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- EMDB-72945: Structure of a GRP94 folding intermediate engaged with a CCDC134-... -

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Basic information

Entry
Database: EMDB / ID: EMD-72945
TitleStructure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon
Map dataTranslocon-only map
Sample
  • Complex: Nascent GRP94 folding intermediate bound to a ribosome-translocon complex
    • Protein or peptide: x 20 types
  • Ligand: x 1 types
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 / sarcoplasmic reticulum lumen / positive regulation of growth hormone secretion / Sec61 translocon complex / 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 / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane / protein N-linked glycosylation / post-translational protein targeting to membrane, translocation / endoplasmic reticulum organization / Trafficking and processing of endosomal TLR / epithelial cell apoptotic process / embryonic hemopoiesis / insulin secretion / Scavenging by Class A Receptors / epidermal growth factor binding / retrograde protein transport, ER to cytosol / azurophil granule membrane / low-density lipoprotein particle receptor binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein phosphatase inhibitor activity / sperm plasma membrane / : / cellular response to ATP / smooth endoplasmic reticulum / Advanced glycosylation endproduct receptor signaling / blastocyst development / regulation of ossification / SRP-dependent cotranslational protein targeting to membrane / protein transmembrane transporter activity / positive regulation of Wnt signaling pathway / response to type II interferon / endoplasmic reticulum unfolded protein response / cytoplasmic microtubule / : / rough endoplasmic reticulum / cellular response to manganese ion / ERAD pathway / response to cytokine / endomembrane system / endocytic vesicle lumen / protein folding chaperone / post-translational protein modification / response to endoplasmic reticulum stress / T cell activation / guanyl-nucleotide exchange factor activity / positive regulation of translation / placenta development / skeletal system development / post-embryonic development / protein localization to plasma membrane / Post-translational protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ATP-dependent protein folding chaperone / enzyme activator activity / positive regulation of insulin secretion / regulation of protein stability / protein modification process / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium channel activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / glucose metabolic process / unfolded protein binding / melanosome / protein folding / protein transport / : / ribosome binding / ER-Phagosome 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. / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / 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. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 / Endoplasmin / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit / Translocon-associated protein subunit alpha / Translocon-associated protein subunit beta / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A / Translocon-associated protein subunit delta / Protein transport protein Sec61 subunit gamma ...Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 / Endoplasmin / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit / Translocon-associated protein subunit alpha / Translocon-associated protein subunit beta / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A / Translocon-associated protein subunit delta / Protein transport protein Sec61 subunit gamma / Protein transport protein Sec61 subunit beta / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258 / Protein transport protein Sec61 subunit alpha isoform 1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2 / Coiled-coil domain-containing protein 134 / Oligosaccharyltransferase complex subunit OSTC / Peptidyl-prolyl cis-trans isomerase FKBP11 / Translocon-associated protein subunit gamma / Stress-associated endoplasmic reticulum protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsYamsek M / Jha R / Keenan RJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM145374 United States
CitationJournal: 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
DepositionSep 29, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72945.png

Downloads & links

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Map

FileDownload / File: emd_72945.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTranslocon-only map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 416 pix.
= 349.44 Å		0.84 Å/pix.
x 416 pix.
= 349.44 Å		0.84 Å/pix.
x 416 pix.
= 349.44 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00395
Minimum - Maximum-0.005121462 - 0.01718846
Average (Standard dev.)0.00082456216 (±0.00093151646)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 349.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half-map 1

Fileemd_72945_half_map_1.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_72945_half_map_2.map
Annotationhalf-map 2
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Sample components

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Entire : Nascent GRP94 folding intermediate bound to a ribosome-translocon...

EntireName: Nascent GRP94 folding intermediate bound to a ribosome-translocon complex
Components
  • Complex: Nascent GRP94 folding intermediate bound to a ribosome-translocon complex
    • Protein or peptide: Translocon-associated protein subunit alpha
    • Protein or peptide: Translocon-associated protein subunit beta
    • Protein or peptide: Translocon-associated protein subunit gamma
    • Protein or peptide: Translocon-associated protein subunit delta
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP11
    • Protein or peptide: Coiled-coil domain-containing protein 134
    • Protein or peptide: Protein transport protein Sec61 subunit alpha isoform 1
    • Protein or peptide: Protein transport protein Sec61 subunit beta
    • Protein or peptide: Protein transport protein Sec61 subunit gamma
    • Protein or peptide: Stress-associated endoplasmic reticulum protein 1
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
    • Protein or peptide: Oligosaccharyltransferase complex subunit OSTC
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
    • Protein or peptide: Endoplasmin
  • Ligand: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate

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Supramolecule #1: Nascent GRP94 folding intermediate bound to a ribosome-translocon...

