6FRK image
Deposition Date 2018-02-16
Release Date 2018-03-28
Last Version Date 2025-07-09
Entry Detail
PDB ID:
6FRK
Keywords:
TRANSLATION
Title:
Structure of a prehandover mammalian ribosomal SRP and SRP receptor targeting complex
Biological Source:
Source Organism:
Saccharomyces cerevisiae (Taxon ID: 4932)
Oryctolagus cuniculus (Taxon ID: 9986)
Canis lupus familiaris (Taxon ID: 9615)
Host Organism:
Oryctolagus cuniculus
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6FRK validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:Canis lupus familiaris RNA, 7SL, cytoplasmic 1 (RN7SL1), SRP RNA
Chain IDs:A (auth: 1)
Chain Length:299
Number of Molecules:1
Biological Source:Canis lupus familiaris
Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:B (auth: 2)
Chain Length:76
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL28
Chain IDs:C (auth: 3)
Chain Length:125
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L12
Chain IDs:D (auth: 4)
Chain Length:163
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:28S ribosomal RNA
Chain IDs:E (auth: 5)
Chain Length:3658
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0
Chain IDs:F (auth: 6)
Chain Length:202
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:G (auth: 7)
Chain Length:120
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:H (auth: 8)
Chain Length:156
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L8
Chain IDs:I (auth: A)
Chain Length:244
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL3
Chain IDs:J (auth: B)
Chain Length:75
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL4
Chain IDs:K (auth: C)
Chain Length:94
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL18
Chain IDs:L (auth: D)
Chain Length:107
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL6
Chain IDs:M (auth: E)
Chain Length:236
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL30
Chain IDs:N (auth: F)
Chain Length:109
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL8
Chain IDs:O (auth: G)
Chain Length:114
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL6
Chain IDs:P (auth: H)
Chain Length:190
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL16
Chain IDs:Q (auth: I)
Chain Length:102
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL5
Chain IDs:R (auth: J)
Chain Length:86
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL13
Chain IDs:S (auth: L)
Chain Length:50
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL14
Chain IDs:T (auth: M)
Chain Length:52
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Chain IDs:U (auth: N)
Chain Length:23
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL13
Chain IDs:V (auth: O)
Chain Length:201
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL22
Chain IDs:W (auth: P)
Chain Length:153
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL18
Chain IDs:X (auth: Q)
Chain Length:187
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL19
Chain IDs:Y (auth: R)
Chain Length:180
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL20
Chain IDs:Z (auth: S)
Chain Length:175
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL21
Chain IDs:AA (auth: T)
Chain Length:11
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL22
Chain IDs:BA (auth: U)
Chain Length:99
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L23
Chain IDs:CA (auth: V)
Chain Length:131
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL24
Chain IDs:DA (auth: W)
Chain Length:63
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL23
Chain IDs:EA (auth: X)
Chain Length:119
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL24
Chain IDs:FA (auth: Y)
Chain Length:657
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Chain IDs:GA (auth: Z)
Chain Length:110
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL15
Chain IDs:HA (auth: a)
Chain Length:244
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Chain IDs:IA (auth: b)
Chain Length:75
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL30
Chain IDs:JA (auth: c)
Chain Length:94
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL31
Chain IDs:KA (auth: d)
Chain Length:107
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL32
Chain IDs:LA (auth: e)
Chain Length:236
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL33
Chain IDs:MA (auth: f)
Chain Length:109
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL34
Chain IDs:NA (auth: g)
Chain Length:114
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL29
Chain IDs:OA (auth: h)
Chain Length:190
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL36
Chain IDs:PA (auth: i)
Chain Length:102
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Chain IDs:QA (auth: j)
Chain Length:86
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL38
Chain IDs:RA (auth: k)
Chain Length:69
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL39
Chain IDs:SA (auth: l)
Chain Length:50
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL40
Chain IDs:TA (auth: m)
Chain Length:52
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL41
Chain IDs:UA (auth: n)
Chain Length:23
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL42
Chain IDs:VA (auth: o)
Chain Length:201
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL43
Chain IDs:WA (auth: p)
Chain Length:153
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Signal recognition particle subunit SRP19
Gene (Uniprot):SRP19
Chain IDs:XA (auth: q)
Chain Length:187
Number of Molecules:1
Biological Source:Canis lupus familiaris
UniProt ID:J9PAS6 Pfam ID:PF01922
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72
Gene (Uniprot):SRP72
Chain IDs:YA (auth: r)
Chain Length:180
Number of Molecules:1
Biological Source:Canis lupus familiaris
UniProt ID:P33731 Pfam ID:PF17004, PF13181, PF08492
Polymer Type:polypeptide(L)
Molecule:Signal sequence
Chain IDs:ZA (auth: t)
Chain Length:11
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Signal recognition particle subunit SRP68
Gene (Uniprot):SRP68
Chain IDs:AB (auth: u)
Chain Length:99
Number of Molecules:1
Biological Source:Canis lupus familiaris
UniProt ID:Q00004 Pfam ID:PF16969
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SRP receptor beta subunit
Gene (Uniprot):SRPRB
Chain IDs:BB (auth: v)
Chain Length:131
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1STG2 Pfam ID:PF09439
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Signal recognition particle 9 kDa protein
Gene (Uniprot):SRP9
Chain IDs:CB (auth: w)
Chain Length:63
Number of Molecules:1
Biological Source:Canis lupus familiaris
UniProt ID:P21262 Pfam ID:PF05486
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Signal recognition particle 54 kDa protein
Gene (Uniprot):SRP54
Chain IDs:DB (auth: x)
Chain Length:119
Number of Molecules:1
Biological Source:Canis lupus familiaris
UniProt ID:P61010 Pfam ID:PF02881, PF00448, PF02978 EC:3.6.5.4
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SRP receptor alpha subunit
Gene (Uniprot):SRPRA
Chain IDs:EB (auth: y)
Chain Length:657
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TCX6 Pfam ID:PF04086, PF02881, PF00448
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Signal recognition particle 14 kDa protein
Gene (Uniprot):SRP14
Chain IDs:FB (auth: z)
Chain Length:110
Number of Molecules:1
Biological Source:Canis lupus familiaris
UniProt ID:P16255 Pfam ID:PF02290
Ligand Molecules
GNP
GTP
MG
ZN
Primary Citation
Structure of a prehandover mammalian ribosomal SRP·SRP receptor targeting complex.
Science 360 323 327 (2018)
PMID: 29567807 DOI: 10.1126/science.aar7924

Abstact

Signal recognition particle (SRP) targets proteins to the endoplasmic reticulum (ER). SRP recognizes the ribosome synthesizing a signal sequence and delivers it to the SRP receptor (SR) on the ER membrane followed by the transfer of the signal sequence to the translocon. Here, we present the cryo-electron microscopy structure of the mammalian translating ribosome in complex with SRP and SR in a conformation preceding signal sequence handover. The structure visualizes all eukaryotic-specific SRP and SR proteins and reveals their roles in stabilizing this conformation by forming a large protein assembly at the distal site of SRP RNA. We provide biochemical evidence that the guanosine triphosphate hydrolysis of SRP·SR is delayed at this stage, possibly to provide a time window for signal sequence handover to the translocon.

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Primary Citation of related structures
6FRK