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

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基本情報

登録情報
データベース: EMDB / ID: EMD-72945
タイトルStructure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon
マップデータTranslocon-only map
試料
  • 複合体: Nascent GRP94 folding intermediate bound to a ribosome-translocon complex
    • タンパク質・ペプチド: x 20種
  • リガンド: x 1種
キーワードRibosome / Membrane protein / Translocon / Transport / N-Glycosylation
機能・相同性
機能・相同性情報


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 / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / 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
類似検索 - 分子機能
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
類似検索 - ドメイン・相同性
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
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.1 Å
データ登録者Yamsek M / Jha R / Keenan RJ
資金援助 米国, 1件
OrganizationGrant number国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM145374 米国
引用ジャーナル: Science / 年: 2024
タイトル: Regulated N-glycosylation controls chaperone function and receptor trafficking.
著者: 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 /
要旨: 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.
履歴
登録2025年9月29日-
ヘッダ(付随情報) 公開2025年11月19日-
マップ公開2025年11月19日-
更新2025年11月19日-
現状2025年11月19日処理サイト: RCSB / 状態: 公開

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構造の表示

添付画像

emd_72945.png

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マップ

ファイルダウンロード / ファイル: emd_72945.map.gz / 形式: CCP4 / 大きさ: 274.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈Translocon-only map
投影像・断面図

画像のコントロール

大きさ
明度
コントラスト
その他
軸Z (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

表面

投影像

断面 (1/3)

断面 (1/2)

断面 (2/3)

画像は Spider により作成

ボクセルのサイズX=Y=Z: 0.84 Å
密度

ヒストグラム

ヒストグラム (対数)
表面レベル登録者による: 0.00395
最小 - 最大-0.005121462 - 0.01718846
平均 (標準偏差)0.00082456216 (±0.00093151646)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ416416416
Spacing416416416
セルA=B=C: 349.44 Å
α=β=γ: 90.0 °

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添付データ

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ハーフマップ: half-map 1

ファイルemd_72945_half_map_1.map
注釈half-map 1
投影像・断面図
軸ZYX

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断面 (1/2)
密度ヒストグラム

ヒストグラム

ヒストグラム (対数)

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ハーフマップ: half-map 2

ファイルemd_72945_half_map_2.map
注釈half-map 2
投影像・断面図
軸ZYX

投影像

断面 (1/2)
密度ヒストグラム

ヒストグラム

ヒストグラム (対数)

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試料の構成要素

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

全体名称: Nascent GRP94 folding intermediate bound to a ribosome-translocon complex
要素
  • 複合体: Nascent GRP94 folding intermediate bound to a ribosome-translocon complex
    • タンパク質・ペプチド: Translocon-associated protein subunit alpha
    • タンパク質・ペプチド: Translocon-associated protein subunit beta
    • タンパク質・ペプチド: Translocon-associated protein subunit gamma
    • タンパク質・ペプチド: Translocon-associated protein subunit delta
    • タンパク質・ペプチド: Peptidyl-prolyl cis-trans isomerase FKBP11
    • タンパク質・ペプチド: Coiled-coil domain-containing protein 134
    • タンパク質・ペプチド: Protein transport protein Sec61 subunit alpha isoform 1
    • タンパク質・ペプチド: Protein transport protein Sec61 subunit beta
    • タンパク質・ペプチド: Protein transport protein Sec61 subunit gamma
    • タンパク質・ペプチド: Stress-associated endoplasmic reticulum protein 1
    • タンパク質・ペプチド: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
    • タンパク質・ペプチド: Oligosaccharyltransferase complex subunit OSTC
    • タンパク質・ペプチド: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4
    • タンパク質・ペプチド: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258
    • タンパク質・ペプチド: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1
    • タンパク質・ペプチド: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2
    • タンパク質・ペプチド: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
    • タンパク質・ペプチド: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
    • タンパク質・ペプチド: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
    • タンパク質・ペプチド: Endoplasmin
  • リガンド: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate

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

超分子名称: Nascent GRP94 folding intermediate bound to a ribosome-translocon complex
タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#20
詳細: Isolated by affinity purification via a Flag-tag on FKBP11
由来(天然)生物種: Homo sapiens (ヒト) / Organelle: Endoplasmic reticulum

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分子 #1: Translocon-associated protein subunit alpha

分子名称: Translocon-associated protein subunit alpha / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 32.263219 KDa
配列文字列: MRLLPRLLLL LLLVFPATVL FRGGPRGLLA VAQDLTEDEE TVEDSIIEDE DDEAEVEEDE PTDLVEDKEE EDVSGEPEAS PSADTTILF VKGEDFPANN IVKFLVGFTN KGTEDFIVES LDASFRYPQD YQFYIQNFTA LPLNTVVPPQ RQATFEYSFI P AEPMGGRP ...文字列:
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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分子 #2: Translocon-associated protein subunit beta

分子名称: Translocon-associated protein subunit beta / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 20.154986 KDa
配列文字列:
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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分子 #3: Translocon-associated protein subunit gamma

