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- PDB-7tut: Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin... -

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Basic information

Entry
Database: PDB / ID: 7tut
TitleStructure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate in complex with the multipass translocon
Components
  • (Protein transport protein Sec61 subunit ...Protein targeting) x 2
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Calcium load-activated calcium channel
  • Coiled-coil domain containing 47
  • Nascent chain
  • Nicalin
  • Obligate partner of TMCO1 insertase
  • P-site tRNA
  • PAT complex subunit Asterix
  • Protein transport protein Sec61 gammaProtein targeting
  • Transmembrane protein 147Transmembrane protein
  • eL13
  • eL14
  • eL15List of Subaru engines
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL23
  • eL24
  • eL27
  • eL28
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL35
  • eL36
  • eL37
  • eL38
  • eL39
  • eL40
  • eL41
  • eL42
  • eL43
  • eL6
  • eL8
  • uL13
  • uL14
  • uL15
  • uL16
  • uL18
  • uL2
  • uL22
  • uL24
  • uL3
  • uL30
  • uL4
  • uL5
  • uL6
KeywordsRIBOSOME / Membrane protein / translocon
Function / homology
Function and homology information


: / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / endoplasmic reticulum Sec complex / pronephric nephron development / rough endoplasmic reticulum membrane / cotranslational protein targeting to membrane / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane ...: / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / endoplasmic reticulum Sec complex / pronephric nephron development / rough endoplasmic reticulum membrane / cotranslational protein targeting to membrane / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / post-translational protein targeting to membrane, translocation / endoplasmic reticulum calcium ion homeostasis / protein folding chaperone complex / ER overload response / protein transmembrane transporter activity / regulation of signal transduction / : / protein folding chaperone / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / post-embryonic development / ribosome binding / 5S rRNA binding / cytosolic large ribosomal subunit / membrane => GO:0016020 / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / calcium ion binding / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / protein-containing complex / RNA binding / nucleoplasm / membrane / plasma membrane / cytoplasm
Similarity search - Function
PAT complex subunit Asterix / PAT complex subunit Asterix / PAT complex subunit CCDC47 / Nicalin / Transmembrane protein 147 / PAT complex subunit CCDC47 / Predicted membrane protein (DUF2053) / Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family ...PAT complex subunit Asterix / PAT complex subunit Asterix / PAT complex subunit CCDC47 / Nicalin / Transmembrane protein 147 / PAT complex subunit CCDC47 / Predicted membrane protein (DUF2053) / Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secY signature 1. / Protein secY signature 2. / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / Peptidase M28 / Peptidase family M28 / Ribosomal protein L19, eukaryotic / Ribosomal L40e family / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L27e signature. / Ribosomal protein L10e signature. / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein L6e signature. / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / 60S ribosomal protein L19 / Ribosomal protein L36e signature. / Ribosomal protein L39e signature. / Ribosomal protein L35Ae signature. / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal L39 protein / Ribosomal protein L31e signature. / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L32e signature. / Ribosomal protein L6 signature 2. / Ribosomal protein L1e signature. / Ribosomal protein L15e signature. / Ribosomal protein L21e signature. / Ribosomal protein L37e signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ribosomal protein L23 signature. / Ubiquitin family / Ribosomal protein L5 signature. / Ribosomal protein L29 signature. / Ubiquitin homologues / Ribosomal protein L15 signature. / Ubiquitin-like domain / Ribosomal protein L14 signature. / Ribosomal protein L22 signature. / Ubiquitin domain profile. / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L30p/L7e / Ribosomal protein L24 signature. / Ribosomal protein L3 signature. