[English] 日本語
Yorodumi
- PDB-9n9j: Structure of a GRP94 folding intermediate engaged with a CCDC134-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9n9j
TitleStructure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon
Components
  • (60S ribosomal protein ...) x 8
  • (Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ...) x 7
  • (Large ribosomal subunit protein ...) x 33
  • (Protein transport protein Sec61 subunit ...) x 3
  • (Translocon-associated protein subunit ...) x 4
  • (tRNA) x 2
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Coiled-coil domain-containing protein 134
  • Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
  • Endoplasmin
  • Oligosaccharyltransferase complex subunit OSTC
  • Peptidyl-prolyl cis-trans isomerase FKBP11
  • Ribosomal protein uL16-like
  • Small ribosomal subunit protein eS32
  • Stress-associated endoplasmic reticulum protein 1
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / Membrane protein / Translocon / Transport / N-Glycosylation
Function / homology
Function and homology information


positive regulation of MyD88-dependent toll-like receptor signaling pathway / : / positive regulation of toll-like receptor signaling pathway / oligosaccharyltransferase complex binding / actin rod assembly / oligosaccharyltransferase complex A / oligosaccharyltransferase complex B / muscle organ morphogenesis / Asparagine N-linked glycosylation / embryonic liver development ...positive regulation of MyD88-dependent toll-like receptor signaling pathway / : / positive regulation of toll-like receptor signaling pathway / oligosaccharyltransferase complex binding / actin rod assembly / oligosaccharyltransferase complex A / oligosaccharyltransferase complex B / muscle organ morphogenesis / Asparagine N-linked glycosylation / embryonic liver development / ATF6 (ATF6-alpha) activates chaperone genes / endoplasmic reticulum Sec complex / pronephric nephron development / endoplasmic reticulum chaperone complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / sequestering of calcium ion / cotranslational protein targeting to membrane / plasma membrane organization / endoplasmic reticulum quality control compartment / Ssh1 translocon complex / protein folding in endoplasmic reticulum / positive regulation of growth hormone secretion / Sec61 translocon complex / sarcoplasmic reticulum lumen / protein targeting to ER / protein insertion into ER membrane / oligosaccharyltransferase complex / post-translational protein targeting to endoplasmic reticulum membrane / positive regulation of organ growth / ventricular system development / : / : / SRP-dependent cotranslational protein targeting to membrane, translocation / XBP1(S) activates chaperone genes / translation at presynapse / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane / exit from mitosis / optic nerve development / protein N-linked glycosylation / post-translational protein targeting to membrane, translocation / endoplasmic reticulum organization / response to insecticide / eukaryotic 80S initiation complex / negative regulation of protein neddylation / regulation of translation involved in cellular response to UV / axial mesoderm development / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / ribosomal protein import into nucleus / Trafficking and processing of endosomal TLR / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 90S preribosome assembly / epithelial cell apoptotic process / alpha-beta T cell differentiation / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / embryonic hemopoiesis / TORC2 complex binding / G1 to G0 transition / insulin secretion / Scavenging by Class A Receptors / epidermal growth factor binding / retrograde protein transport, ER to cytosol / middle ear morphogenesis / azurophil granule membrane / low-density lipoprotein particle receptor binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein phosphatase inhibitor activity / cytoplasmic side of rough endoplasmic reticulum membrane / : / sperm plasma membrane / negative regulation of ubiquitin protein ligase activity / homeostatic process / cellular response to ATP / macrophage chemotaxis / lung morphogenesis / smooth endoplasmic reticulum / positive regulation of natural killer cell proliferation / male meiosis I / Advanced glycosylation endproduct receptor signaling / Protein hydroxylation / Peptide chain elongation / Selenocysteine synthesis / regulation of ossification / Formation of a pool of free 40S subunits / cellular response to actinomycin D / protein transmembrane transporter activity / Eukaryotic Translation Termination / blastocyst development / negative regulation of ubiquitin-dependent protein catabolic process / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / Viral mRNA Translation / positive regulation of signal transduction by p53 class mediator / positive regulation of Wnt signaling pathway
