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- PDB-3jaj: Structure of the engaged state of the mammalian SRP-ribosome complex -

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Basic information

Entry
Database: PDB / ID: 3jaj
TitleStructure of the engaged 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
  • Nascent chain
  • SRP 7S RNA
  • SRP14
  • SRP19
  • SRP54
  • SRP68
  • SRP9
  • 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 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Sep 7, 2022Group: Database references / Derived calculations / Refinement description
Category: database_2 / em_3d_fitting ...database_2 / em_3d_fitting / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting.overall_b_value / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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
2: Nascent chain
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)3,367,732259
Polymers3,363,43689
Non-polymers4,296170
Water00
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)
#55: 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)
#56: 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)
#57: 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)
#58: 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)
#59: 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)
#60: 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)
#61: 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)
#62: 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)
#63: 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)
#64: 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)
#65: 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)
#66: 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)
#67: 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)
#68: 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)
#69: 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)
#70: 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)
#71: 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)
#72: 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)
#73: 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)
#74: 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)
#75: 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)
#76: 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)
#77: 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)
#78: 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)
#79: 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)
#80: 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)
#81: 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)
#82: 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)
#83: 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)
#84: 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)
#85: 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)
#86: 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)
#87: 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)
#50: 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)
#51: 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)
#54: 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)
#52: 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)
#53: 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)
#88: Protein SRP9


Mass: 8705.137 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#89: 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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Protein/peptide , 1 types, 1 molecules 2

#49: Protein/peptide Nascent chain


Mass: 3359.454 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

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


Mass: 24.305 Da / Num. of mol.: 166 / Source method: obtained synthetically / Formula: Mg
#91: 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
1Engaged ribosome SRP complexRIBOSOME0
280S 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, 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 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: Jun 16, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 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
EM software
IDNameCategory
1Cootmodel fitting
2REFMACmodel fitting
3UCSF Chimeramodel fitting
4RELION3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Single particle / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52061 / 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 building
IDSpaceTarget criteriaProtocolDetails
1RECIPROCALR-factor
2REALRIGID BODY FITMETHOD--rigid body
Atomic model building
IDPDB-ID 3D fitting-ID
11WGW

1wgw

1
34P3E

4p3e

1
41.0E+801
51E8S

1e8s

1
73J7O

3j7o

1
83J7P

3j7p

1
21QB2

1qb2

2
RefinementDetails: Hydrogens have been added in their riding positions
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms100682 127216 170 0 228068

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