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- PDB-7obr: RNC-SRP early complex -

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Basic information

Entry
Database: PDB / ID: 7obr
TitleRNC-SRP early complex
Components
  • (60S RIBOSOMAL PROTEIN ...) x 19
  • (Ribosomal protein ...) x 7
  • (Signal recognition particle ...) x 6
  • 28S rRNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Dipeptidyl aminopeptidase B
  • SRP RNA
  • eL18
  • eL21
  • eL28
  • eL31
  • eL32
  • eL33
  • eL38
  • eL39
  • eL42
  • eL43
  • uL15
  • uL22
  • uL23
  • uL29
  • uL3
  • uL30
KeywordsRNA BINDING PROTEIN / SRP SRP receptor / co-translational protein targeting / endoplasmic reticulum / signal peptide
Function / homology
Function and homology information


PI3K Cascade / PIP3 activates AKT signaling / FLT3 Signaling / Negative regulation of FLT3 / FLT3 signaling through SRC family kinases / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / RAF/MAP kinase cascade / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling ...PI3K Cascade / PIP3 activates AKT signaling / FLT3 Signaling / Negative regulation of FLT3 / FLT3 signaling through SRC family kinases / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / RAF/MAP kinase cascade / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / signal recognition particle, endoplasmic reticulum targeting / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Cyclin D associated events in G1 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of FLT3 / Regulation of BACH1 activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Termination of translesion DNA synthesis / Ovarian tumor domain proteases / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Iron uptake and transport / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / DNA Damage Recognition in GG-NER / Activation of NF-kappaB in B cells / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1
Similarity search - Function
Flt3 ligand / flt3 ligand / Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Putative TPR-like repeat / Signal recognition particle, SRP9 subunit / SRP9 domain / Signal recognition particle SRP9 ...Flt3 ligand / flt3 ligand / Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Putative TPR-like repeat / Signal recognition particle, SRP9 subunit / SRP9 domain / Signal recognition particle SRP9 / Signal recognition particle 9 kDa protein (SRP9) / Signal recognition particle, SRP14 subunit / Signal recognition particle, SRP9/SRP14 subunit / Signal recognition particle 14kD protein / 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 / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / 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 / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Four-helical cytokine-like, core / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Tetratricopeptide repeat / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L41 / Ribosomal protein L41 / metallochaperone-like domain / TRASH domain / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L44 / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature.
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Fms related receptor tyrosine kinase 3 ligand / Large ribosomal subunit protein eL42 ...GUANOSINE-5'-DIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Fms related receptor tyrosine kinase 3 ligand / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL2 / 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 eL22 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL34 / Signal recognition particle 19 kDa protein / Signal recognition particle 14 kDa protein / Dipeptidyl aminopeptidase B / Signal recognition particle 9 kDa protein / Signal recognition particle subunit SRP72 / Signal recognition particle subunit SRP54 / Ubiquitin-ribosomal protein eL40 fusion protein / Signal recognition particle subunit SRP68 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Canis lupus familiaris (dog)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsJomaa, A. / Ban, N.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Citation
Journal: Cell Rep / Year: 2021
Title: Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle.
Authors: Ahmad Jomaa / Simon Eitzinger / Zikun Zhu / Sowmya Chandrasekar / Kan Kobayashi / Shu-Ou Shan / Nenad Ban /
Abstract: 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 ...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.
#1: Journal: Cell Rep / Year: 2021
Title: Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle
Authors: Jomaa, A. / Eitzinger, S. / Zhu, Z. / Chandrasekar, S. / Kobayashi, K. / Shan, S. / Ban, N.
History
DepositionApr 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author

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Structure visualization

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Assembly

Deposited unit
1: SRP RNA
5: 28S rRNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
A: 60S ribosomal protein L8
B: uL3
C: 60S ribosomal protein L4
D: 60S ribosomal protein L5
E: 60S ribosomal protein L6
F: uL30
G: 60S ribosomal protein L7a
H: 60S ribosomal protein L9
I: 60S ribosomal protein L10
J: Ribosomal protein L11
L: 60S ribosomal protein L13
M: 60S ribosomal protein L14
N: Ribosomal protein L15
O: 60S ribosomal protein L13a
P: uL22
Q: eL18
R: 60S RIBOSOMAL PROTEIN EL19
S: 60S ribosomal protein L18a
T: eL21
U: Ribosomal protein L22
V: Ribosomal protein L23
W: Ribosomal protein L24
X: uL23
Y: Ribosomal protein L26
Z: 60S ribosomal protein L27
a: uL15
b: 60S ribosomal protein L29
c: 60S ribosomal protein L30
d: eL31
e: eL32
f: eL33
g: 60S ribosomal protein L34
h: uL29
i: 60S ribosomal protein L36
j: Ribosomal protein L37
k: eL38
l: eL39
m: 60S RIBOSOMAL PROTEIN EL40
n: 60s ribosomal protein l41
o: eL42
p: eL43
q: Signal recognition particle 19
r: eL28
s: Dipeptidyl aminopeptidase B
t: Signal recognition particle 14 kDa protein
u: Signal recognition particle subunit SRP68
w: Signal recognition particle 9 kDa protein
x: Signal recognition particle 54 kDa protein
z: Signal recognition particle subunit SRP72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,355,431156
Polymers2,352,30353
Non-polymers3,128103
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area418630 Å2
ΔGint-4192 kcal/mol
Surface area761220 Å2
MethodPISA

