ISDA

Deposition Date 2021-04-23

Release Date 2021-07-21

Last Version Date 2024-11-20

Entry Detail

PDB ID:

7OBR

Keywords:

RNA BINDING PROTEIN

Title:

RNC-SRP early complex

Biological Source:

Source Organism:

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Taxon ID: 559292)
Canis lupus familiaris (Taxon ID: 9615)
Oryctolagus cuniculus (Taxon ID: 9986)

Host Organism:

Oryctolagus cuniculus

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.80 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:SRP RNA
Chain IDs:A (auth: 1)
Chain Length:249
Number of Molecules:1
Biological Source:Canis lupus familiaris

Polymer Type:polyribonucleotide
Molecule:28S rRNA
Chain IDs:B (auth: 5)
Chain Length:3493
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

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

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8
Gene (Uniprot):ZNF34
Chain IDs:E (auth: A)
Chain Length:245
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:A0A5F9D5B2 Pfam ID:PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL3
Gene (Uniprot):RPL3
Chain IDs:F (auth: B)
Chain Length:223
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TL06 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Gene (Uniprot):RPL4
Chain IDs:G (auth: C)
Chain Length:413
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SVW5 Pfam ID:PF00573, PF14374

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Chain IDs:H (auth: D)
Chain Length:125
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:P19949

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):RPL6
Chain IDs:I (auth: E)
Chain Length:157
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SKF7 Pfam ID:PF03868, PF01159

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL30
Gene (Uniprot):RPL7
Chain IDs:J (auth: F)
Chain Length:110
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SV32 Pfam ID:PF08079, PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Gene (Uniprot):RPL7A
Chain IDs:K (auth: G)
Chain Length:129
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1STW0 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Gene (Uniprot):RPL9
Chain IDs:L (auth: H)
Chain Length:123
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SWI6 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:M (auth: I)
Chain Length:214
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:B7NZQ2 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L11
Gene (Uniprot):RPL11
Chain IDs:N (auth: J)
Chain Length:178
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TUB8 Pfam ID:PF00281, PF00673

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Chain IDs:O (auth: L)
Chain Length:210
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Chain IDs:P (auth: M)
Chain Length:52
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SZ12 Pfam ID:PF01929

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Gene (Uniprot):RPL15
Chain IDs:Q (auth: N)
Chain Length:25
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1T0C1 Pfam ID:PF00827

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Chain IDs:R (auth: O)
Chain Length:199
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

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

UniProt ID:G1SCJ6 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL18
Chain IDs:T (auth: Q)
Chain Length:144
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TX70 Pfam ID:PF17135

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN EL19
Gene (Uniprot):RPL19
Chain IDs:U (auth: R)
Chain Length:180
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:Q3T0W9 Pfam ID:PF01280

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Gene (Uniprot):RPL18A
Chain IDs:V (auth: S)
Chain Length:175
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TTY7 Pfam ID:PF01775

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL21
Gene (Uniprot):RPL21
Chain IDs:W (auth: T)
Chain Length:110
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SHQ2 Pfam ID:PF01157

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L22
Gene (Uniprot):RPL22
Chain IDs:X (auth: U)
Chain Length:99
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TSG1 Pfam ID:PF01776

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L23
Gene (Uniprot):RPL23
Chain IDs:Y (auth: V)
Chain Length:140
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1T6D1 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L24
Gene (Uniprot):RPL24
Chain IDs:Z (auth: W)
Chain Length:86
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SE28 Pfam ID:PF01246

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL23
Gene (Uniprot):RPL23A
Chain IDs:AA (auth: X)
Chain Length:156
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SE76 Pfam ID:PF03939, PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L26
Gene (Uniprot):RPL26
Chain IDs:BA (auth: Y)
Chain Length:145
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SQH0 Pfam ID:PF16906, PF00467

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):RPL27
Chain IDs:CA (auth: Z)
Chain Length:671
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TXF6 Pfam ID:PF00467, PF01777

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL15
Gene (Uniprot):RPL27A
Chain IDs:DA (auth: a)
Chain Length:245
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SNY0 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Chain IDs:EA (auth: b)
Chain Length:223
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SGR6 Pfam ID:PF01779

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:FA (auth: c)
Chain Length:413
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TDL2 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL31
Gene (Uniprot):RPL31
Chain IDs:GA (auth: d)
Chain Length:125
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SHG0 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL32
Gene (Uniprot):RPL32
Chain IDs:HA (auth: e)
Chain Length:157
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TUN8 Pfam ID:PF01655