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eL40 fusion protein / Coiled-coil domain containing 47 / Transmembrane protein 147 / Nicalin ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eL40 fusion protein / Coiled-coil domain containing 47 / Transmembrane protein 147 / Nicalin / PAT complex subunit Asterix / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL30 / Ribosomal protein L19 / Large ribosomal subunit protein uL3 / Uncharacterized protein / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL34 / Protein transport protein Sec61 subunit alpha isoform 1 / Protein transport protein Sec61 subunit beta / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Canis lupus (gray wolf)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsKim, M.K. / Lewis, A.J.O. / Keenan, R.J. / Hegde, R.S.
Funding support United States, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A022_1007 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM130051 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM086487 United States
CitationJournal: Nature / Year: 2022
Title: Mechanism of an intramembrane chaperone for multipass membrane proteins.
Authors: Luka Smalinskaitė / Min Kyung Kim / Aaron J O Lewis / Robert J Keenan / Ramanujan S Hegde /
Abstract: Multipass membrane proteins play numerous roles in biology and include receptors, transporters, ion channels and enzymes. How multipass proteins are co-translationally inserted and folded at the ...Multipass membrane proteins play numerous roles in biology and include receptors, transporters, ion channels and enzymes. How multipass proteins are co-translationally inserted and folded at the endoplasmic reticulum is not well understood. The prevailing model posits that each transmembrane domain (TMD) of a multipass protein successively passes into the lipid bilayer through a front-side lateral gate of the Sec61 protein translocation channel. The PAT complex, an intramembrane chaperone comprising Asterix and CCDC47, engages early TMDs of multipass proteins to promote their biogenesis by an unknown mechanism. Here, biochemical and structural analysis of intermediates during multipass protein biogenesis showed that the nascent chain is not engaged with Sec61, which is occluded and latched closed by CCDC47. Instead, Asterix binds to and redirects the substrate to a location behind Sec61, where the PAT complex contributes to a multipass translocon surrounding a semi-enclosed, lipid-filled cavity. Detection of multiple TMDs in this cavity after their emergence from the ribosome suggests that multipass proteins insert and fold behind Sec61. Accordingly, biogenesis of several multipass proteins was unimpeded by inhibitors of the Sec61 lateral gate. These findings elucidate the mechanism of an intramembrane chaperone and suggest a new framework for multipass membrane protein biogenesis at the endoplasmic reticulum.
History
DepositionFeb 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 16, 2022Group: Data collection / Database references / Structure summary
Category: citation / em_software / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uL2
C: uL4
D: uL18
E: eL6
F: uL30
G: eL8
H: uL6
I: uL16
J: uL5
L: eL13
M: eL14
N: eL15
O: uL13
P: uL22
Q: eL18
R: eL19
S: eL20
T: eL21
U: eL22
V: uL14
W: eL24
X: eL23
Y: uL24
Z: eL27
a: uL15
b: eL29
c: eL30
d: eL31
e: eL32
f: eL33
g: eL34
h: eL35
i: eL36
j: eL37
k: eL38
l: eL39
m: eL40
n: eL41
o: eL42
p: eL43
q: P-site tRNA
r: eL28
u: 5S ribosomal RNA
v: 5.8S ribosomal RNA
w: uL3
B: Nascent chain
1: Protein transport protein Sec61 subunit alpha isoform 1
2: Protein transport protein Sec61 subunit beta
3: Protein transport protein Sec61 gamma
4: Coiled-coil domain containing 47
5: PAT complex subunit Asterix
7: Nicalin
6: Transmembrane protein 147
8: Calcium load-activated calcium channel
K: 28S ribosomal RNA
9: Obligate partner of TMCO1 insertase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,395,950281
Polymers2,390,27556
Non-polymers5,674225
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, immunoprecipitation, cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 49 types, 49 molecules ACDEFGHIJLMNOPQRSTUVWXYZabcdef...

