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- PDB-3jan: Structure of the scanning state of the mammalian SRP-ribosome complex -

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Basic information

Entry
Database: PDB / ID: 3jan
TitleStructure of the scanning state of the mammalian SRP-ribosome complex
Components
  • (Ribosomal protein ...) x 77
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • SRP 7S RNA
  • SRP14
  • SRP19
  • SRP54
  • SRP68
  • SRP9Signal recognition particle 9
  • Val tRNA
KeywordsRIBOSOME / mammalian / SRP / translocation / translation
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsVoorhees, R.M. / Hegde, R.S.
CitationJournal: Elife / Year: 2015
Title: Structures of the scanning and engaged states of the mammalian SRP-ribosome complex.
Authors: Rebecca M Voorhees / Ramanujan S Hegde /
Abstract: The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially ...The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially engaging those with hydrophobic targeting signals, and delivers these ribosome-nascent chain complexes to the membrane. Here, we present structures of native mammalian SRP-ribosome complexes in the scanning and engaged states. These structures reveal the near-identical SRP architecture of these two states, show many of the SRP-ribosome interactions at atomic resolution, and suggest how the polypeptide-binding M domain selectively engages hydrophobic signals. The scanning M domain, pre-positioned at the ribosomal exit tunnel, is auto-inhibited by a C-terminal amphipathic helix occluding its hydrophobic binding groove. Upon engagement, the hydrophobic targeting signal displaces this amphipathic helix, which then acts as a protective lid over the signal. Biochemical experiments suggest how scanning and engagement are coordinated with translation elongation to minimize exposure of hydrophobic signals during membrane targeting.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references

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Structure visualization

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Assembly

Deposited unit
A: Ribosomal protein uL2
D: Ribosomal protein uL18
G: Ribosomal protein eL8
H: Ribosomal protein uL6
J: Ribosomal protein uL5
L: Ribosomal protein eL13
M: Ribosomal protein eL14
N: Ribosomal protein eL15
O: Ribosomal protein uL13
Q: Ribosomal protein eL18
R: Ribosomal protein eL19
S: Ribosomal protein eL20
T: Ribosomal protein eL21
U: Ribosomal protein eL22
V: Ribosomal protein uL14
X: Ribosomal protein uL23
Y: Ribosomal protein uL24
Z: Ribosomal protein eL27
a: Ribosomal protein uL15
b: Ribosomal protein eL29
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
k: Ribosomal protein eL38
l: Ribosomal protein eL39
m: Ribosomal protein eL40
o: Ribosomal protein eL42
5: 28S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
B: Ribosomal protein uL3
C: Ribosomal protein uL4
E: Ribosomal protein eL6
F: Ribosomal protein uL30
I: Ribosomal protein uL16
P: Ribosomal protein uL22
W: Ribosomal protein eL24
j: Ribosomal protein eL37
n: Ribosomal protein eL41
p: Ribosomal protein eL43
r: Ribosomal protein eL28
K: Ribosomal protein uL11
q: Ribosomal protein uL10
z: SRP54
3: Val tRNA
4: SRP 7S RNA
9: SRP19
6: SRP68
S2: 18S ribosomal RNA
SA: Ribosomal protein uS2
SB: Ribosomal protein eS1
SC: Ribosomal protein uS5
SE: Ribosomal protein eS4
SG: Ribosomal protein eS6
SH: Ribosomal protein eS7
SI: Ribosomal protein eS8
SJ: Ribosomal protein uS4
SL: Ribosomal protein uS17
SN: Ribosomal protein uS15
SO: Ribosomal protein uS11
SV: Ribosomal protein eS21
SW: Ribosomal protein uS8
SX: Ribosomal protein uS12
SY: Ribosomal protein eS24
Sa: Ribosomal protein eS26
Sb: Ribosomal protein eS27
Se: Ribosomal protein eS30
SD: Ribosomal protein uS3
SF: Ribosomal protein uS7
SK: Ribosomal protein eS10
SM: Ribosomal protein eS12
SP: Ribosomal protein uS19
SQ: Ribosomal protein uS9
SR: Ribosomal protein eS17
SS: Ribosomal protein uS13
ST: Ribosomal protein eS19
SU: Ribosomal protein uS10
SZ: Ribosomal protein es25
Sc: Ribosomal protein eS28
Sd: Ribosomal protein uS14
Sf: Ribosomal protein eS31
Sg: Ribosomal protein RACK1
S1: SRP9
S4: SRP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,364,373258
Polymers3,360,07788
Non-polymers4,296170
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Ribosomal protein ... , 77 types, 77 molecules ADGHJLMNOQRSTUVXYZabcdefghiklm...

