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PDBsum entry 2xzm

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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
2xzm
Jmol
Contents
Protein chains
67 a.a. *
207 a.a. *
196 a.a. *
215 a.a. *
98 a.a. *
80 a.a. *
104 a.a. *
93 a.a. *
98 a.a. *
204 a.a. *
229 a.a. *
179 a.a. *
230 a.a. *
89 a.a. *
192 a.a. *
129 a.a. *
143 a.a. *
105 a.a. *
140 a.a. *
141 a.a. *
154 a.a. *
53 a.a. *
150 a.a. *
148 a.a. *
157 a.a. *
338 a.a. *
125 a.a. *
150 a.a. *
124 a.a. *
121 a.a. *
259 a.a. *
68 a.a. *
235 a.a. *
97 a.a. *
DNA/RNA
Metals
_MG ×92
_ZN ×4
Waters ×552
* Residue conservation analysis
PDB id:
2xzm
Name: Ribosome
Title: Crystal structure of the eukaryotic 40s ribosomal subunit in complex with initiation factor 1. This file contains the 40s subunit and initiation factor for molecule 1
Structure: Ribosomal protein s28e containing protein. Chain: 1. Synonym: rps28e, 40s ribosomal protein rps28e. 40s ribosomal protein s8. Chain: 2. Synonym: rps8e, 40s ribosomal protein rps8e. 40s ribosomal protein rps7e. Chain: 3. Synonym: rps7e.
Source: Tetrahymena thermophila. Organism_taxid: 5911. Atcc: 30382. Expressed in: escherichia coli. Expression_system_taxid: 562. Atcc: 30382
Resolution:
3.93Å     R-factor:   0.206     R-free:   0.243
Authors: J.Rabl,M.Leibundgut,S.F.Ataide,A.Haag,N.Ban
Key ref: J.Rabl et al. (2011). Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1. Science, 331, 730-736. PubMed id: 21205638
Date:
26-Nov-10     Release date:   19-Jan-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q234G5  (Q234G5_TETTS) -  40S ribosomal protein S28e, putative
Seq:
Struc:
68 a.a.
67 a.a.
Protein chain
Pfam   ArchSchema ?
Q22AV0  (Q22AV0_TETTS) -  40S ribosomal protein S8
Seq:
Struc:
208 a.a.
207 a.a.
Protein chain
Pfam   ArchSchema ?
E6PBS5  (E6PBS5_TETTH) -  40S ribosomal protein rpS7e
Seq:
Struc:
197 a.a.
196 a.a.
Protein chain
Pfam   ArchSchema ?
Q23DE3  (RS3A_TETTS) -  40S ribosomal protein S3a
Seq:
Struc:
265 a.a.
215 a.a.
Protein chain
Pfam   ArchSchema ?
Q23PT4  (Q23PT4_TETTS) -  Uncharacterized protein
Seq:
Struc:
229 a.a.
98 a.a.*
Protein chain
Pfam   ArchSchema ?
Q22CK0  (Q22CK0_TETTS) -  40S ribosomal protein S27
Seq:
Struc:
81 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
Q24F70  (Q24F70_TETTS) -  40S ribosomal protein S10, putative
Seq:
Struc:
162 a.a.
104 a.a.
Protein chain
Pfam   ArchSchema ?
E6PBU3  (E6PBU3_TETTH) -  40S ribosomal protein rpS25e
Seq:
Struc:
143 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
E6PBU9  (E6PBU9_TETTH) -  40S ribosomal protein rpS31e
Seq:
Struc:
189 a.a.
98 a.a.*
Protein chain
Pfam   ArchSchema ?
E6PBR9  (E6PBR9_TETTH) -  40S ribosomal protein SA
Seq:
Struc:
241 a.a.
204 a.a.
Protein chain
Pfam   ArchSchema ?
Q22AV9  (Q22AV9_TETTS) -  40S ribosomal protein S3
Seq:
Struc:
243 a.a.
229 a.a.
Protein chain
Pfam   ArchSchema ?
Q230V2  (Q230V2_TETTS) -  Ribosomal protein S9 component of cytosolic 80S ribosome and 40S small subunit
Seq:
Struc:
238 a.a.
179 a.a.
Protein chain
Pfam   ArchSchema ?
Q23KG1  (Q23KG1_TETTS) -  40S ribosomal protein S2, putative
Seq:
Struc:
296 a.a.
230 a.a.
Protein chain
Pfam   ArchSchema ?
E6PBV1  (E6PBV1_TETTH) -  EIF1
Seq:
Struc:
101 a.a.
89 a.a.
Protein chain
Pfam   ArchSchema ?
Q22WU7  (Q22WU7_TETTS) -  40S ribosomal protein S5
Seq:
Struc:
200 a.a.
192 a.a.
Protein chain
Pfam   ArchSchema ?
Q238Q8  (Q238Q8_TETTS) -  Uncharacterized protein
Seq:
Struc:
130 a.a.
129 a.a.
Protein chain
Pfam   ArchSchema ?
E6PBT4  (E6PBT4_TETTH) -  40S ribosomal protein rpS16e
Seq:
Struc:
145 a.a.
143 a.a.
Protein chain
Pfam   ArchSchema ?
Q22DC6  (Q22DC6_TETTS) -  40S ribosomal protein S20
Seq:
Struc:
170 a.a.
105 a.a.
Protein chain
Pfam   ArchSchema ?
E6PBT2  (E6PBT2_TETTH) -  40S ribosomal protein rpS14e
Seq:
Struc:
151 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P06147  (RS12_TETTH) -  40S ribosomal protein S12
Seq:
Struc:
142 a.a.
141 a.a.
Protein chain
Pfam   ArchSchema ?
E6PBT6  (E6PBT6_TETTH) -  40S ribosomal protein rpS18e
Seq:
Struc:
155 a.a.
154 a.a.
Protein chain
Pfam   ArchSchema ?
Q22MB0  (Q22MB0_TETTS) -  40S ribosomal protein S29
Seq:
Struc:
55 a.a.
53 a.a.
Protein chain
Pfam   ArchSchema ?
E6PBT1  (E6PBT1_TETTH) -  40S ribosomal protein rpS13e
Seq:
Struc:
153 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
E6PBU2  (E6PBU2_TETTH) -  40S ribosomal protein S24
Seq:
Struc:
149 a.a.
148 a.a.
Protein chain
Pfam   ArchSchema ?
Q22B78  (Q22B78_TETTS) -  40S ribosomal protein S11, putative
Seq:
Struc:
157 a.a.
157 a.a.
Protein chain
Pfam   ArchSchema ?
Q24D42  (Q24D42_TETTS) -  Receptor of activated kinase C 1A, component of 40S small ribosomal subunit
Seq:
Struc:
343 a.a.
338 a.a.
Protein chain
Pfam   ArchSchema ?
E6PBT3  (E6PBT3_TETTH) -  40S ribosomal protein rpS15e
Seq:
Struc:
144 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
E6PBT7  (E6PBT7_TETTH) -  40S ribosomal protein rpS19e
Seq:
Struc:
155 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
Q22W26  (Q22W26_TETTS) -  40S ribosomal protein S12
Seq:
Struc:
126 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
E6PBT5  (E6PBT5_TETTH) -  40S ribosomal protein rpS17e
Seq:
Struc:
130 a.a.
121 a.a.
Protein chain
Pfam   ArchSchema ?
P0C233  (RS4_TETTH) -  40S ribosomal protein S4
Seq:
Struc:
259 a.a.
259 a.a.*
Protein chain
Pfam   ArchSchema ?
E6PBU8  (E6PBU8_TETTH) -  40S ribosomal protein rpS30e
Seq:
Struc:
80 a.a.
68 a.a.
Protein chain
Pfam   ArchSchema ?
A4VD76  (A4VD76_TETTS) -  40S ribosomal protein S6
Seq:
Struc:
293 a.a.
235 a.a.
Protein chain
Pfam   ArchSchema ?
E6PBT9  (E6PBT9_TETTH) -  40S ribosomal protein rpS21e
Seq:
Struc:
97 a.a.
97 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 113 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   6 terms 
  Biological process     ribosomal small subunit biogenesis   9 terms 
  Biochemical function     structural constituent of ribosome     7 terms  