Similarity search - Function
Keratinocyte-associated protein 2 / Coiled-coil domain-containing protein 134 / Keratinocyte-associated protein 2 / ERK and JNK pathways, inhibitor / Stress-associated endoplasmic reticulum protein / Ribosome associated membrane protein RAMP4 / : / Translocon-associated protein (TRAP), alpha subunit / Translocon-associated / Translocon-associated protein subunit beta ...Keratinocyte-associated protein 2 / Coiled-coil domain-containing protein 134 / Keratinocyte-associated protein 2 / ERK and JNK pathways, inhibitor / Stress-associated endoplasmic reticulum protein / Ribosome associated membrane protein RAMP4 / : / Translocon-associated protein (TRAP), alpha subunit / Translocon-associated / Translocon-associated protein subunit beta / Translocon-associated protein subunit gamma / : / : / : / Translocon-associated protein (TRAP), alpha subunit / Translocon-associated protein, delta subunit precursor (TRAP-delta) / Translocon-associated protein beta (TRAPB) / Translocon-associated protein, gamma subunit (TRAP-gamma) / Ribophorin II third domain / Ribophorin II second domain / Ribophorin II N-terminal domain / : / : / OST48 middle domain / : / Ribophorin_II, C-terminal domain / Peptidyl-prolyl cis-trans isomerase FKBP2/11 / DAD/Ost2 / Oligosaccharyltransferase complex subunit / DAD family / Oligosaccharyltransferase subunit 5 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48kDa subunit / Oligosaccharyltransferase complex subunit OSTC / OST48, N-terminal domain / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit Swp1 / Oligosaccaryltransferase / Oligosaccharyltransferase subunit ost4p superfamily / Oligosaccaryltransferase / : / AglB core domain / Ribophorin I / Ribophorin I / Oligosaccharyl transferase complex, subunit OST3/OST6 / OST3 / OST6 family, transporter family / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / Endoplasmic reticulum targeting sequence. / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / HSP90, C-terminal domain / Ribosomal L28e protein family / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / metallochaperone-like domain / TRASH domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e
Similarity search - Domain/homology
Chem-ELU / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 / Large ribosomal subunit protein uL10 ...Chem-ELU / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 / Large ribosomal subunit protein uL10 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 / Endoplasmin / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL29 / Translocon-associated protein subunit alpha / Translocon-associated protein subunit beta / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL14 / Translocon-associated protein subunit delta / Protein transport protein Sec61 subunit gamma / Protein transport protein Sec61 subunit beta / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Protein transport protein Sec61 subunit alpha isoform 1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2 / Ribosomal protein uL16-like / Coiled-coil domain-containing protein 134 / Oligosaccharyltransferase complex subunit OSTC / Peptidyl-prolyl cis-trans isomerase FKBP11 / Translocon-associated protein subunit gamma / Large ribosomal subunit protein eL36 / Stress-associated endoplasmic reticulum protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYamsek, M. / Jha, R. / Keenan, R.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM145374 United States
Citation
Journal: Nature / Year: 2025
Title: Structural basis of regulated N-glycosylation at the secretory translocon.
Authors: Melvin Yamsek / Mengxiao Ma / Roshan Jha / Yu Wan / Qianru Li / Frank Zhong / Katherine DeLong / Zhe Ji / Rajat Rohatgi / Robert J Keenan /
Abstract: Most human secretory pathway proteins are N-glycosylated by oligosaccharyltransferase (OST) complexes as they enter the endoplasmic reticulum (ER). Recent work revealed a substrate-assisted mechanism ...Most human secretory pathway proteins are N-glycosylated by oligosaccharyltransferase (OST) complexes as they enter the endoplasmic reticulum (ER). Recent work revealed a substrate-assisted mechanism by which N-glycosylation of the chaperone glucose-regulated protein 94 (GRP94) is regulated to control cell surface receptor signalling. Here we report the structure of a natively isolated GRP94 folding intermediate tethered to a specialized CCDC134-bound translocon. Together with functional analysis, the data reveal how a conserved N-terminal extension in GRP94 inhibits OST-A and how structural rearrangements within the translocon shield the tethered nascent chain from inappropriate OST-B glycosylation. These interactions depend on a hydrophobic CCDC134 groove, which recognizes a non-native conformation of nascent GRP94. Our results define a mechanism of regulated N-glycosylation and illustrate how the nascent chain remodels the translocon to facilitate its own biogenesis.