#1: Protein Ribosomal protein uL2 /


Mass: 26570.105 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#2: Protein Ribosomal protein uL18 /


Mass: 33942.223 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#3: Protein Ribosomal protein eL8 /


Mass: 27258.246 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#4: Protein Ribosomal protein uL6 /


Mass: 21655.268 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#5: Protein Ribosomal protein uL5 /


Mass: 19359.393 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#6: Protein Ribosomal protein eL13 /


Mass: 24234.566 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#7: Protein Ribosomal protein eL14 /


Mass: 16129.309 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#8: Protein Ribosomal protein eL15 /


Mass: 24076.088 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#9: Protein Ribosomal protein uL13 /


Mass: 23435.090 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#10: Protein Ribosomal protein eL18 /


Mass: 21457.391 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#11: Protein Ribosomal protein eL19 /


Mass: 21613.033 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#12: Protein Ribosomal protein eL20 /


Mass: 20696.363 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#13: Protein Ribosomal protein eL21 /


Mass: 18478.791 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#14: Protein Ribosomal protein eL22 /


Mass: 11481.249 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#15: Protein Ribosomal protein uL14 /


Mass: 13972.425 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#16: Protein Ribosomal protein uL23 /


Mass: 13856.360 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#17: Protein Ribosomal protein uL24 /


Mass: 15891.787 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#18: Protein Ribosomal protein eL27 /


Mass: 15704.635 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#19: Protein Ribosomal protein uL15 /


Mass: 16503.391 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#20: Protein Ribosomal protein eL29 /


Mass: 8722.283 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#21: Protein Ribosomal protein eL30 /


Mass: 10496.355 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#22: Protein Ribosomal protein eL31 /


Mass: 12635.694 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#23: Protein Ribosomal protein eL32 /


Mass: 15022.021 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#24: Protein Ribosomal protein eL33 /


Mass: 12433.548 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#25: Protein Ribosomal protein eL34 /


Mass: 12994.621 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#26: Protein Ribosomal protein uL29 /


Mass: 14460.454 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein Ribosomal protein eL36 /


Mass: 11915.396 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#28: Protein Ribosomal protein eL38 /


Mass: 8107.752 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#29: Protein/peptide Ribosomal protein eL39 /


Mass: 6295.562 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#30: Protein Ribosomal protein eL40 /


Mass: 6199.574 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#31: Protein Ribosomal protein eL42 /


Mass: 12198.603 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#35: Protein Ribosomal protein uL3 /


Mass: 44759.359 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#36: Protein Ribosomal protein uL4 /


Mass: 41635.141 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#37: Protein Ribosomal protein eL6 /


Mass: 27052.178 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#38: Protein Ribosomal protein uL30 /


Mass: 26590.725 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#39: Protein Ribosomal protein uL16 /


Mass: 24465.791 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#40: Protein Ribosomal protein uL22 /


Mass: 17757.627 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#41: Protein Ribosomal protein eL24 /


Mass: 7512.774 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#42: Protein Ribosomal protein eL37 /


Mass: 10102.944 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: Protein/peptide Ribosomal protein eL41 /


Mass: 3213.075 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: Protein Ribosomal protein eL43 /


Mass: 10168.153 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#45: Protein Ribosomal protein eL28 /


Mass: 14301.777 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#46: Protein Ribosomal protein uL11 /


Mass: 17689.461 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#47: Protein Ribosomal protein uL10 /


Mass: 22217.840 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#54: Protein Ribosomal protein uS2 /


Mass: 23360.791 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#55: Protein Ribosomal protein eS1 /


Mass: 24688.990 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#56: Protein Ribosomal protein uS5 /


Mass: 24091.453 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#57: Protein Ribosomal protein eS4 /


Mass: 29523.674 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#58: Protein Ribosomal protein eS6 /


Mass: 27471.535 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#59: Protein Ribosomal protein eS7 /


Mass: 21603.229 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#60: Protein Ribosomal protein eS8 /


