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- PDB-7qwq: Ternary complex of ribosome nascent chain with SRP and NAC -

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Basic information

Entry
Database: PDB / ID: 7qwq
TitleTernary complex of ribosome nascent chain with SRP and NAC
Components
  • (60S ribosomal protein ...) x 23
  • (Ribosomal protein ...) x 10
  • (Signal recognition particle ...) x 3
  • 28S rRNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Isoform 2 of Transcription factor BTF3
  • L8
  • Nascent chain preprolactin
  • Nascent polypeptide-associated complex subunit alpha
  • Ribosomal_L18_c domain-containing protein
  • Ribosomal_L23eN domain-containing protein
  • SRP RNA 7SL
  • Ubiquitin A-52 residue ribosomal protein fusion product 1
  • eL18
  • eL42
  • eL43
  • uL3
  • uL30
KeywordsRIBOSOME / SRP / NAC / nascent chain / co-translational / Endoplasmic reticulum / co-translational protein targeting / co-translational folding
Function / homology
Function and homology information


PI3K Cascade / PIP3 activates AKT signaling / FLT3 Signaling / FLT3 signaling through SRC family kinases / RAF/MAP kinase cascade / Negative regulation of FLT3 / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / endoplasmic reticulum signal sequence receptor activity / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / negative regulation of striated muscle cell apoptotic process ...PI3K Cascade / PIP3 activates AKT signaling / FLT3 Signaling / FLT3 signaling through SRC family kinases / RAF/MAP kinase cascade / Negative regulation of FLT3 / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / endoplasmic reticulum signal sequence receptor activity / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / negative regulation of striated muscle cell apoptotic process / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / signal recognition particle, endoplasmic reticulum targeting / regulation of skeletal muscle fiber development / granulocyte differentiation / positive regulation of cell proliferation involved in heart morphogenesis / positive regulation of skeletal muscle tissue growth / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / signal recognition particle / cardiac ventricle development / signal recognition particle binding / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / cotranslational protein targeting to membrane / exocrine pancreas development / signal-recognition-particle GTPase / heart trabecula morphogenesis / dendritic cell differentiation / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / skeletal muscle tissue regeneration / SRP-dependent cotranslational protein targeting to membrane / embryonic hemopoiesis / ribonucleoprotein complex binding / ubiquitin ligase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / positive regulation of signal transduction by p53 class mediator / neutrophil chemotaxis / B cell differentiation / protein-RNA complex assembly / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / cytokine activity / wound healing / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Dengue Virus Genome Translation and Replication / receptor tyrosine kinase binding / GDP binding / protein transport / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit rRNA binding / killing of cells of another organism / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / cytoplasmic translation / transcription coactivator activity / tRNA binding / nuclear speck / postsynaptic density / response to xenobiotic stimulus / rRNA binding / ribosome / translation / structural constituent of ribosome / ribonucleoprotein complex / protein domain specific binding / mRNA binding / positive regulation of cell population proliferation / GTPase activity / nucleolus / synapse / GTP binding / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / : / DNA-templated transcription / RNA binding / extracellular exosome / nucleoplasm / zinc ion binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Flt3 ligand / flt3 ligand / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein ...Flt3 ligand / flt3 ligand / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Nascent polypeptide-associated complex subunit alpha / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / Signal recognition particle, SRP54 subunit / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. / NAC / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Four-helical cytokine-like, core / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / : / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L6e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal L40e family / Ribosomal protein L36e signature. / Ribosomal protein L30e signature 1. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / : / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ribosomal protein L44e / Ribosomal protein L44 / 60S ribosomal protein L35 / Ribosomal protein L6e / Ribosomal protein L7A/L8 / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 60S ribosomal protein L6E / Ribosomal protein L7, eukaryotic / : / Ribosomal protein L30, N-terminal / Ribosomal protein L39e, conserved site / Ribosomal L30 N-terminal domain / Ribosomal protein L39e signature. / Ribosomal protein L34Ae