#1: Journal: Science / Year: 2024
Title: Regulated N-glycosylation controls chaperone function and receptor trafficking.
Authors: Mengxiao Ma / Ramin Dubey / Annie Jen / Ganesh V Pusapati / Bharti Singal / Evgenia Shishkova / Katherine A Overmyer / Valérie Cormier-Daire / Juliette Fedry / L Aravind / Joshua J Coon / Rajat Rohatgi /
Abstract: One-fifth of human proteins are N-glycosylated in the endoplasmic reticulum (ER) by two oligosaccharyltransferases, OST-A and OST-B. Contrary to the prevailing view of N-glycosylation as a ...One-fifth of human proteins are N-glycosylated in the endoplasmic reticulum (ER) by two oligosaccharyltransferases, OST-A and OST-B. Contrary to the prevailing view of N-glycosylation as a housekeeping function, we identified an ER pathway that modulates the activity of OST-A. Genetic analyses linked OST-A to HSP90B1, an ER chaperone for membrane receptors, and CCDC134, an ER luminal protein. During its translocation into the ER, an N-terminal peptide in HSP90B1 templates the assembly of a translocon complex containing CCDC134 and OST-A that protects HSP90B1 during folding, preventing its hyperglycosylation and degradation. Disruption of this pathway impairs WNT and IGF1R signaling and causes the bone developmental disorder osteogenesis imperfecta. Thus, N-glycosylation can be regulated by specificity factors in the ER to control cell surface receptor signaling and tissue development.
History
DepositionFeb 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Dec 10, 2025Group: Data collection / Database references / Category: em_admin / pdbx_database_related / Item: _em_admin.last_update
Revision 1.1Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / pdbx_database_related / Data content type: EM metadata / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
5: Translocon-associated protein subunit alpha
6: Translocon-associated protein subunit beta
7: Translocon-associated protein subunit gamma
8: Translocon-associated protein subunit delta
A: Peptidyl-prolyl cis-trans isomerase FKBP11
B: Coiled-coil domain-containing protein 134
D: Protein transport protein Sec61 subunit alpha isoform 1
E: Protein transport protein Sec61 subunit beta
F: Protein transport protein Sec61 subunit gamma
G: Stress-associated endoplasmic reticulum protein 1
I: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
J: Oligosaccharyltransferase complex subunit OSTC
K2: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4
L2: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258
L5: 28S ribosomal RNA
L7: 5S ribosomal RNA
L8: 5.8S ribosomal RNA
LA: 60S ribosomal protein L8
LB: 60S ribosomal protein L3
LC: Large ribosomal subunit protein uL4
LD: Large ribosomal subunit protein uL18
LE: Large ribosomal subunit protein eL6
LF: 60S ribosomal protein L7
LG: Large ribosomal subunit protein eL8
LH: Large ribosomal subunit protein uL6
LI: Ribosomal protein uL16-like
LL: Large ribosomal subunit protein eL13
LM: Large ribosomal subunit protein eL14
LN: Large ribosomal subunit protein eL15
LO: Large ribosomal subunit protein uL13
LP: Large ribosomal subunit protein uL22
LQ: Large ribosomal subunit protein eL18
LR: Large ribosomal subunit protein eL19
LS: Large ribosomal subunit protein eL20
LT: Large ribosomal subunit protein eL21
LU: Large ribosomal subunit protein eL22
LV: Large ribosomal subunit protein uL14
LW: Large ribosomal subunit protein eL24
LX: Large ribosomal subunit protein uL23
LY: Large ribosomal subunit protein uL24
LZ: Large ribosomal subunit protein eL27
La: 60S ribosomal protein L27a
Lb: 60S ribosomal protein L29
Lc: Large ribosomal subunit protein eL30
Ld: Large ribosomal subunit protein eL31
Le: Large ribosomal subunit protein eL32
Lf: Large ribosomal subunit protein eL33
Lg: Large ribosomal subunit protein eL34
Lh: Large ribosomal subunit protein uL29
Li: Large ribosomal subunit protein eL36
Lj: Large ribosomal subunit protein eL37
Lk: Large ribosomal subunit protein eL38
Ll: Large ribosomal subunit protein eL39
Lm: Ubiquitin-60S ribosomal protein L40
Ln: Small ribosomal subunit protein eS32
Lo: Large ribosomal subunit protein eL42
Lp: Large ribosomal subunit protein eL43
Lr: 60S ribosomal protein L28
Ls: 60S acidic ribosomal protein P0
Lt: 60S ribosomal protein L12
Lz: 60S ribosomal protein L10a
M2: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1
N: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2
N2: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
O2: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
P2: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
u3: tRNA
v3: tRNA
y3: Endoplasmin
LJ: Large ribosomal subunit protein uL5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,334,539306
Polymers3,324,62370
Non-polymers9,916236
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
Translocon-associated protein subunit ... , 4 types, 4 molecules 5678

