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- PDB-9ygy: Structure of a GRP94 folding intermediate engaged with a CCDC134-... -

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Basic information

Entry
Database: PDB / ID: 9ygy
TitleStructure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon
Components
  • (Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ...) x 7
  • (Protein transport protein Sec61 subunit ...) x 3
  • (Translocon-associated protein subunit ...) x 4
  • Coiled-coil domain-containing protein 134
  • Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
  • Endoplasmin
  • Oligosaccharyltransferase complex subunit OSTC
  • Peptidyl-prolyl cis-trans isomerase FKBP11
  • Stress-associated endoplasmic reticulum protein 1
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
Chem-ELU / 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 ...Chem-ELU / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 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: Yamsek, M. / Ma, M. / Jha, R. / Wan, Y. / Li, Q. / Zhong, F. / DeLong, K. / Ji, Z. / Rohatgi, R. / Keenan, R.J.
#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
DepositionSep 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
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
y3: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)645,91425
Polymers641,81820
Non-polymers4,0965
Water00
1


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

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Components

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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

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Protein , 6 types, 6 molecules ABGJN2y3

#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
#17: 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
#20: 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

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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

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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
#15: 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
#16: 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
#18: 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
#19: 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

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Sugars , 4 types, 4 molecules

#21: 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
#22: 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
#23: 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
#24: 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

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Non-polymers , 1 types, 1 molecules

#25: 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: obtained synthetically / Formula: C20H38O7P2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: Nascent GRP94 folding intermediate bound to a ribosome-translocon complex
Type: COMPLEX
Details: Isolated by affinity purification via a Flag-tag on FKBP11
Entity ID: #1-#20 / 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.

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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

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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: 4.1 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

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