ISDA

Deposition Date 2015-06-17

Release Date 2015-08-05

Last Version Date 2024-11-06

Entry Detail

PDB ID:

3JAN

Keywords:

RIBOSOME

Title:

Structure of the scanning state of the mammalian SRP-ribosome complex

Biological Source:

Source Organism:

Oryctolagus cuniculus (Taxon ID: 9986)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.75 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:Val tRNA
Chain IDs:WA (auth: 3)
Chain Length:76
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polyribonucleotide
Molecule:SRP 7S RNA
Chain IDs:XA (auth: 4)
Chain Length:206
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polyribonucleotide
Molecule:28S ribosomal RNA
Chain IDs:FA (auth: 5)
Chain Length:3658
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:SRP68
Chain IDs:ZA (auth: 6)
Chain Length:179
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:GA (auth: 7)
Chain Length:120
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:HA (auth: 8)
Chain Length:156
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:SRP19
Chain IDs:YA (auth: 9)
Chain Length:105
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL2
Chain IDs:A
Chain Length:244
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL3
Chain IDs:IA (auth: B)
Chain Length:394
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL4
Chain IDs:JA (auth: C)
Chain Length:94
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL18
Chain IDs:B (auth: D)
Chain Length:107
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL6
Chain IDs:KA (auth: E)
Chain Length:128
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL30
Chain IDs:LA (auth: F)
Chain Length:109
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL8
Chain IDs:C (auth: G)
Chain Length:238
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL6
Chain IDs:D (auth: H)
Chain Length:190
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL16
Chain IDs:MA (auth: I)
Chain Length:102
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL5
Chain IDs:E (auth: J)
Chain Length:86
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL11
Chain IDs:TA (auth: K)
Chain Length:163
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL13
Chain IDs:F (auth: L)
Chain Length:50
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL14
Chain IDs:G (auth: M)
Chain Length:52
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL15
Chain IDs:H (auth: N)
Chain Length:23
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL13
Chain IDs:I (auth: O)
Chain Length:104
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL22
Chain IDs:NA (auth: P)
Chain Length:153
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL18
Chain IDs:J (auth: Q)
Chain Length:202
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL19
Chain IDs:K (auth: R)
Chain Length:125
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL20
Chain IDs:L (auth: S)
Chain Length:175
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:SRP9
Chain IDs:IC (auth: S1)
Chain Length:74
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:AB (auth: S2)
Chain Length:1742
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:SRP14
Chain IDs:JC (auth: S4)
Chain Length:76
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS2
Chain IDs:BB (auth: SA)
Chain Length:208
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS1
Chain IDs:CB (auth: SB)
Chain Length:83
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS5
Chain IDs:DB (auth: SC)
Chain Length:64
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS3
Chain IDs:TB (auth: SD)
Chain Length:227
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS4
Chain IDs:EB (auth: SE)
Chain Length:57
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS7
Chain IDs:UB (auth: SF)
Chain Length:71
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS6
Chain IDs:FB (auth: SG)
Chain Length:237
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS7
Chain IDs:GB (auth: SH)
Chain Length:189
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS8
Chain IDs:HB (auth: SI)
Chain Length:206
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS4
Chain IDs:IB (auth: SJ)
Chain Length:185
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS10
Chain IDs:VB (auth: SK)
Chain Length:98
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS17
Chain IDs:JB (auth: SL)
Chain Length:152
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS12
Chain IDs:WB (auth: SM)
Chain Length:124
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS15
Chain IDs:KB (auth: SN)
Chain Length:149
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS11
Chain IDs:LB (auth: SO)
Chain Length:136
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS19
Chain IDs:XB (auth: SP)
Chain Length:96
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS9
Chain IDs:YB (auth: SQ)
Chain Length:141
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS17
Chain IDs:ZB (auth: SR)
Chain Length:129
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS13
Chain IDs:AC (auth: SS)
Chain Length:137
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS19
Chain IDs:BC (auth: ST)
Chain Length:141
