4V7E

Model of the small subunit RNA based on a 5.5 A cryo-EM map of Triticum aestivum translating 80S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion.

Gogala, M.Becker, T.Beatrix, B.Armache, J.P.Barrio-Garcia, C.Berninghausen, O.Beckmann, R.

(2014) Nature 506: 107-110

  • DOI: 10.1038/nature12950
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The biogenesis of secretory as well as transmembrane proteins requires the activity of the universally conserved protein-conducting channel (PCC), the Sec61 complex (SecY complex in bacteria). In eukaryotic cells the PCC is located in the membrane of ...

    The biogenesis of secretory as well as transmembrane proteins requires the activity of the universally conserved protein-conducting channel (PCC), the Sec61 complex (SecY complex in bacteria). In eukaryotic cells the PCC is located in the membrane of the endoplasmic reticulum where it can bind to translating ribosomes for co-translational protein transport. The Sec complex consists of three subunits (Sec61α, β and γ) and provides an aqueous environment for the translocation of hydrophilic peptides as well as a lateral opening in the Sec61α subunit that has been proposed to act as a gate for the membrane partitioning of hydrophobic domains. A plug helix and a so-called pore ring are believed to seal the PCC against ion flow and are proposed to rearrange for accommodation of translocating peptides. Several crystal and cryo-electron microscopy structures revealed different conformations of closed and partially open Sec61 and SecY complexes. However, in none of these samples has the translocation state been unambiguously defined biochemically. Here we present cryo-electron microscopy structures of ribosome-bound Sec61 complexes engaged in translocation or membrane insertion of nascent peptides. Our data show that a hydrophilic peptide can translocate through the Sec complex with an essentially closed lateral gate and an only slightly rearranged central channel. Membrane insertion of a hydrophobic domain seems to occur with the Sec complex opening the proposed lateral gate while rearranging the plug to maintain an ion permeability barrier. Taken together, we provide a structural model for the basic activities of the Sec61 complex as a protein-conducting channel.


    Related Citations: 
    • Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
      Armache, J.P.,Jarasch, A.,Anger, A.M.,Villa, E.,Becker, T.,Bhushan, S.,Jossinet, F.,Habeck, M.,Dindar, G.,Franckenberg, S.,Marquez, V.,Mielke, T.,Thomm, M.,Berninghausen, O.,Beatrix, B.,Soding, J.,Westhof, E.,Wilson, D.N.,Beckmann, R.
      (2010) Proc.Natl.Acad.Sci.USA 107: 19748
    • Localization of eukaryote-specific ribosomal proteins in a 5.5- angstrom cryo-EM map of the 80S eukaryotic ribosome.
      Armache, J.P.,Jarasch, A.,Anger, A.M.,Villa, E.,Becker, T.,Bhushan, S.,Jossinet, F.,Habeck, M.,Dindar, G.,Franckenberg, S.,Marquez, V.,Mielke, T.,Thomm, M.,Berninghausen, O.,Beatrix, B.,Soding, J.,Westhof, E.,Wilson, D.N.,Beckmann, R.
      (2010) Proc.Natl.Acad.Sci.USA 107: 19754