SupramoleculeName: Nascent GRP94 folding intermediate bound to a ribosome-translocon complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Details: Isolated by affinity purification via a Flag-tag on FKBP11
Source (natural)Organism: Homo sapiens (human) / Organelle: Endoplasmic reticulum

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Macromolecule #1: Translocon-associated protein subunit alpha

MacromoleculeName: Translocon-associated protein subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.263219 KDa
SequenceString: MRLLPRLLLL LLLVFPATVL FRGGPRGLLA VAQDLTEDEE TVEDSIIEDE DDEAEVEEDE PTDLVEDKEE EDVSGEPEAS PSADTTILF VKGEDFPANN IVKFLVGFTN KGTEDFIVES LDASFRYPQD YQFYIQNFTA LPLNTVVPPQ RQATFEYSFI P AEPMGGRP ...String:
MRLLPRLLLL LLLVFPATVL FRGGPRGLLA VAQDLTEDEE TVEDSIIEDE DDEAEVEEDE PTDLVEDKEE EDVSGEPEAS PSADTTILF VKGEDFPANN IVKFLVGFTN KGTEDFIVES LDASFRYPQD YQFYIQNFTA LPLNTVVPPQ RQATFEYSFI P AEPMGGRP FGLVINLNYK DLNGNVFQDA VFNQTVTVIE REDGLDGETI FMYMFLAGLG LLVIVGLHQL LESRKRKRPI QK VEMGTSS QNDVDMSWIP QETLNQINKA SPRRLPRKRA QKRSVGSDE

UniProtKB: Translocon-associated protein subunit alpha

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Macromolecule #2: Translocon-associated protein subunit beta

MacromoleculeName: Translocon-associated protein subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.154986 KDa
SequenceString:
MRLLSFVVLA LFAVTQAEEG ARLLASKSLL NRYAVEGRDL TLQYNIYNVG SSAALDVELS DDSFPPEDFG IVSGMLNVKW DRIAPASNV SHTVVLRPLK AGYFNFTSAT ITYLAQEDGP VVIGSTSAPG QGGILAQREF DRRFSPHFLD WAAFGVMTLP S IGIPLLLW YSSKRKYDTP KTKKN

UniProtKB: Translocon-associated protein subunit beta

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Macromolecule #3: Translocon-associated protein subunit gamma

MacromoleculeName: Translocon-associated protein subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.106465 KDa
SequenceString:
MAPKGSSKQQ SEEDLLLQDF SRNLSAKSSA LFFGNAFIVS AIPIWLYWRI WHMDLIQSAV LYSVMTLVST YLVAFAYKNV KFVLKHKVA QKREDAVSKE VTRKLSEADN RKMSRKEKDE RILWKKNEVA DYEATTFSIF YNNTLFLVVV IVASFFILKN F NPTVNYIL SISASSGLIA LLSTGSK

UniProtKB: Translocon-associated protein subunit gamma

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Macromolecule #4: Translocon-associated protein subunit delta

MacromoleculeName: Translocon-associated protein subunit delta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.015547 KDa
SequenceString:
MAAMASLGAL ALLLLSSLSR CSAEACLEPQ ITPSYYTTSD AVISTETVFI VEISLTCKNR VQNMALYADV GGKQFPVTRG QDVGRYQVS WSLDHKSAHA GTYEVRFFDE ESYSLLRKAQ RNNEDISIIP PLFTVSVDHR GTWNGPWVST EVLAAAIGLV I YYLAFSAK SHIQA

UniProtKB: Translocon-associated protein subunit delta

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Macromolecule #5: Peptidyl-prolyl cis-trans isomerase FKBP11

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP11 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.213393 KDa
SequenceString: MTLRPSLLPL HLLLLLLLSA AVCRAEAGLE TESPVRTLQV ETLVEPPEPC AEPAAFGDTL HIHYTGSLVD GRIIDTSLTR DPLVIELGQ KQVIPGLEQS LLDMCVGEKR RAIIPSHLAY GKRGFPPSVP ADAVVQYDVE LIALIRANYW LKLVKGILPL V GMAMVPAL ...String:
MTLRPSLLPL HLLLLLLLSA AVCRAEAGLE TESPVRTLQV ETLVEPPEPC AEPAAFGDTL HIHYTGSLVD GRIIDTSLTR DPLVIELGQ KQVIPGLEQS LLDMCVGEKR RAIIPSHLAY GKRGFPPSVP ADAVVQYDVE LIALIRANYW LKLVKGILPL V GMAMVPAL LGLIGYHLYR KANRPKVSKK KLKEEKRNKS KKK