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Fms related receptor tyrosine kinase 3 ligand / Ubiquitin-ribosomal protein eL40 fusion protein ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Fms related receptor tyrosine kinase 3 ligand / Ubiquitin-ribosomal protein eL40 fusion protein / Ribosomal protein L36a / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL29 / Uncharacterized protein / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL34 / Signal recognition particle 19 kDa protein / Transcription factor BTF3 / Signal recognition particle subunit SRP54 / Nascent polypeptide-associated complex subunit alpha / Large ribosomal subunit protein eL19 / Signal recognition particle subunit SRP68 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsJomaa, A. / Gamerdinger, M. / Hsieh, H. / Wallisch, A. / Chandrasekaran, V. / Ulusoy, Z. / Scaiola, A. / Hegde, R. / Shan, S. / Ban, N. / Deuerling, E.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Science / Year: 2022
Title: Mechanism of signal sequence handover from NAC to SRP on ribosomes during ER-protein targeting.
Authors: Ahmad Jomaa / Martin Gamerdinger / Hao-Hsuan Hsieh / Annalena Wallisch / Viswanathan Chandrasekaran / Zeynel Ulusoy / Alain Scaiola / Ramanujan S Hegde / Shu-Ou Shan / Nenad Ban / Elke Deuerling /
Abstract: The nascent polypeptide-associated complex (NAC) interacts with newly synthesized proteins at the ribosomal tunnel exit and competes with the signal recognition particle (SRP) to prevent mistargeting ...The nascent polypeptide-associated complex (NAC) interacts with newly synthesized proteins at the ribosomal tunnel exit and competes with the signal recognition particle (SRP) to prevent mistargeting of cytosolic and mitochondrial polypeptides to the endoplasmic reticulum (ER). How NAC antagonizes SRP and how this is overcome by ER targeting signals are unknown. Here, we found that NAC uses two domains with opposing effects to control SRP access. The core globular domain prevented SRP from binding to signal-less ribosomes, whereas a flexibly attached domain transiently captured SRP to permit scanning of nascent chains. The emergence of an ER-targeting signal destabilized NAC's globular domain and facilitated SRP access to the nascent chain. These findings elucidate how NAC hands over the signal sequence to SRP and imparts specificity of protein localization.
History
DepositionJan 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Source and taxonomy / Structure summary
Category: em_entity_assembly / em_entity_assembly_naturalsource ...em_entity_assembly / em_entity_assembly_naturalsource / em_entity_assembly_recombinant / entity_src_nat
Item: _entity_src_nat.common_name
Revision 1.2Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
1: SRP RNA 7SL
q: Signal recognition particle 19 kDa protein
s: Nascent chain preprolactin
u: Isoform 2 of Transcription factor BTF3
v: Signal recognition particle subunit SRP68
x: Signal recognition particle 54 kDa protein
A: L8
b: 60S ribosomal protein L29
5: 28S rRNA
B: uL3
c: 60S ribosomal protein L30
C: 60S ribosomal protein L4
d: Ribosomal protein L31
D: Ribosomal_L18_c domain-containing protein
e: Ribosomal protein L32
E: 60S ribosomal protein L6
f: 60S ribosomal protein L35a
F: uL30
g: 60S ribosomal protein L34
G: 60S ribosomal protein L7a
h: 60S ribosomal protein L35
H: 60S ribosomal protein L9
i: 60S ribosomal protein L36
I: 60S ribosomal protein L10
j: Ribosomal protein L37
J: Ribosomal protein L11
k: 60S ribosomal protein L38
L: 60S ribosomal protein L13
l: Ribosomal protein L39
M: 60S ribosomal protein L14
m: Ubiquitin A-52 residue ribosomal protein fusion product 1
N: Ribosomal protein L15
n: 60s ribosomal protein l41
O: 60S ribosomal protein L13a
o: eL42
P: 60S ribosomal protein L17
p: eL43
Q: eL18
r: 60S ribosomal protein L28
R: 60S ribosomal protein L19
S: 60S ribosomal protein L18a
T: 60S ribosomal protein L21
U: Ribosomal protein L22
V: Ribosomal protein L23
W: Ribosomal protein L24
X: Ribosomal_L23eN domain-containing protein
7: 5S ribosomal RNA
Y: Ribosomal protein L26
8: 5.8S ribosomal RNA
Z: 60S ribosomal protein L27
a: 60S ribosomal protein L27a
t: Nascent polypeptide-associated complex subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,747,362154
Polymers2,744,67852
Non-polymers2,685102
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 4 types, 4 molecules 1578

#1: RNA chain SRP RNA 7SL


Mass: 54095.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: GenBank: 23924
#9: RNA chain 28S rRNA


Mass: 1539032.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#47: RNA chain 5S ribosomal RNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_4
#49: RNA chain 5.8S ribosomal RNA


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_3

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Signal recognition particle ... , 3 types, 3 molecules qvx

#2: Protein Signal recognition particle 19 kDa protein / SRP19


Mass: 16183.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP19 / Production host: Escherichia coli (E. coli) / References: UniProt: P09132
#5: Protein Signal recognition particle subunit SRP68 / SRP68 / Signal recognition particle 68 kDa protein


Mass: 70831.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHB9
#6: Protein Signal recognition particle 54 kDa protein / SRP54


Mass: 55847.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: mutant G226E / Source: (gene. exp.) Homo sapiens (human) / Gene: SRP54 / Production host: Escherichia coli (E. coli)
References: UniProt: P61011, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

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Protein , 12 types, 12 molecules suABDFmopQXt