#1: Protein Translocon-associated protein subunit alpha / TRAP-alpha / Signal sequence receptor subunit alpha / SSR-alpha


Mass: 32263.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P43307
#2: Protein Translocon-associated protein subunit beta / TRAP-beta / Signal sequence receptor subunit beta / SSR-beta


Mass: 20154.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P43308
#3: Protein Translocon-associated protein subunit gamma / TRAP-gamma / Signal sequence receptor subunit gamma / SSR-gamma


Mass: 21106.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNL2
#4: Protein Translocon-associated protein subunit delta / TRAP-delta / Signal sequence receptor subunit delta / SSR-delta


Mass: 19015.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51571

+
Protein , 9 types, 9 molecules ABGJLILmLsN2y3

#5: Protein Peptidyl-prolyl cis-trans isomerase FKBP11 / PPIase FKBP11 / 19 kDa FK506-binding protein / 19 kDa FKBP / FKBP-19 / FK506-binding protein 11 / ...PPIase FKBP11 / 19 kDa FK506-binding protein / 19 kDa FKBP / FKBP-19 / FK506-binding protein 11 / FKBP-11 / Rotamase


Mass: 22213.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NYL4, peptidylprolyl isomerase
#6: Protein Coiled-coil domain-containing protein 134


Mass: 26598.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H6E4
#10: Protein Stress-associated endoplasmic reticulum protein 1 / Ribosome-attached membrane protein 4


Mass: 7384.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6X1
#12: Protein Oligosaccharyltransferase complex subunit OSTC / Hydrophobic protein HSF-28


Mass: 16844.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRP0
#26: Protein Ribosomal protein uL16-like / 60S ribosomal protein L10-like / Large ribosomal subunit protein uL16-like


Mass: 24570.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96L21
#54: Protein Ubiquitin-60S ribosomal protein L40 / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987
#59: Protein 60S acidic ribosomal protein P0 / 60S ribosomal protein L10E / Large ribosomal subunit protein uL10


Mass: 34309.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05388
#64: Protein Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit / DDOST 48 kDa subunit / Oligosaccharyl transferase 48 kDa subunit


Mass: 50854.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39656
#69: Protein Endoplasmin / 94 kDa glucose-regulated protein / GRP-94 / Heat shock protein 90 kDa beta member 1 / Heat shock ...94 kDa glucose-regulated protein / GRP-94 / Heat shock protein 90 kDa beta member 1 / Heat shock protein family C member 4 / Tumor rejection antigen 1 / gp96 homolog


Mass: 96254.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P14625, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

+
Protein transport protein Sec61 subunit ... , 3 types, 3 molecules DEF

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


Mass: 52304.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61619
#8: Protein Protein transport protein Sec61 subunit beta