 

 
Science 331:730-736 (2011)
PubMed id: 21205638  
 
 
Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1.
J.Rabl, M.Leibundgut, S.F.Ataide, A.Haag, N.Ban.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23262488 M.E.Filbin, B.S.Vollmar, D.Shi, T.Gonen, and J.S.Kieft (2013).
HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation.
  Nat Struct Mol Biol, 20, 150-158.  
23395961 Y.Hashem, A.des Georges, J.Fu, S.N.Buss, F.Jossinet, A.Jobe, Q.Zhang, H.Y.Liao, R.A.Grassucci, C.Bajaj, E.Westhof, S.Madison-Antenucci, and J.Frank (2013).
High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome.
  Nature, 494, 385-389.
PDB codes: 3zeq 3zex 3zey 3zf7
23142978 B.Bradatsch, C.Leidig, S.Granneman, M.Gnädig, D.Tollervey, B.Böttcher, R.Beckmann, and E.Hurt (2012).
Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel.
  Nat Struct Mol Biol, 19, 1234-1241.
PDB code: 3j2i
23142985 B.J.Greber, D.Boehringer, C.Montellese, and N.Ban (2012).
Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit.
  Nat Struct Mol Biol, 19, 1228-1233.
PDB codes: 4b6a 4b6b
22664984 C.E.Aitken, and J.R.Lorsch (2012).
A mechanistic overview of translation initiation in eukaryotes.
  Nat Struct Mol Biol, 19, 568-576.  
22664983 S.Melnikov, A.Ben-Shem, N.Garreau de Loubresse, L.Jenner, G.Yusupova, and M.Yusupov (2012).
One core, two shells: bacterial and eukaryotic ribosomes.
  Nat Struct Mol Biol, 19, 560-567.  
22358840 T.Becker, S.Franckenberg, S.Wickles, C.J.Shoemaker, A.M.Anger, J.P.Armache, H.Sieber, C.Ungewickell, O.Berninghausen, I.Daberkow, A.Karcher, M.Thomm, K.P.Hopfner, R.Green, and R.Beckmann (2012).
Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.
  Nature, 482, 501-506.
PDB codes: 3j15 3j16
22002225 B.S.Shin, J.R.Kim, S.E.Walker, J.Dong, J.R.Lorsch, and T.E.Dever (2011).
Initiation factor eIF2γ promotes eIF2-GTP-Met-tRNAi(Met) ternary complex binding to the 40S ribosome.
  Nat Struct Mol Biol, 18, 1227-1234.  
21419622 F.A.Rey, and W.I.Sundquist (2011).
Macromolecular assemblages.
  Curr Opin Struct Biol, 21, 221-222.  
21623367 T.Becker, J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, H.Sieber, B.A.Motaal, T.Mielke, O.Berninghausen, and R.Beckmann (2011).
Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome.
  Nat Struct Mol Biol, 18, 715-720.
PDB code: 3izq
21310988 V.Ramakrishnan (2011).
Molecular biology. The eukaryotic ribosome.
  Science, 331, 681-682.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.