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL33
Gene (Uniprot):RPL35A
Chain IDs:IA (auth: f)
Chain Length:110
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SF08 Pfam ID:PF01247

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34
Chain IDs:JA (auth: g)
Chain Length:129
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TXG5 Pfam ID:PF01199

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL29
Gene (Uniprot):RPL35
Chain IDs:KA (auth: h)
Chain Length:123
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SIT5 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):RPL36
Chain IDs:LA (auth: i)
Chain Length:214
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TTQ5 Pfam ID:PF01158

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Gene (Uniprot):RPL37
Chain IDs:MA (auth: j)
Chain Length:178
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:U3KPD5 Pfam ID:PF01907

Polymer Type:polypeptide(L)
Molecule:eL38
Chain IDs:NA (auth: k)
Chain Length:69
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL39
Gene (Uniprot):RPL39
Chain IDs:OA (auth: l)
Chain Length:210
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SYU7 Pfam ID:PF00832

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN EL40
Gene (Uniprot):UBA52
Chain IDs:PA (auth: m)
Chain Length:52
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:P63048 Pfam ID:PF01020

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60s ribosomal protein l41
Gene (Uniprot):RPL41
Chain IDs:QA (auth: n)
Chain Length:25
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:A0A087WNH4 Pfam ID:PF05162

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL42
Chain IDs:RA (auth: o)
Chain Length:199
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:A0A5F9D391 Pfam ID:PF00935

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL43
Gene (Uniprot):RPL37A
Chain IDs:SA (auth: p)
Chain Length:153
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SY53 Pfam ID:PF01780

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Signal recognition particle 19
Gene (Uniprot):SRP19
Chain IDs:TA (auth: q)
Chain Length:144
Number of Molecules:1
Biological Source:Canis lupus familiaris

UniProt ID:J9PAS6 Pfam ID:PF01922

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL28
Gene (Uniprot):RPL28
Chain IDs:UA (auth: r)
Chain Length:180
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1U7L1 Pfam ID:PF01778

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Dipeptidyl aminopeptidase B
Gene (Uniprot):DAP2
Chain IDs:VA (auth: s)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P18962

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Signal recognition particle 14 kDa protein
Gene (Uniprot):SRP14
Chain IDs:WA (auth: t)
Chain Length:110
Number of Molecules:1
Biological Source:Canis lupus familiaris

UniProt ID:P16255 Pfam ID:PF02290

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Signal recognition particle subunit SRP68
Gene (Uniprot):SRP68
Chain IDs:XA (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:Signal recognition particle 9 kDa protein
Gene (Uniprot):SRP9
Chain IDs:YA (auth: w)
Chain Length:86
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:ZA (auth: x)
Chain Length:156
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:Signal recognition particle subunit SRP72
Gene (Uniprot):SRP72
Chain IDs:AB (auth: z)
Chain Length:671
Number of Molecules:1
Biological Source:Canis lupus familiaris

UniProt ID:P33731 Pfam ID:PF17004, PF13181, PF08492

Ligand Molecules

GDP

Primary Citation

Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle.

Jomaa, A, Eitzinger, S, Zhu, Z, Chandrasekar, S, Kobayashi, K, Shan, S.O, Ban, N, Jomaa, A, Eitzinger, S, Zhu, Z, Chandrasekar, S, Kobayashi, K, Shan, S, Ban, N.Show

Cell Rep 36 109350 109350 (2021)

PMID: 34260909 DOI: 10.1016/j.celrep.2021.109350

Abstact

Co-translational protein targeting to membranes by the signal recognition particle (SRP) is a universally conserved pathway from bacteria to humans. In mammals, SRP and its receptor (SR) have many additional RNA features and protein components compared to the bacterial system, which were recently shown to play regulatory roles. Due to its complexity, the mammalian SRP targeting process is mechanistically not well understood. In particular, it is not clear how SRP recognizes translating ribosomes with exposed signal sequences and how the GTPase activity of SRP and SR is regulated. Here, we present electron cryo-microscopy structures of SRP and SRP·SR in complex with the translating ribosome. The structures reveal the specific molecular interactions between SRP and the emerging signal sequence and the elements that regulate GTPase activity of SRP·SR. Our results suggest the molecular mechanism of how eukaryote-specific elements regulate the early and late stages of SRP-dependent protein targeting.

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Protein

Chemical

Disease

Primary Citation of related structures