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP11

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Macromolecule #6: Coiled-coil domain-containing protein 134

MacromoleculeName: Coiled-coil domain-containing protein 134 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.598648 KDa
SequenceString: MDLLQFLAFL FVLLLSGMGA TGTLRTSLDP SLEIYKKMFE VKRREQLLAL KNLAQLNDIH QQYKILDVML KGLFKVLEDS RTVLTAADV LPDGPFPQDE KLKDAFSHVV ENTAFFGDVV LRFPRIVHYY FDHNSNWNLL IRWGISFCNQ TGVFNQGPHS P ILSLMAQE ...String:
MDLLQFLAFL FVLLLSGMGA TGTLRTSLDP SLEIYKKMFE VKRREQLLAL KNLAQLNDIH QQYKILDVML KGLFKVLEDS RTVLTAADV LPDGPFPQDE KLKDAFSHVV ENTAFFGDVV LRFPRIVHYY FDHNSNWNLL IRWGISFCNQ TGVFNQGPHS P ILSLMAQE LGISEKDSNF QNPFKIDRTE FIPSTDPFQK ALREEEKRRK KEEKRKEIRK GPRISRSQSE L

UniProtKB: Coiled-coil domain-containing protein 134

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Macromolecule #7: Protein transport protein Sec61 subunit alpha isoform 1

MacromoleculeName: Protein transport protein Sec61 subunit alpha isoform 1
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.304406 KDa
SequenceString: MAIKFLEVIK PFCVILPEIQ KPERKIQFKE KVLWTAITLF IFLVCCQIPL FGIMSSDSAD PFYWMRVILA SNRGTLMELG ISPIVTSGL IMQLLAGAKI IEVGDTPKDR ALFNGAQKLF GMIITIGQSI VYVMTGMYGD PSEMGAGICL LITIQLFVAG L IVLLLDEL ...String:
MAIKFLEVIK PFCVILPEIQ KPERKIQFKE KVLWTAITLF IFLVCCQIPL FGIMSSDSAD PFYWMRVILA SNRGTLMELG ISPIVTSGL IMQLLAGAKI IEVGDTPKDR ALFNGAQKLF GMIITIGQSI VYVMTGMYGD PSEMGAGICL LITIQLFVAG L IVLLLDEL LQKGYGLGSG ISLFIATNIC ETIVWKAFSP TTVNTGRGME FEGAIIALFH LLATRTDKVR ALREAFYRQN LP NLMNLIA TIFVFAVVIY FQGFRVDLPI KSARYRGQYN TYPIKLFYTS NIPIILQSAL VSNLYVISQM LSARFSGNLL VSL LGTWSD TSSGGPARAY PVGGLCYYLS PPESFGSVLE DPVHAVVYIV FMLGSCAFFS KTWIEVSGSS AKDVAKQLKE QQMV MRGHR ETSMVHELNR YIPTAAAFGG LCIGALSVLA DFLGAIGSGT GILLAVTIIY QYFEIFVKEQ SEVGSMGALL F

UniProtKB: Protein transport protein Sec61 subunit alpha isoform 1

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Macromolecule #8: Protein transport protein Sec61 subunit beta

MacromoleculeName: Protein transport protein Sec61 subunit beta / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.987456 KDa
SequenceString:
MPGPTPSGTN VGSSGRSPSK AVAARAAGST VRQRKNASCG TRSAGRTTSA GTGGMWRFYT EDSPGLKVGP VPVLVMSLLF IASVFMLHI WGKYTRS

UniProtKB: Protein transport protein Sec61 subunit beta

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Macromolecule #9: Protein transport protein Sec61 subunit gamma

MacromoleculeName: Protein transport protein Sec61 subunit gamma / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.752325 KDa
SequenceString:
MDQVMQFVEP SRQFVKDSIR LVKRCTKPDR KEFQKIAMAT AIGFAIMGFI GFFVKLIHIP INNIIVGG

UniProtKB: Protein transport protein Sec61 subunit gamma

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Macromolecule #10: Stress-associated endoplasmic reticulum protein 1