#3: Protein Nascent chain preprolactin


Mass: 9549.763 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: this will need to changed to UNK / Source: (gene. exp.) Homo sapiens (human) / Production host: Oryctolagus cuniculus (rabbit)
#4: Protein Isoform 2 of Transcription factor BTF3 / Nascent polypeptide-associated complex subunit beta / NAC-beta / RNA polymerase B transcription factor 3


Mass: 17724.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTF3, NACB, OK/SW-cl.8 / Production host: Escherichia coli (E. coli) / References: UniProt: P20290
#7: Protein L8


Mass: 26570.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#10: Protein uL3


Mass: 46107.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: G1TL06
#14: Protein Ribosomal_L18_c domain-containing protein


Mass: 34481.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#18: Protein uL30


Mass: 26662.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SV32
#31: Protein Ubiquitin A-52 residue ribosomal protein fusion product 1 / Ubiquitin-60S ribosomal protein L40


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2U3YV30
#35: Protein eL42


Mass: 16130.169 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9D391
#37: Protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#38: Protein eL18


Mass: 21457.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#46: Protein Ribosomal_L23eN domain-containing protein / uL23


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#52: Protein Nascent polypeptide-associated complex subunit alpha / NAC-alpha / Alpha-NAC


Mass: 23406.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NACA, HSD48 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13765

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60S ribosomal protein ... , 23 types, 23 molecules bcCEfgGhHiIkLMnOPrRSTZa

#8: Protein 60S ribosomal protein L29


Mass: 24608.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN82
#11: Protein 60S ribosomal protein L30


Mass: 12821.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#12: Protein 60S ribosomal protein L4


Mass: 46388.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#16: Protein 60S ribosomal protein L6


Mass: 33055.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#17: Protein 60S ribosomal protein L35a / eL33


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#19: Protein 60S ribosomal protein L34


Mass: 14557.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U945
#20: Protein 60S ribosomal protein L7a


Mass: 36267.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0
#21: Protein 60S ribosomal protein L35 / uL29


Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#22: Protein 60S ribosomal protein L9


Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6
#23: Protein 60S ribosomal protein L36


Mass: 11888.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#24: Protein 60S ribosomal protein L10 / Ribosomal protein L10 (Predicted)


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#27: Protein 60S ribosomal protein L38


Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B5FYZ2
#28: Protein 60S ribosomal protein L13


Mass: 24216.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: APSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPASGPLRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPR ...Details: APSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPASGPLRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPR RRNKSTESLQANVQRLKEYRSKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKE AAEQDVEKKK
Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV0
#30: Protein 60S ribosomal protein L14


Mass: 23810.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KNW6
#33: Protein/peptide 60s ribosomal protein l41 / eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4
#34: Protein 60S ribosomal protein L13a


Mass: 56501.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A287B929
#36: Protein 60S ribosomal protein L17


Mass: 17758.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#39: Protein 60S ribosomal protein L28 / eL28


Mass: 15783.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#40: Protein 60S ribosomal protein L19 / eL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q3T0W9
#41: Protein 60S ribosomal protein L18a


Mass: 20696.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#42: Protein 60S ribosomal protein L21 / eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#50: Protein 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#51: Protein 60S ribosomal protein L27a


Mass: 16620.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0

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Ribosomal protein ... , 10 types, 10 molecules dejJlNUVWY

#13: Protein Ribosomal protein L31 / eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#15: Protein Ribosomal protein L32 / eL32


Mass: 18350.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUN8
#25: Protein Ribosomal protein L37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#26: Protein Ribosomal protein L11


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#29: Protein Ribosomal protein L39 / eL39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYU7
#32: Protein Ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#43: Protein Ribosomal protein L22


Mass: 11836.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: Protein Ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#45: Protein Ribosomal protein L24 / eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#48: Protein Ribosomal protein L26


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0

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Non-polymers , 2 types, 102 molecules

#53: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 97 / Source method: obtained synthetically / Formula: Mg
#54: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Ternary ribosome-nascent chain SRP NAC complexCOMPLEX#1-#520MULTIPLE SOURCES
2RibosomeRIBOSOME#7-#521NATURAL
3SRP RNA 7SLCOMPLEX#11RECOMBINANT
4Signal recognition particle proteinsCOMPLEX#2, #5-#61RECOMBINANT
5Nascent chain preprolactinCOMPLEX#31RECOMBINANT
6Isoform 2 of Transcription factor BTF3COMPLEX#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Oryctolagus cuniculus (rabbit)9986
23Homo sapiens (human)9606
34Homo sapiens (human)9606
45Homo sapiens (human)9606
56Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Escherichia coli (E. coli)562
24Escherichia coli (E. coli)562
35Oryctolagus cuniculus (rabbit)9986
46Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51843 / Symmetry type: POINT

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