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- PDB-5aka: EM structure of ribosome-SRP-FtsY complex in closed state -

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Entry
Database: PDB / ID: 5aka
TitleEM structure of ribosome-SRP-FtsY complex in closed state
Components
  • (50S RIBOSOMAL PROTEIN ...) x 29
  • 23S ribosomal RNA
  • 4.5S ribosomal RNA
  • 5S ribosomal RNA
  • ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
  • SIGNAL RECOGNITION PARTICLE PROTEIN
KeywordsRIBOSOME / PROTEIN TARGETING / SIGNAL RECOGNITION PARTICLE / SIGNAL SEQUENCE
Function / homology
Function and homology information


signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / negative regulation of cytoplasmic translational initiation / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / negative regulation of cytoplasmic translational initiation / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / regulation of cell growth / translational initiation / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / GTPase activity / mRNA binding / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Signal recognition particle protein / 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 protein / 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 / Ribosomal protein L25, short-form / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / : / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L16 / : / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L21 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Signal recognition particle protein / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 Å
Authorsvon Loeffelholz, O. / Jiang, Q. / Ariosa, A. / Karuppasamy, M. / Huard, K. / Berger, I. / Shan, S. / Schaffitzel, C.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Ribosome-SRP-FtsY cotranslational targeting complex in the closed state.
Authors: Ottilie von Loeffelholz / Qiyang Jiang / Aileen Ariosa / Manikandan Karuppasamy / Karine Huard / Imre Berger / Shu-ou Shan / Christiane Schaffitzel /
Abstract: The signal recognition particle (SRP)-dependent pathway is essential for correct targeting of proteins to the membrane and subsequent insertion in the membrane or secretion. In Escherichia coli, the ...The signal recognition particle (SRP)-dependent pathway is essential for correct targeting of proteins to the membrane and subsequent insertion in the membrane or secretion. In Escherichia coli, the SRP and its receptor FtsY bind to ribosome-nascent chain complexes with signal sequences and undergo a series of distinct conformational changes, which ensures accurate timing and fidelity of protein targeting. Initial recruitment of the SRP receptor FtsY to the SRP-RNC complex results in GTP-independent binding of the SRP-FtsY GTPases at the SRP RNA tetraloop. In the presence of GTP, a closed state is adopted by the SRP-FtsY complex. The cryo-EM structure of the closed state reveals an ordered SRP RNA and SRP M domain with a signal sequence-bound. Van der Waals interactions between the finger loop and ribosomal protein L24 lead to a constricted signal sequence-binding pocket possibly preventing premature release of the signal sequence. Conserved M-domain residues contact ribosomal RNA helices 24 and 59. The SRP-FtsY GTPases are detached from the RNA tetraloop and flexible, thus liberating the ribosomal exit site for binding of the translocation machinery.
History
DepositionMar 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2May 6, 2015Group: Other
Revision 2.0Aug 2, 2017Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / em_image_scans / em_software / entity / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name / _entity.pdbx_description / _entity.src_method
Revision 2.1Dec 20, 2017Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.page_last / _citation_author.name
Revision 2.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
0: 50S RIBOSOMAL PROTEIN L32
1: 50S RIBOSOMAL PROTEIN L33
2: 50S RIBOSOMAL PROTEIN L34
3: 50S RIBOSOMAL PROTEIN L35
4: 50S RIBOSOMAL PROTEIN L36
5: SIGNAL RECOGNITION PARTICLE PROTEIN
6: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
7: 4.5S ribosomal RNA
A: 5S ribosomal RNA
B: 23S ribosomal RNA
C: 50S RIBOSOMAL PROTEIN L2
D: 50S RIBOSOMAL PROTEIN L3
E: 50S RIBOSOMAL PROTEIN L4
F: 50S RIBOSOMAL PROTEIN L5
G: 50S RIBOSOMAL PROTEIN L6
H: 50S RIBOSOMAL PROTEIN L9
I: 50S RIBOSOMAL PROTEIN L11
J: 50S RIBOSOMAL PROTEIN L13
K: 50S RIBOSOMAL PROTEIN L14
L: 50S RIBOSOMAL PROTEIN L15
M: 50S RIBOSOMAL PROTEIN L16
N: 50S RIBOSOMAL PROTEIN L17
O: 50S RIBOSOMAL PROTEIN L18
P: 50S RIBOSOMAL PROTEIN L19
Q: 50S RIBOSOMAL PROTEIN L20
R: 50S RIBOSOMAL PROTEIN L21
S: 50S RIBOSOMAL PROTEIN L22
T: 50S RIBOSOMAL PROTEIN L23
U: 50S RIBOSOMAL PROTEIN L24
V: 50S RIBOSOMAL PROTEIN L25
W: 50S RIBOSOMAL PROTEIN L27
X: 50S RIBOSOMAL PROTEIN L29
Y: 50S RIBOSOMAL PROTEIN L30
Z: 50S RIBOSOMAL PROTEIN L31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,394,622144
Polymers1,391,94834
Non-polymers2,674110
Water9,116506
1