MacromoleculeName: Stress-associated endoplasmic reticulum protein 1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.384762 KDa
SequenceString:
MVAKQRIRMA NEKHSKNITQ RGNVAKTSRN APEEKASVGP WLLALFIFVV CGSAIFQIIQ SIRMGM

UniProtKB: Stress-associated endoplasmic reticulum protein 1

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Macromolecule #11: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.60732 KDa
SequenceString: MTKFGFLRLS YEKQDTLLKL LILSMAAVLS FSTRLFAVLR FESVIHEFDP YFNYRTTRFL AEEGFYKFHN WFDDRAWYPL GRIIGGTIY PGLMITSAAI YHVLHFFHIT IDIRNVCVFL APLFSSFTTI VTYHLTKELK DAGAGLLAAA MIAVVPGYIS R SVAGSYDN ...String:
MTKFGFLRLS YEKQDTLLKL LILSMAAVLS FSTRLFAVLR FESVIHEFDP YFNYRTTRFL AEEGFYKFHN WFDDRAWYPL GRIIGGTIY PGLMITSAAI YHVLHFFHIT IDIRNVCVFL APLFSSFTTI VTYHLTKELK DAGAGLLAAA MIAVVPGYIS R SVAGSYDN EGIAIFCMLL TYYMWIKAVK TGSICWAAKC ALAYFYMVSS WGGYVFLINL IPLHVLVLML TGRFSHRIYV AY CTVYCLG TILSMQISFV GFQPVLSSEH MAAFGVFGLC QIHAFVDYLR SKLNPQQFEV LFRSVISLVG FVLLTVGALL MLT GKISPW TGRFYSLLDP SYAKNNIPII ASVSEHQPTT WSSYYFDLQL LVFMFPVGLY YCFSNLSDAR IFIIMYGVTS MYFS AVMVR LMLVLAPVMC ILSGIGVSQV LSTYMKNLDI SRPDKKSKKQ QDSTYPIKNE VASGMILVMA FFLITYTFHS TWVTS EAYS SPSIVLSARG GDGSRIIFDD FREAYYWLRH NTPEDAKVMS WWDYGYQITA MANRTILVDN NTWNNTHISR VGQAMA STE EKAYEIMREL DVSYVLVIFG GLTGYSSDDI NKFLWMVRIG GSTDTGKHIK ENDYYTPTGE FRVDREGSPV LLNCLMY KM CYYRFGQVYT EAKRPPGFDR VRNAEIGNKD FELDVLEEAY TTEHWLVRIY KVKDLDNRGL SRT

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A

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Macromolecule #12: Oligosaccharyltransferase complex subunit OSTC

MacromoleculeName: Oligosaccharyltransferase complex subunit OSTC / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.844215 KDa
SequenceString:
METLYRVPFL VLECPNLKLK KPPWLHMPSA MTVYALVVVS YFLITGGIIY DVIVEPPSVG SMTDEHGHQR PVAFLAYRVN GQYIMEGLA SSFLFTMGGL GFIILDRSNA PNIPKLNRFL LLFIGFVCVL LSFFMARVFM RMKLPGYLMG

UniProtKB: Oligosaccharyltransferase complex subunit OSTC

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Macromolecule #13: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4
type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.196004 KDa
SequenceString:
MITDVQLAIF ANMLGVSLFL LVVLYHYVAV NNPKKQE

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4

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Macromolecule #14: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258
type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.083804 KDa
SequenceString:
MELEAMSRYT SPVNPAVFPH LTVVLLAIGM FFTAWFFVYE VTSTKYTRDI YKELLISLVA SLFMGFGVLF LLLWVGIYV

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258

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Macromolecule #15: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.503631 KDa
SequenceString:
MSASVVSVIS RFLEEYLSST PQRLKLLDAY LLYILLTGAL QFGYCLLVGT FPFNSFLSGF ISCVGSFILA VCLRIQINPQ NKADFQGIS PERAFADFLF ASTILHLVVM NFVG

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1

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Macromolecule #16: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.689456 KDa
SequenceString:
MVVGTGTSLA LSSLLSLLLF AGMQMYSRQL ASTEWLTIQG GLLGSGLFVF SLTAFNNLEN LVFGKGFQAK IFPEILLCLL LALFASGLI HRVCVTTCFI FSMVGLYYIN KISSTLYQAA APVLTPAKVT GKSKKRN