Mass: 9987.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60468
#9: Protein Protein transport protein Sec61 subunit gamma


Mass: 7752.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60059

+
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ... , 7 types, 7 molecules IK2L2M2NO2P2

#11: Protein Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A / Oligosaccharyl transferase subunit STT3A / STT3-A / B5 / Integral membrane protein 1 / ...Oligosaccharyl transferase subunit STT3A / STT3-A / B5 / Integral membrane protein 1 / Transmembrane protein TMC


Mass: 80607.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P46977, dolichyl-diphosphooligosaccharide-protein glycotransferase
#13: Protein/peptide Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4


Mass: 4196.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0C6T2
#14: Protein Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258 / Oligosaccharyl transferase subunit TMEM258 / Transmembrane protein 258


Mass: 9083.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61165
#62: Protein Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 / Oligosaccharyl transferase subunit DAD1 / Defender against cell death 1 / DAD-1


Mass: 12503.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61803
#63: Protein Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2 / Oligosaccharyl transferase subunit KCP2 / Keratinocyte-associated protein 2 / KCP-2


Mass: 14689.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N6L1
#65: Protein Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kDa subunit / Ribophorin I / RPN- ...Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kDa subunit / Ribophorin I / RPN-I / Ribophorin-1


Mass: 68656.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04843
#66: Protein Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa subunit / RIBIIR / Ribophorin ...Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa subunit / RIBIIR / Ribophorin II / RPN-II / Ribophorin-2


Mass: 69347.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04844

+
RNA chain , 5 types, 5 molecules L5L7L8u3v3

#15: RNA chain 28S ribosomal RNA


Mass: 1638922.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#16: RNA chain 5S ribosomal RNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898
#17: RNA chain 5.8S ribosomal RNA


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853
#67: RNA chain tRNA


Mass: 24414.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#68: RNA chain tRNA


Mass: 24436.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

+
60S ribosomal protein ... , 8 types, 8 molecules LALBLFLaLbLrLtLz

#18: Protein 60S ribosomal protein L8 / Large ribosomal subunit protein uL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#19: Protein 60S ribosomal protein L3 / HIV-1 TAR RNA-binding protein B / TARBP-B / Large ribosomal subunit protein uL3


Mass: 46211.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#23: Protein 60S ribosomal protein L7 / Large ribosomal subunit protein uL30


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#42: Protein 60S ribosomal protein L27a / Large ribosomal subunit protein uL15


Mass: 16604.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#43: Protein 60S ribosomal protein L29 / Cell surface heparin-binding protein HIP / Large ribosomal subunit protein eL29


Mass: 17804.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47914
#58: Protein 60S ribosomal protein L28 / Large ribosomal subunit protein eL28


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779
#60: Protein 60S ribosomal protein L12 / Large ribosomal subunit protein uL11


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30050
#61: Protein 60S ribosomal protein L10a / CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down- ...CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down-regulated protein 6 / NEDD-6


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62906

+
Large ribosomal subunit protein ... , 33 types, 33 molecules LCLDLELGLHLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLcLdLeLfLgLhLiLjLkLl...

#20: Protein Large ribosomal subunit protein uL4 / 60S ribosomal protein L4 / 60S ribosomal protein L1


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#21: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#22: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding ...60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107


Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#24: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a / PLA-X polypeptide / Surfeit locus protein 3


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#25: Protein Large ribosomal subunit protein uL6 / 60S ribosomal protein L9


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#27: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13 / Breast basic conserved protein 1


Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#28: Protein Large ribosomal subunit protein eL14 / 60S ribosomal protein L14 / CAG-ISL 7


Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#29: Protein Large ribosomal subunit protein eL15 / 60S ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#30: Protein Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a / 23 kDa highly basic protein


Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#31: Protein Large ribosomal subunit protein uL22 / 60S ribosomal protein L17 / 60S ribosomal protein L23 / PD-1


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#32: Protein Large ribosomal subunit protein eL18 / 60S ribosomal protein L18