Mass: 24003.012 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#61: Protein Ribosomal protein uS4 /


Mass: 21649.633 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#62: Protein Ribosomal protein uS17 /


Mass: 17657.842 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#63: Protein Ribosomal protein uS15 /


Mass: 17057.113 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#64: Protein Ribosomal protein uS11 /


Mass: 14544.659 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#65: Protein Ribosomal protein eS21 /


Mass: 8977.214 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#66: Protein Ribosomal protein uS8 /


Mass: 14734.357 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#67: Protein Ribosomal protein uS12 /


Mass: 15636.409 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#68: Protein Ribosomal protein eS24 /


Mass: 14604.264 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#69: Protein Ribosomal protein eS26 /


Mass: 11184.231 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#70: Protein Ribosomal protein eS27 /


Mass: 9348.990 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#71: Protein Ribosomal protein eS30 /


Mass: 6440.627 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#72: Protein Ribosomal protein uS3 /


Mass: 25172.561 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#73: Protein Ribosomal protein uS7 /


Mass: 21525.941 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#74: Protein Ribosomal protein eS10 /


Mass: 11773.953 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#75: Protein Ribosomal protein eS12 /


Mass: 13776.030 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#76: Protein Ribosomal protein uS19 /


Mass: 11541.736 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#77: Protein Ribosomal protein uS9 /


Mass: 15975.753 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#78: Protein Ribosomal protein eS17 /


Mass: 14969.445 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#79: Protein Ribosomal protein uS13 /


Mass: 16170.774 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#80: Protein Ribosomal protein eS19 /


Mass: 15668.050 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#81: Protein Ribosomal protein uS10 /


Mass: 11724.857 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#82: Protein Ribosomal protein es25 /


Mass: 8526.119 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#83: Protein Ribosomal protein eS28 /


Mass: 7263.394 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#84: Protein Ribosomal protein uS14 /


Mass: 6199.237 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#85: Protein Ribosomal protein eS31 /


Mass: 8358.903 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#86: Protein Ribosomal protein RACK1 /


Mass: 34669.113 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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RNA chain , 6 types, 6 molecules 57834S2

#32: RNA chain 28S ribosomal RNA /


Mass: 1185357.625 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#33: RNA chain 5S ribosomal RNA /


Mass: 38691.914 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#34: RNA chain 5.8S ribosomal RNA /


Mass: 50143.648 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#49: RNA chain Val tRNA


Mass: 24437.535 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: RNA chain SRP 7S RNA


Mass: 66779.680 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#53: RNA chain 18S ribosomal RNA /


Mass: 561958.812 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Protein , 5 types, 5 molecules z96S1S4

#48: Protein SRP54


Mass: 46695.121 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#51: Protein SRP19


Mass: 12159.153 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#52: Protein SRP68


Mass: 21324.430 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#87: Protein SRP9 / Signal recognition particle 9


Mass: 8705.137 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#88: Protein SRP14


Mass: 8665.137 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Non-polymers , 2 types, 170 molecules

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


Mass: 24.305 Da / Num. of mol.: 166 / Source method: obtained synthetically / Formula: Mg
#90: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Sequence detailsPROTEIN AND RNA IN THIS ENTRY ARE FROM ORYCTOLAGUS CUNICULUS, BUT THE MODELED SEQUENCES ARE FROM SUS SCROFA.

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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
IDNameTypeParent-IDSynonym
1Scanning ribosome SRP complexRIBOSOME0
280S ribosomeEukaryotic ribosomeRIBOSOME1mammalian ribosome
3Signal recognition particle1SRP
Buffer solutionName: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT
pH: 7.5
Details: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow-discharged holey carbon grids (Quantifoil R2/2) coated with a ~70-Angstrom-thick layer of amorphous carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Details: 3 uL of sample was incubated on the grid for 30 seconds at 277 K, blotted for 3 seconds, then flash-frozen in liquid ethane (FEI VITROBOT MARK IV).
Method: 3 uL of sample was incubated on the grid for 30 seconds at 277 K before blotting for 3 seconds

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Nov 14, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0124 / Classification: refinement
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Single particleSingle particle analysis / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27627 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å / Details: gold-standard / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--rigid body
Atomic model buildingPDB-ID: 3JAJ

3jaj

RefinementDetails: Hydrogens have been added in their riding positions
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms100449 127216 170 0 227835

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