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Components

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RNA chain , 4 types, 4 molecules 1578

#1: RNA chain SRP RNA


Mass: 80677.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog)
#2: RNA chain 28S rRNA


Mass: 1131535.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#3: 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
#4: 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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60S RIBOSOMAL PROTEIN ... , 19 types, 19 molecules ACDEGHILMORSZbcgimn

#5: Protein 60S ribosomal protein L8


Mass: 26701.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9D5B2
#7: 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
#8: Protein 60S ribosomal protein L5


Mass: 34481.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#9: Protein 60S ribosomal protein L6


Mass: 28529.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#11: 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
#12: 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
#13: 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
#15: Protein 60S ribosomal protein L13


Mass: 24216.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV0
#16: 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
#18: Protein 60S ribosomal protein L13a


Mass: 23248.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A287B929
#21: Protein 60S RIBOSOMAL PROTEIN EL19


Mass: 21613.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q3T0W9
#22: 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) / References: UniProt: G1TTY7
#29: 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
#31: 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
#32: Protein 60S ribosomal protein L30


Mass: 10496.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#36: 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
#38: 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
#42: Protein 60S RIBOSOMAL PROTEIN EL40


Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P63048
#43: 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

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Protein , 17 types, 17 molecules BFPQTXadefhkloprs

#6: Protein uL3


Mass: 45976.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#10: 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
#19: Protein uL22


Mass: 17758.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TVT6
#20: Protein eL18


Mass: 21457.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TX70
#23: Protein eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#27: 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
#30: Protein uL15


Mass: 16489.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#33: Protein eL31


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


Mass: 18350.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUN8
#35: Protein eL33


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#37: Protein uL29


Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#40: Protein eL38


Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#41: Protein eL39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYU7
#44: Protein eL42


Mass: 12329.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9D391
#45: 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
#47: Protein eL28


Mass: 15783.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#48: Protein Dipeptidyl aminopeptidase B / DPAP B / YSCV


Mass: 7746.921 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: DAP2, YHR028C / Production host: Oryctolagus cuniculus (rabbit)
References: UniProt: P18962, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases

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Ribosomal protein ... , 7 types, 7 molecules JNUVWYj

#14: 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
#17: 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
#24: Protein Ribosomal protein L22


Mass: 11481.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TSG1
#25: 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
#26: Protein Ribosomal protein L24


Mass: 7512.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#28: 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
#39: 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

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Signal recognition particle ... , 6 types, 6 molecules qtuwxz

#46: Protein Signal recognition particle 19


Mass: 16183.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: J9PAS6
#49: Protein Signal recognition particle 14 kDa protein / SRP14


Mass: 12512.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P16255
#50: Protein Signal recognition particle subunit SRP68 / SRP68 / Signal recognition particle 68 kDa protein


Mass: 70376.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: Q00004
#51: Protein Signal recognition particle 9 kDa protein / SRP9


Mass: 10061.663 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P21262
#52: Protein Signal recognition particle 54 kDa protein / SRP54


Mass: 55775.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P61010
#53: Protein Signal recognition particle subunit SRP72 / SRP72 / Signal recognition particle 72 kDa protein


Mass: 74608.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P33731

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Non-polymers , 3 types, 103 molecules

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


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


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#56: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM

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Details

Has ligand of interestY

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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
1RNC-SRP complexCOMPLEX#1-#530MULTIPLE SOURCES
2RNC-SRP complexCOMPLEX#1-#45, #471NATURAL
3RNC-SRP complexCOMPLEX#1, #46, #49-#531NATURAL
4polypeptide nascent chainCOMPLEX#481RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Oryctolagus cuniculus (rabbit)9986
23Canis lupus familiaris (dog)9615
34Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43135 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6FRK

6frk

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