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2

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Macromolecule #17: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.854578 KDa
SequenceString: MGYFRCARAG SFGRRRKMEP STAARAWALF WLLLPLLGAV CASGPRTLVL LDNLNVRETH SLFFRSLKDR GFELTFKTAD DPSLSLIKY GEFLYDNLII FSPSVEDFGG NINVETISAF IDGGGSVLVA ASSDIGDPLR ELGSECGIEF DEEKTAVIDH H NYDISDLG ...String:
MGYFRCARAG SFGRRRKMEP STAARAWALF WLLLPLLGAV CASGPRTLVL LDNLNVRETH SLFFRSLKDR GFELTFKTAD DPSLSLIKY GEFLYDNLII FSPSVEDFGG NINVETISAF IDGGGSVLVA ASSDIGDPLR ELGSECGIEF DEEKTAVIDH H NYDISDLG QHTLIVADTE NLLKAPTIVG KSSLNPILFR GVGMVADPDN PLVLDILTGS STSYSFFPDK PITQYPHAVG KN TLLIAGL QARNNARVIF SGSLDFFSDS FFNSAVQKAA PGSQRYSQTG NYELAVALSR WVFKEEGVLR VGPVSHHRVG ETA PPNAYT VTDLVEYSIV IQQLSNGKWV PFDGDDIQLE FVRIDPFVRT FLKKKGGKYS VQFKLPDVYG VFQFKVDYNR LGYT HLYSS TQVSVRPLQH TQYERFIPSA YPYYASAFSM MLGLFIFSIV FLHMKEKEKS D

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit

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Macromolecule #18: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.656156 KDa
SequenceString: MEAPAAGLFL LLLLGTWAPA PGSASSEAPP LINEDVKRTV DLSSHLAKVT AEVVLAHLGG GSTSRATSFL LALEPELEAR LAHLGVQVK GEDEEENNLE VRETKIKGKS GRFFTVKLPV ALDPGAKISV IVETVYTHVL HPYPTQITQS EKQFVVFEGN H YFYSPYPT ...String:
MEAPAAGLFL LLLLGTWAPA PGSASSEAPP LINEDVKRTV DLSSHLAKVT AEVVLAHLGG GSTSRATSFL LALEPELEAR LAHLGVQVK GEDEEENNLE VRETKIKGKS GRFFTVKLPV ALDPGAKISV IVETVYTHVL HPYPTQITQS EKQFVVFEGN H YFYSPYPT KTQTMRVKLA SRNVESYTKL GNPTRSEDLL DYGPFRDVPA YSQDTFKVHY ENNSPFLTIT SMTRVIEVSH WG NIAVEEN VDLKHTGAVL KGPFSRYDYQ RQPDSGISSI RSFKTILPAA AQDVYYRDEI GNVSTSHLLI LDDSVEMEIR PRF PLFGGW KTHYIVGYNL PSYEYLYNLG DQYALKMRFV DHVFDEQVID SLTVKIILPE GAKNIEIDSP YEISRAPDEL HYTY LDTFG RPVIVAYKKN LVEQHIQDIV VHYTFNKVLM LQEPLLVVAA FYILFFTVII YVRLDFSITK DPAAEARMKV ACITE QVLT LVNKRIGLYR HFDETVNRYK QSRDISTLNS GKKSLETEHK ALTSEIALLQ SRLKTEGSDL CDRVSEMQKL DAQVKE LVL KSAVEAERLV AGKLKKDTYI ENEKLISGKR QELVTKIDHI LDAL

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1

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Macromolecule #19: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.347508 KDa
SequenceString: MAPPGSSTVF LLALTIIAST WALTPTHYLT KHDVERLKAS LDRPFTNLES AFYSIVGLSS LGAQVPDAKK ACTYIRSNLD PSNVDSLFY AAQASQALSG CEISISNETK DLLLAAVSED SSVTQIYHAV AALSGFGLPL ASQEALSALT ARLSKEETVL A TVQALQTA ...String:
MAPPGSSTVF LLALTIIAST WALTPTHYLT KHDVERLKAS LDRPFTNLES AFYSIVGLSS LGAQVPDAKK ACTYIRSNLD PSNVDSLFY AAQASQALSG CEISISNETK DLLLAAVSED SSVTQIYHAV AALSGFGLPL ASQEALSALT ARLSKEETVL A TVQALQTA SHLSQQADLR SIVEEIEDLV ARLDELGGVY LQFEEGLETT ALFVAATYKL MDHVGTEPSI KEDQVIQLMN AI FSKKNFE SLSEAFSVAS AAAVLSHNRY HVPVVVVPEG SASDTHEQAI LRLQVTNVLS QPLTQATVKL EHAKSVASRA TVL QKTSFT PVGDVFELNF MNVKFSSGYY DFLVEVEGDN RYIANTVELR VKISTEVGIT NVDLSTVDKD QSIAPKTTRV TYPA KAKGT FIADSHQNFA LFFQLVDVNT GAELTPHQTF VRLHNQKTGQ EVVFVAEPDN KNVYKFELDT SERKIEFDSA SGTYT LYLI IGDATLKNPI LWNVADVVIK FPEEEAPSTV LSQNLFTPKQ EIQHLFREPE KRPPTVVSNT FTALILSPLL LLFALW IRI GANVSNFTFA PSTIIFHLGH AAMLGLMYVY WTQLNMFQTL KYLAILGSVT FLAGNRMLAQ QAVKRTAH