    Organizational Affiliation

    Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24E
BY
138N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8E
BI
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10E
BK
183N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12E
BM
171N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S31e
Bf
155N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
BX
142N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
RACK1
Bg
380Triticum aestivumMutation(s): 0 
Gene Names: TaGB1
Find proteins for Q8LNY6 (Triticum aestivum)
Go to UniProtKB:  Q8LNY6
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
BD
208Triticum aestivumMutation(s): 0 
Find proteins for Q8L804 (Triticum aestivum)
Go to UniProtKB:  Q8L804
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4E
BE
265N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7
BF
191N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9
BQ
149N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10
BU
128N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11
BO
151N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
BS
152Triticum aestivumMutation(s): 0 
Find proteins for Q8L806 (Triticum aestivum)
Go to UniProtKB:  Q8L806
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
BN
151N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17
BL
160N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19E
BT
146N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19
BP
154N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25E
BZ
108N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28E
Bc
65Triticum aestivumMutation(s): 0 
Find proteins for Q7X9K4 (Triticum aestivum)
Go to UniProtKB:  Q7X9K4
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
BW
130N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14
Bd
56Triticum aestivumMutation(s): 0 
Gene Names: RPS29
Find proteins for Q5I7K3 (Triticum aestivum)
Go to Gene View: RPS29
Go to UniProtKB:  Q5I7K3
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27E
Bb
86N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30E
Be
62N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
BA
260N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17E
BR
141N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1E
BB
262N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21E
BV
82N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26E
Ba
133N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4
BJ
195N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
BC
263N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
BG
245N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7E
BH
189Triticum aestivumMutation(s): 0 
Find proteins for Q5I7K2 (Triticum aestivum)
Go to UniProtKB:  Q5I7K2
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8E
CG
257N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21E
CT
164Triticum aestivumMutation(s): 0 
Gene Names: RPL21
Find proteins for F4YWL9 (Triticum aestivum)
Go to Gene View: RPL21
Go to UniProtKB:  F4YWL9
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27E
CZ
136N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L1
Cz
216Triticum aestivumMutation(s): 0 
Find proteins for Q5I7L3 (Triticum aestivum)
Go to UniProtKB:  Q5I7L3
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2
CA
261N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
CJ
180Triticum aestivumMutation(s): 0 
Find proteins for Q5I7L2 (Triticum aestivum)
Go to UniProtKB:  Q5I7L2
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6
CH
190N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14
CV
140Triticum aestivumMutation(s): 0 
Find proteins for Q5I7K4 (Triticum aestivum)
Go to UniProtKB:  Q5I7K4
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15E
CN
200N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15
Ca
144N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18E
CQ
188Triticum aestivumMutation(s): 0 
Find proteins for Q5I7L0 (Triticum aestivum)
Go to UniProtKB:  Q5I7L0
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18
CD
304N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19E
CR
209Triticum aestivumMutation(s): 0 
Find proteins for Q7XY20 (Triticum aestivum)
Go to UniProtKB:  Q7XY20
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22
CP
171N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23
CX
152N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24E
CW
162N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24
CY
150N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28E
Cr
147N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30E
Cc
112Triticum aestivumMutation(s): 0 
Find proteins for Q5I7K9 (Triticum aestivum)
Go to UniProtKB:  Q5I7K9
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31E
Cd
123N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32E
Ce
133N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37E
Cj
94N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39E
Cl
51Triticum aestivumMutation(s): 0 
Find proteins for Q5I7K7 (Triticum aestivum)
Go to UniProtKB:  Q5I7K7
Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L44E
Co
105N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14E
CM
134N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20
CS
178N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22E
CU
130N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36E
Ci
112Triticum aestivumMutation(s): 0 
Find proteins for Q5I7L5 (Triticum aestivum)
Go to UniProtKB:  Q5I7L5
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11
CK
166N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein P1
Cu, Cv
110Triticum aestivumMutation(s): 0 
Find proteins for Q5I7K5 (Triticum aestivum)
Go to UniProtKB:  Q5I7K5
Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
Acidic ribosomal protein P2
Cs, Ct
113N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
Ch
124Triticum aestivumMutation(s): 0 
Gene Names: RPL35
Find proteins for Q8L805 (Triticum aestivum)
Go to Gene View: RPL35
Go to UniProtKB:  Q8L805
Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
CF
244Triticum aestivumMutation(s): 0 
Find proteins for Q5I7K6 (Triticum aestivum)
Go to UniProtKB:  Q5I7K6
Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
Cq
319N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
CB
389Triticum aestivumMutation(s): 0 
Gene Names: RPL3 (RPL3-A1, RPL3A-1)
Find proteins for Q7X744 (Triticum aestivum)
Go to Gene View: RPL3
Go to UniProtKB:  Q7X744
Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4
CC
405N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13
CO
206Triticum aestivumMutation(s): 0 
Find proteins for Q5I7L1 (Triticum aestivum)
Go to UniProtKB:  Q5I7L1
Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43E
Cp
92Triticum aestivumMutation(s): 0 
Find proteins for D8L9P6 (Triticum aestivum)
Go to UniProtKB:  D8L9P6
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16
CI
224N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41E
Cn
25N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L40E
Cm
53N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13E
CL
208N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6E
CE
219Triticum aestivumMutation(s): 0 
Find proteins for Q5I7L4 (Triticum aestivum)
Go to UniProtKB:  Q5I7L4
Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33E
Cf
111N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38E
Ck
69N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29E
Cb
60N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34E
Cg
119Triticum aestivumMutation(s): 0 
Find proteins for Q5I7K8 (Triticum aestivum)
Go to UniProtKB:  Q5I7K8
Entity ID: 1
MoleculeChainsLengthOrganism
18S ribosomal RNAAd1810Triticum aestivum
Entity ID: 2
MoleculeChainsLengthOrganism
P-site tRNAAe75Triticum aestivum
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3'Af11Triticum aestivum
Entity ID: 84
MoleculeChainsLengthOrganism
60S ribosomal RNAAa3391Triticum aestivum
Entity ID: 85
MoleculeChainsLengthOrganism
5.8S ribosomal RNAAc160Triticum aestivum
Entity ID: 86
MoleculeChainsLengthOrganism
5S ribosomal RNAAb120Triticum aestivum
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
BG
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2015-04-15
    Type: Other
  • Version 1.3: 2018-07-18
    Type: Data collection