#1: Protein uL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#2: Protein uL4


Mass: 46388.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#3: Protein uL18


Mass: 34481.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#4: Protein eL6


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#5: Protein uL30


Mass: 29201.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB1
#6: Protein eL8


Mass: 36221.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0
#7: Protein uL6


Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6
#8: Protein uL16


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#9: Protein uL5


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#10: Protein eL13


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV0
#11: Protein eL14


Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#12: Protein eL15 / List of Subaru engines


Mass: 24193.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#13: Protein uL13


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#14: Protein uL22


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TVT6
#15: Protein eL18


Mass: 21653.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#16: Protein eL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJR3
#17: Protein eL20


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#18: Protein eL21 /


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#19: Protein eL22


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TSG1
#20: Protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#21: Protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#22: Protein eL23


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#23: Protein uL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#24: Protein eL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#25: Protein uL15


Mass: 16620.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#26: Protein eL29


Mass: 24931.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#27: Protein eL30


Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#28: Protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#29: Protein eL32 / CD59


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#30: Protein eL33


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#31: Protein eL34 /


Mass: 13196.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U945
#32: Protein eL35


Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#33: Protein eL36


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#34: Protein eL37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#35: Protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U001
#36: Protein eL39


Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#37: Protein eL40 / Ubiquitin-60S ribosomal protein L40


Mass: 11699.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2K5PSA0
#39: Protein eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U344
#40: Protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#42: Protein eL28


Mass: 15783.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#45: Protein uL3


Mass: 46107.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#46: Protein Nascent chain


Mass: 28622.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#49: Protein Protein transport protein Sec61 gamma / Protein targeting


Mass: 7752.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus (gray wolf)
#50: Protein Coiled-coil domain containing 47


Mass: 55803.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus (gray wolf) / References: UniProt: A0A8C0RJF2
#51: Protein PAT complex subunit Asterix


Mass: 12077.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus (gray wolf) / References: UniProt: A0A8C0TSD6
#52: Protein Nicalin


Mass: 63172.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus (gray wolf) / References: UniProt: A0A8C0S144
#53: Protein Transmembrane protein 147 / Transmembrane protein


Mass: 25309.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus (gray wolf) / References: UniProt: A0A8C0RUW0
#54: Protein Calcium load-activated calcium channel


Mass: 21205.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus (gray wolf)
#56: Protein Obligate partner of TMCO1 insertase


Mass: 14822.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus (gray wolf)

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Protein/peptide , 1 types, 1 molecules n

#38: Protein/peptide eL41 / 60s ribosomal protein l41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4

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RNA chain , 4 types, 4 molecules quvK

#41: RNA chain P-site tRNA


Mass: 24632.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: RNA chain 5S ribosomal RNA /


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: X06789.1
#44: 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)
#55: RNA chain 28S ribosomal RNA /


Mass: 1148115.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Protein transport protein Sec61 subunit ... , 2 types, 2 molecules 12

#47: Protein Protein transport protein Sec61 subunit alpha isoform 1 / Protein targeting / Sec61 alpha-1


Mass: 52279.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus (gray wolf) / References: UniProt: P38377
#48: Protein Protein transport protein Sec61 subunit beta / Protein targeting


Mass: 9987.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus (gray wolf) / References: UniProt: P60467

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Non-polymers , 2 types, 225 molecules

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


Mass: 24.305 Da / Num. of mol.: 220 / Source method: obtained synthetically / Formula: Mg
#58: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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: 80S ribosome translating a stalled, four-TMD nascent chain (derived from rhodopsin), and bound to components of the multi-pass translocon
Type: RIBOSOME / Details: Sample prepared by in vitro translation / Entity ID: #1-#56 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Buffer solutionpH: 7.5
Details: 50 mM HEPES-KOH, pH 7.5, 200 mM potassium acetate, 5 mM magnesium acetate, 0.25% digitonin, 50 mM biotin
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Blot for 4 seconds with Whatman filter papers at a blot force of -15 before plunging.

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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 defocus max: 2700 nm / Nominal defocus min: 1900 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13755

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
7UCSF ChimeraX1.3model fitting
8Coot0.95model fitting
10PHENIX1.19.2-4158model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136812 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 276.11 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025163576
ELECTRON MICROSCOPYf_angle_d0.6585239707
ELECTRON MICROSCOPYf_chiral_restr0.041229684
ELECTRON MICROSCOPYf_plane_restr0.007815790
ELECTRON MICROSCOPYf_dihedral_angle_d16.618674100

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