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2

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Macromolecule #20: Endoplasmin

MacromoleculeName: Endoplasmin / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.254234 KDa
SequenceString: MRALWVLGLC CVLLTFGSVR ADDEVDVDGT VEEDLGKSRE GSRTDDEVVQ REEEAIQLDG LNASQIRELR EKSEKFAFQA EVNRMMKLI INSLYKNKEI FLRELISNAS DALDKIRLIS LTDENALSGN EELTVKIKCD KEKNLLHVTD TGVGMTREEL V KNLGTIAK ...String:
MRALWVLGLC CVLLTFGSVR ADDEVDVDGT VEEDLGKSRE GSRTDDEVVQ REEEAIQLDG LNASQIRELR EKSEKFAFQA EVNRMMKLI INSLYKNKEI FLRELISNAS DALDKIRLIS LTDENALSGN EELTVKIKCD KEKNLLHVTD TGVGMTREEL V KNLGTIAK SGTSEFLNKM TEAQEDGQST SELIGQFGVG FYSAFLVADK VIVTSKHNND TQHIWESDSN EFSVIADPRG NT LGRGTTI TLVLKEEASD YLELDTIKNL VKKYSQFINF PIYVWSSKTE TVEEPMEEEE AAKEEKEESD DEAAVEEEEE EKK PKTKKV EKTVWDWELM NDIKPIWQRP SKEVEEDEYK AFYKSFSKES DDPMAYIHFT AEGEVTFKSI LFVPTSAPRG LFDE YGSKK SDYIKLYVRR VFITDDFHDM MPKYLNFVKG VVDSDDLPLN VSRETLQQHK LLKVIRKKLV RKTLDMIKKI ADDKY NDTF WKEFGTNIKL GVIEDHSNRT RLAKLLRFQS SHHPTDITSL DQYVERMKEK QDKIYFMAGS SRKEAESSPF VERLLK KGY EVIYLTEPVD EYCIQALPEF DGKRFQNVAK EGVKFDESEK TKESREAVEK EFEPLLNWMK DKALKDKIEK AVVSQRL TE SPCALVASQY GWSGNMERIM KAQAYQTGKD ISTNYYASQK KTFEINPRHP LIRDMLRRIK EDEDDKTVLD LAVVLFET A TLRSGYLLPD TKAYGDRIER MLRLSLNIDP DAKVEEEPEE EPEETAEDTT EDTEQDEDEE MDVGTDEEEE TAKESTAEK DEL(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

UniProtKB: Endoplasmin

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Macromolecule #25: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,1...

MacromoleculeName: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate
type: ligand / ID: 25 / Number of copies: 1 / Formula: ELU
Molecular weightTheoretical: 452.459 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.056 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES, pH 7.4
200.0 mMCH3CO2KPotassium Acetate
2.0 mMMgCl2Magnesium Chloride
1.0 mMC10H17N3O6SGlutathione
0.15 % (w/v)C56H92O29Digitonin
0.5 mg/mLC120H169N31O49S3xFlag Peptide

Details: HEPES buffer was adjusted to pH 7.4 with potassium hydroxide.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
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..
DetailsNative ribosome-translocon complexes isolated from HEK293 microsomes by affinity purification via a Flag-tag on FKBP11

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6569 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 53000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 741983
CTF correctionType: NONE
Startup modelType of model: OTHER / Details: Unpublished ribosome-translocon map
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 55750
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4

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Atomic model buiding 1

DetailsTightly restrained real-space refinement in Coot and Phenix
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9ygy:
Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon

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