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#33: Protein Large ribosomal subunit protein eL19 / 60S ribosomal protein L19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#34: Protein Large ribosomal subunit protein eL20 / 60S ribosomal protein L18a


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#35: Protein Large ribosomal subunit protein eL21 / 60S ribosomal protein L21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#36: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated ...60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#37: Protein Large ribosomal subunit protein uL14 / 60S ribosomal protein L23 / 60S ribosomal protein L17


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62829
#38: Protein Large ribosomal subunit protein eL24 / 60S ribosomal protein L24 / 60S ribosomal protein L30


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83731
#39: Protein Large ribosomal subunit protein uL23 / 60S ribosomal protein L23a


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#40: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#41: Protein Large ribosomal subunit protein eL27 / 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#44: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#45: Protein Large ribosomal subunit protein eL31 / 60S ribosomal protein L31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#46: Protein Large ribosomal subunit protein eL32 / 60S ribosomal protein L32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#47: Protein Large ribosomal subunit protein eL33 / 60S ribosomal protein L35a / Cell growth-inhibiting gene 33 protein


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#48: Protein Large ribosomal subunit protein eL34 / 60S ribosomal protein L34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#49: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#50: Protein Large ribosomal subunit protein eL36 / 60S ribosomal protein L36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#51: Protein Large ribosomal subunit protein eL37 / 60S ribosomal protein L37 / G1.16


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#52: Protein Large ribosomal subunit protein eL38 / 60S ribosomal protein L38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#53: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#56: Protein Large ribosomal subunit protein eL42 / 60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / ...60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881
#57: Protein Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513
#70: Protein Large ribosomal subunit protein uL5 / 60S ribosomal protein L11 / CLL-associated antigen KW-12


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913

+
Protein/peptide , 1 types, 1 molecules Ln

#55: Protein/peptide Small ribosomal subunit protein eS32 / 60S ribosomal protein L41 / HG12 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945

+
Sugars , 4 types, 4 molecules

#71: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#72: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#73: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g6-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#74: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

+
Non-polymers , 4 types, 233 molecules

#75: Chemical ChemComp-ELU / phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate


Mass: 452.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C20H38O7P2 / Feature type: SUBJECT OF INVESTIGATION
#76: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 226
Source method: isolated from a genetically manipulated source
Formula: Mg
#77: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: Zn
#78: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

+
Details

Has ligand of interestY
Has protein modificationY
Sequence detailsChain y3 residues 558-600 are part of the natively isolated GRP94 nascent chain. However, because ...Chain y3 residues 558-600 are part of the natively isolated GRP94 nascent chain. However, because of the way the sample is prepared, nascent chain density in this part of the structure reflects a mixture of different length GRP94 chains, and thus sequence cannot be assigned to it.

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Nascent GRP94 folding intermediate bound to a ribosome-translocon complex
Type: RIBOSOME
Details: Isolated by affinity purification via a Flag-tag on FKBP11
Entity ID: #1-#26, #70, #27-#69 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Organelle: Endoplasmic reticulum
Buffer solutionpH: 7.4
Details: HEPES buffer was adjusted to pH 7.4 with potassium hydroxide.
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES, pH 7.4C8H18N2O4S1
2200 mMPotassium AcetateCH3CO2K1
32 mMMagnesium ChlorideMgCl21
41 mMGlutathioneC10H17N3O6S1
50.15 % (w/v)DigitoninC56H92O291
60.5 mg/mL3xFlag PeptideC120H169N31O49S1
SpecimenConc.: 0.056 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Native ribosome-translocon complexes isolated from HEK293 microsomes by affinity purification via a Flag-tag on FKBP11
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: Three microliters of affinity-purified RTCs were applied to the grid, incubated for 60 seconds, blotted for 7 seconds, drained for 0.5 seconds, and frozen in liquid nitrogen-cooled ethane.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 53000 X / Nominal defocus max: 1900 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6569

-
Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.21.2_5419+SVNmodel refinement
13RELION53D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 741983
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55750 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Tightly restrained real-space refinement in Coot and Phenix
RefinementCross valid method: NONE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • 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

-
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

Read more