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- PDB-6frk: Structure of a prehandover mammalian ribosomal SRP and SRP recept... -

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Entry
Database: PDB / ID: 6frk
TitleStructure of a prehandover mammalian ribosomal SRP and SRP receptor targeting complex
Components
  • (60S ribosomal protein ...) x 2
  • (Ribosomal protein ...) x 41
  • (SRP receptor ...Signal recognition particle receptor) x 2
  • (Signal recognition particle ...) x 6
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Canis lupus familiaris RNA, 7SL, cytoplasmic 1 (RN7SL1), SRP RNA
  • Signal sequence
  • tRNATransfer RNA
KeywordsTRANSLATION / ER membrane targeting ribosome Signal recognition particle
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / granulocyte differentiation / negative regulation of translational elongation / signal-recognition-particle GTPase / protein targeting to ER ...SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / granulocyte differentiation / negative regulation of translational elongation / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane / TPR domain binding / ribonucleoprotein complex binding / cytoplasmic microtubule / neutrophil chemotaxis / GDP binding / ribosome binding / nuclear speck / GTPase activity / GTP binding / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / ATP hydrolysis activity / nucleoplasm / nucleus / cytosol
Similarity search - Function
Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle receptor, beta subunit / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Signal recognition particle receptor beta subunit / Putative TPR-like repeat / Signal recognition particle, SRP9 subunit ...Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle receptor, beta subunit / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Signal recognition particle receptor beta subunit / 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 / Longin-like domain superfamily / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / Signal recognition particle receptor subunit beta / SRP receptor subunit alpha / Signal recognition particle 19 kDa protein ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / Signal recognition particle receptor subunit beta / SRP receptor subunit alpha / Signal recognition particle 19 kDa protein / Signal recognition particle 14 kDa protein / Signal recognition particle 9 kDa protein / Signal recognition particle subunit SRP72 / Signal recognition particle subunit SRP54 / Signal recognition particle subunit SRP68
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Oryctolagus cuniculus (rabbit)
Canis lupus familiaris (dog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKobayashi, K. / Jomaa, A. / Ban, N.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation51NF40_141735 Switzerland
Swiss National Science Foundation310030B_163478 Switzerland
CitationJournal: Science / Year: 2018
Title: Structure of a prehandover mammalian ribosomal SRP·SRP receptor targeting complex.
Authors: Kan Kobayashi / Ahmad Jomaa / Jae Ho Lee / Sowmya Chandrasekar / Daniel Boehringer / Shu-Ou Shan / Nenad Ban /
Abstract: 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 ...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.
History
DepositionFeb 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

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Assembly

Deposited unit
1: Canis lupus familiaris RNA, 7SL, cytoplasmic 1 (RN7SL1), SRP RNA
2: tRNA
3: Ribosomal protein eL28
4: Ribosomal protein L12
5: 28S ribosomal RNA
6: 60S acidic ribosomal protein P0
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
A: Ribosomal protein L8
B: Ribosomal protein uL3
C: Ribosomal protein uL4
D: Ribosomal protein uL18
E: Ribosomal protein eL6
F: Ribosomal protein uL30
G: Ribosomal protein eL8
H: Ribosomal protein uL6
I: Ribosomal protein uL16
J: Ribosomal protein uL5
L: Ribosomal protein eL13
M: Ribosomal protein eL14
N: Ribosomal protein L15
O: Ribosomal protein uL13
P: Ribosomal protein uL22
Q: Ribosomal protein eL18
R: Ribosomal protein eL19
S: Ribosomal protein eL20
T: Ribosomal protein eL21
U: Ribosomal protein eL22
V: Ribosomal protein L23
W: Ribosomal protein eL24
X: Ribosomal protein uL23
Y: Ribosomal protein uL24
Z: 60S ribosomal protein L27
a: Ribosomal protein uL15
b: 60S ribosomal protein L29
c: Ribosomal protein eL30
d: Ribosomal protein eL31
e: Ribosomal protein eL32
f: Ribosomal protein eL33
g: Ribosomal protein eL34
h: Ribosomal protein uL29
i: Ribosomal protein eL36
j: Ribosomal protein L37
k: Ribosomal protein eL38
l: Ribosomal protein eL39
m: Ribosomal protein eL40
n: Ribosomal protein eL41
o: Ribosomal protein eL42
p: Ribosomal protein eL43
q: Signal recognition particle subunit SRP19
r: Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72
t: Signal sequence
u: Signal recognition particle subunit SRP68
v: SRP receptor beta subunit
w: Signal recognition particle 9 kDa protein
x: Signal recognition particle 54 kDa protein
y: SRP receptor alpha subunit
z: Signal recognition particle 14 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,504,828197
Polymers2,499,83158
Non-polymers4,996139
Water0
1


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

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Components

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RNA chain , 5 types, 5 molecules 12578

#1: RNA chain Canis lupus familiaris RNA, 7SL, cytoplasmic 1 (RN7SL1), SRP RNA


Mass: 96826.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: REF: 577019609
#2: RNA chain tRNA / Transfer RNA


Mass: 24437.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#5: RNA chain 28S ribosomal RNA /


Mass: 1185357.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#7: 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)
#8: 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)

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Ribosomal protein ... , 41 types, 41 molecules 34ABCDEFGHIJLMNOPQRSTUVWXYacde...