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS10
Chain IDs:CC (auth: SU)
Chain Length:104
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS21
Chain IDs:MB (auth: SV)
Chain Length:82
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS8
Chain IDs:NB (auth: SW)
Chain Length:129
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS12
Chain IDs:OB (auth: SX)
Chain Length:141
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS24
Chain IDs:PB (auth: SY)
Chain Length:126
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein es25
Chain IDs:DC (auth: SZ)
Chain Length:75
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS26
Chain IDs:QB (auth: Sa)
Chain Length:208
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS27
Chain IDs:RB (auth: Sb)
Chain Length:83
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS28
Chain IDs:EC (auth: Sc)
Chain Length:64
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS14
Chain IDs:FC (auth: Sd)
Chain Length:227
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS30
Chain IDs:SB (auth: Se)
Chain Length:57
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS31
Chain IDs:GC (auth: Sf)
Chain Length:71
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein RACK1
Chain IDs:HC (auth: Sg)
Chain Length:237
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL21
Chain IDs:M (auth: T)
Chain Length:159
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL22
Chain IDs:N (auth: U)
Chain Length:99
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL14
Chain IDs:O (auth: V)
Chain Length:131
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL24
Chain IDs:OA (auth: W)
Chain Length:63
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL23
Chain IDs:P (auth: X)
Chain Length:119
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL24
Chain IDs:Q (auth: Y)
Chain Length:134
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL27
Chain IDs:R (auth: Z)
Chain Length:426
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL15
Chain IDs:S (auth: a)
Chain Length:244
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL29
Chain IDs:T (auth: b)
Chain Length:394
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL30
Chain IDs:U (auth: c)
Chain Length:94
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL31
Chain IDs:V (auth: d)
Chain Length:107
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL32
Chain IDs:W (auth: e)
Chain Length:128
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL33
Chain IDs:X (auth: f)
Chain Length:109
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL34
Chain IDs:Y (auth: g)
Chain Length:238
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL29
Chain IDs:Z (auth: h)
Chain Length:190
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL36
Chain IDs:AA (auth: i)
Chain Length:102
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL37
Chain IDs:PA (auth: j)
Chain Length:86
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL38
Chain IDs:BA (auth: k)
Chain Length:163
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL39
Chain IDs:CA (auth: l)
Chain Length:50
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL40
Chain IDs:DA (auth: m)
Chain Length:52
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL41
Chain IDs:QA (auth: n)
Chain Length:23
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL42
Chain IDs:EA (auth: o)
Chain Length:104
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL43
Chain IDs:RA (auth: p)
Chain Length:153
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL10
Chain IDs:UA (auth: q)
Chain Length:202
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL28
Chain IDs:SA (auth: r)
Chain Length:125
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:SRP54
Chain IDs:VA (auth: z)
Chain Length:426
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Ligand Molecules

Primary Citation

Structures of the scanning and engaged states of the mammalian SRP-ribosome complex.

Voorhees, R.M, Hegde, R.S.Show

Elife 4 ? ? (2015)

PMID: 26158507 DOI: 10.7554/eLife.07975

Abstact

The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially engaging those with hydrophobic targeting signals, and delivers these ribosome-nascent chain complexes to the membrane. Here, we present structures of native mammalian SRP-ribosome complexes in the scanning and engaged states. These structures reveal the near-identical SRP architecture of these two states, show many of the SRP-ribosome interactions at atomic resolution, and suggest how the polypeptide-binding M domain selectively engages hydrophobic signals. The scanning M domain, pre-positioned at the ribosomal exit tunnel, is auto-inhibited by a C-terminal amphipathic helix occluding its hydrophobic binding groove. Upon engagement, the hydrophobic targeting signal displaces this amphipathic helix, which then acts as a protective lid over the signal. Biochemical experiments suggest how scanning and engagement are coordinated with translation elongation to minimize exposure of hydrophobic signals during membrane targeting.

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Protein

Chemical

Disease

Primary Citation of related structures