cytosolic small ribosomal su...
  • Y

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • Z

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • a

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • b

  • cytosolic small ribosomal su...
  • c

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • d

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • e

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • g


    h


    z


    Primary referenceStructures of the human and Drosophila 80S ribosome., Anger AM, Armache JP, Berninghausen O, Habeck M, Subklewe M, Wilson DN, Beckmann R, Nature. 2013 May 2;497(7447):80-5. doi: 10.1038/nature12104. PMID:23636399
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (822 Kb) [Save to disk]
  • Biological Unit Coordinates (3j3a.pdb1.gz) 807 Kb
  • CSU: Contacts of Structural Units for 3J3A
  • Retrieve 3J3A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3J3A from S2C, [Save to disk]
  • View 3J3A in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3J3A
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3J3A, from MSDmotif at EBI
  • Fold representative 3j3a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j3a_Y] [3j3a_I] [3j3a_e] [3j3a_A] [3j3a_V] [3j3a] [3j3a_Z] [3j3a_F] [3j3a_Q] [3j3a_L] [3j3a_M] [3j3a_C] [3j3a_h] [3j3a_N] [3j3a_D] [3j3a_G] [3j3a_B] [3j3a_O] [3j3a_H] [3j3a_W] [3j3a_X] [3j3a_J] [3j3a_f] [3j3a_c] [3j3a_K] [3j3a_U] [3j3a_P] [3j3a_S] [3j3a_a] [3j3a_d] [3j3a_g] [3j3a_E] [3j3a_R] [3j3a_T] [3j3a_z] [3j3a_b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3J3A: [S4 ] by SMART
  • Alignments of the sequence of 3J3A with the sequences similar proteins can be viewed for 3J3A's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3J3A
  • Community annotation for 3J3A at PDBWiki (http://pdbwiki.org)

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