#3: Protein Ribosomal protein eL28 /


Mass: 14301.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#4: Protein Ribosomal protein L12 /


Mass: 17689.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#9: Protein Ribosomal protein L8 /


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


Mass: 44759.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#11: Protein Ribosomal protein uL4 /


Mass: 41635.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#12: Protein Ribosomal protein uL18 /


Mass: 33942.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#13: Protein Ribosomal protein eL6 /


Mass: 27052.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#14: Protein Ribosomal protein uL30 /


Mass: 26590.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#15: Protein Ribosomal protein eL8 /


Mass: 27258.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#16: Protein Ribosomal protein uL6 /


Mass: 21655.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#17: Protein Ribosomal protein uL16 /


Mass: 24465.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#18: Protein Ribosomal protein uL5 /


Mass: 19359.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#19: Protein Ribosomal protein eL13 /


Mass: 24234.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#20: Protein Ribosomal protein eL14 /


Mass: 16129.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#21: Protein Ribosomal protein L15 /


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#22: Protein Ribosomal protein uL13 /


Mass: 23435.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#23: Protein Ribosomal protein uL22 /


Mass: 17757.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#24: Protein Ribosomal protein eL18 /


Mass: 21457.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#25: Protein Ribosomal protein eL19 /


Mass: 21613.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#26: Protein Ribosomal protein eL20 /


Mass: 20696.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein Ribosomal protein eL21 /


Mass: 18478.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#28: Protein Ribosomal protein eL22 /


Mass: 11481.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#29: Protein Ribosomal protein L23 /


Mass: 13972.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#30: Protein Ribosomal protein eL24 /


Mass: 7512.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#31: Protein Ribosomal protein uL23 /


Mass: 13856.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#32: Protein Ribosomal protein uL24 /


Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#34: Protein Ribosomal protein uL15 /


Mass: 16503.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#36: Protein Ribosomal protein eL30 /


Mass: 10496.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#37: Protein Ribosomal protein eL31 /


Mass: 12635.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#38: Protein Ribosomal protein eL32 /


Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#39: Protein Ribosomal protein eL33 /


Mass: 12433.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#40: Protein Ribosomal protein eL34 /


Mass: 12994.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#41: Protein Ribosomal protein uL29 /


Mass: 14460.454 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#42: Protein Ribosomal protein eL36 /


Mass: 11915.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: Protein Ribosomal protein L37 /


Mass: 10102.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: Protein Ribosomal protein eL38 /


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


Mass: 6295.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#46: Protein Ribosomal protein eL40 /


Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#47: Protein/peptide Ribosomal protein eL41 /


Mass: 3213.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#48: Protein Ribosomal protein eL42 /


Mass: 12198.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#49: Protein Ribosomal protein eL43 /


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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60S ribosomal protein ... , 2 types, 2 molecules Zb

#33: Protein 60S ribosomal protein L27 /


Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#35: Protein 60S ribosomal protein L29 /


Mass: 8722.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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

#50: Protein Signal recognition particle subunit SRP19 /


Mass: 12159.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: J9PAS6
#51: Protein Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72,Signal recognition particle subunit SRP72 / / SRP72 / Signal recognition particle 72 kDa protein


Mass: 67314.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P33731
#53: Protein Signal recognition particle subunit SRP68 / / SRP68 / Signal recognition particle 68 kDa protein


Mass: 65569.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: Q00004
#55: Protein Signal recognition particle 9 kDa protein / SRP9


Mass: 8694.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P21262
#56: 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
#58: 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

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SRP receptor ... , 2 types, 2 molecules vy

#54: Protein SRP receptor beta subunit


Mass: 23588.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: SRPRB / Production host: Escherichia coli (E. coli) / References: UniProt: G1STG2
#57: Protein SRP receptor alpha subunit


Mass: 72232.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: SRPRA / Production host: Escherichia coli (E. coli) / References: UniProt: G1TCX6

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Protein / Protein/peptide , 2 types, 2 molecules 6t

#52: Protein/peptide Signal sequence /


Mass: 1262.751 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Oryctolagus cuniculus (rabbit)
#6: Protein 60S acidic ribosomal protein P0 /


Mass: 22217.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Non-polymers , 4 types, 139 molecules

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


Mass: 24.305 Da / Num. of mol.: 133 / Source method: obtained synthetically / Formula: Mg
#60: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#61: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#62: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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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
1Translating ribosome bound to SRP and SRP receptorCOMPLEX#1-#580MULTIPLE SOURCES
2RibosomeRIBOSOME#2-#49, #521NATURAL
3SRPCOMPLEX#1, #50-#51, #53, #55-#56, #581NATURAL
4SRP receptorSignal recognition particle receptorCOMPLEX#54, #571RECOMBINANT
5Signal sequenceCOMPLEX#521RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Oryctolagus cuniculus (rabbit)9986
23Canis lupus familiaris (dog)9615
34Oryctolagus cuniculus (rabbit)9986
45Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
14Escherichia coli (E. coli)562
25Oryctolagus cuniculus (rabbit)9986
Buffer solutionpH: 7.6
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: 100 % / Chamber temperature: 277 K

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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 FIELDBright-field microscopy / Nominal magnification: 59000 X / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1EMAN1.9particle selection
7UCSF Chimeramodel fitting
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45800 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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