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

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Components

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50S RIBOSOMAL PROTEIN ... , 29 types, 29 molecules 01234CDEFGHIJKLMNOPQRSTUVWXYZ

#1: Protein 50S RIBOSOMAL PROTEIN L32


Mass: 6332.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7N4
#2: Protein 50S RIBOSOMAL PROTEIN L33


Mass: 6257.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7N9
#3: Protein/peptide 50S RIBOSOMAL PROTEIN L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7P5
#4: Protein 50S RIBOSOMAL PROTEIN L35 / RIBOSOMAL PROTEIN A


Mass: 7181.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7Q1
#5: Protein/peptide 50S RIBOSOMAL PROTEIN L36 / RIBOSOMAL PROTEIN B


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7Q6
#11: Protein 50S RIBOSOMAL PROTEIN L2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P60422
#12: Protein 50S RIBOSOMAL PROTEIN L3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P60438
#13: Protein 50S RIBOSOMAL PROTEIN L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P60723
#14: Protein 50S RIBOSOMAL PROTEIN L5


Mass: 20202.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P62399
#15: Protein 50S RIBOSOMAL PROTEIN L6


Mass: 18801.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0AG55
#16: Protein 50S RIBOSOMAL PROTEIN L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7R1
#17: Protein 50S RIBOSOMAL PROTEIN L11


Mass: 14763.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7J7
#18: Protein 50S RIBOSOMAL PROTEIN L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0AA10
#19: Protein 50S RIBOSOMAL PROTEIN L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0ADY3
#20: Protein 50S RIBOSOMAL PROTEIN L15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P02413
#21: Protein 50S RIBOSOMAL PROTEIN L16


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0ADY7
#22: Protein 50S RIBOSOMAL PROTEIN L17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0AG44
#23: Protein 50S RIBOSOMAL PROTEIN L18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0C018
#24: Protein 50S RIBOSOMAL PROTEIN L19


Mass: 13028.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7K6
#25: Protein 50S RIBOSOMAL PROTEIN L20


Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7L3
#26: Protein 50S RIBOSOMAL PROTEIN L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0AG48
#27: Protein 50S RIBOSOMAL PROTEIN L22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P61175
#28: Protein 50S RIBOSOMAL PROTEIN L23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0ADZ0
#29: Protein 50S RIBOSOMAL PROTEIN L24


Mass: 11208.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P60624
#30: Protein 50S RIBOSOMAL PROTEIN L25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P68919
#31: Protein 50S RIBOSOMAL PROTEIN L27


Mass: 9015.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7L8
#32: Protein 50S RIBOSOMAL PROTEIN L29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7M6
#33: Protein 50S RIBOSOMAL PROTEIN L30


Mass: 6423.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0AG51
#34: Protein 50S RIBOSOMAL PROTEIN L31


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7M9

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RNA chain , 3 types, 3 molecules 7AB

#8: RNA chain 4.5S ribosomal RNA


Mass: 24029.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria)
#9: RNA chain 5S ribosomal RNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: GenBank: 731469900
#10: RNA chain 23S ribosomal RNA


Mass: 941612.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: GenBank: 731469900

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Protein / Protein/peptide , 2 types, 2 molecules 56

#6: Protein SIGNAL RECOGNITION PARTICLE PROTEIN / FIFTY-FOUR HOMOLOG / FFH / P48


Mass: 12358.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0AGD7
#7: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 586.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria)

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Non-polymers , 2 types, 616 molecules

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


Mass: 24.305 Da / Num. of mol.: 110 / Source method: obtained synthetically / Formula: Mg
#36: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

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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

ComponentName: E.COLI SRP-FTSY BINDS TO E.COLI RIBOSOME WITH LEP50 NASCENT CHAIN
Type: RIBOSOME
Buffer solutionName: 50MM HEPES-KOH, 100MM KOAC, 8MM MG(OAC)2, 500UG/ML CHLORAMPHENICO
pH: 7.5
Details: 50MM HEPES-KOH, 100MM KOAC, 8MM MG(OAC)2, 500UG/ML CHLORAMPHENICO
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHAN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jan 24, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 77769 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Image recordingElectron dose: 24 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1CNSmodel fitting
2Cootmodel fitting
3HHpredmodel fitting
4UCSF Chimeramodel fitting
5RELION3D reconstruction
6Xmipp33D reconstruction
CTF correctionDetails: PER MICROGRAPH
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 5.7 Å / Num. of particles: 32170 / Nominal pixel size: 2 Å / Actual pixel size: 2 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2917. (DEPOSITION ID: 13058).
Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementHighest resolution: 5.7 Å
Refinement stepCycle: LAST / Highest resolution: 5.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27028 65093 110 506 92737

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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