分子名称: Translocon-associated protein subunit gamma / タイプ: protein_or_peptide / ID: 3 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 21.106465 KDa
配列文字列:
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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分子 #4: Translocon-associated protein subunit delta

分子名称: Translocon-associated protein subunit delta / タイプ: protein_or_peptide / ID: 4 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 19.015547 KDa
配列文字列:
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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分子 #5: Peptidyl-prolyl cis-trans isomerase FKBP11

分子名称: Peptidyl-prolyl cis-trans isomerase FKBP11 / タイプ: protein_or_peptide / ID: 5 / コピー数: 1 / 光学異性体: LEVO / EC番号: peptidylprolyl isomerase
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 22.213393 KDa
配列文字列: MTLRPSLLPL HLLLLLLLSA AVCRAEAGLE TESPVRTLQV ETLVEPPEPC AEPAAFGDTL HIHYTGSLVD GRIIDTSLTR DPLVIELGQ KQVIPGLEQS LLDMCVGEKR RAIIPSHLAY GKRGFPPSVP ADAVVQYDVE LIALIRANYW LKLVKGILPL V GMAMVPAL ...文字列:
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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分子 #6: Coiled-coil domain-containing protein 134

分子名称: Coiled-coil domain-containing protein 134 / タイプ: protein_or_peptide / ID: 6 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 26.598648 KDa
配列文字列: MDLLQFLAFL FVLLLSGMGA TGTLRTSLDP SLEIYKKMFE VKRREQLLAL KNLAQLNDIH QQYKILDVML KGLFKVLEDS RTVLTAADV LPDGPFPQDE KLKDAFSHVV ENTAFFGDVV LRFPRIVHYY FDHNSNWNLL IRWGISFCNQ TGVFNQGPHS P ILSLMAQE ...文字列:
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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分子 #7: Protein transport protein Sec61 subunit alpha isoform 1

分子名称: Protein transport protein Sec61 subunit alpha isoform 1
タイプ: protein_or_peptide / ID: 7 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 52.304406 KDa
配列文字列: MAIKFLEVIK PFCVILPEIQ KPERKIQFKE KVLWTAITLF IFLVCCQIPL FGIMSSDSAD PFYWMRVILA SNRGTLMELG ISPIVTSGL IMQLLAGAKI IEVGDTPKDR ALFNGAQKLF GMIITIGQSI VYVMTGMYGD PSEMGAGICL LITIQLFVAG L IVLLLDEL ...文字列:
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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分子 #8: Protein transport protein Sec61 subunit beta

分子名称: Protein transport protein Sec61 subunit beta / タイプ: protein_or_peptide / ID: 8 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 9.987456 KDa
配列文字列:
MPGPTPSGTN VGSSGRSPSK AVAARAAGST VRQRKNASCG TRSAGRTTSA GTGGMWRFYT EDSPGLKVGP VPVLVMSLLF IASVFMLHI WGKYTRS

UniProtKB: Protein transport protein Sec61 subunit beta

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分子 #9: Protein transport protein Sec61 subunit gamma

分子名称: Protein transport protein Sec61 subunit gamma / タイプ: protein_or_peptide / ID: 9 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 7.752325 KDa
配列文字列:
MDQVMQFVEP SRQFVKDSIR LVKRCTKPDR KEFQKIAMAT AIGFAIMGFI GFFVKLIHIP INNIIVGG

UniProtKB: Protein transport protein Sec61 subunit gamma

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分子 #10: Stress-associated endoplasmic reticulum protein 1

分子名称: Stress-associated endoplasmic reticulum protein 1 / タイプ: protein_or_peptide / ID: 10 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 7.384762 KDa
配列文字列:
MVAKQRIRMA NEKHSKNITQ RGNVAKTSRN APEEKASVGP WLLALFIFVV CGSAIFQIIQ SIRMGM

UniProtKB: Stress-associated endoplasmic reticulum protein 1

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

分子名称: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
タイプ: protein_or_peptide / ID: 11 / コピー数: 1 / 光学異性体: LEVO
EC番号: dolichyl-diphosphooligosaccharide-protein glycotransferase
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 80.60732 KDa
配列文字列: MTKFGFLRLS YEKQDTLLKL LILSMAAVLS FSTRLFAVLR FESVIHEFDP YFNYRTTRFL AEEGFYKFHN WFDDRAWYPL GRIIGGTIY PGLMITSAAI YHVLHFFHIT IDIRNVCVFL APLFSSFTTI VTYHLTKELK DAGAGLLAAA MIAVVPGYIS R SVAGSYDN ...文字列:
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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分子 #12: Oligosaccharyltransferase complex subunit OSTC

分子名称: Oligosaccharyltransferase complex subunit OSTC / タイプ: protein_or_peptide / ID: 12 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 16.844215 KDa
配列文字列:
METLYRVPFL VLECPNLKLK KPPWLHMPSA MTVYALVVVS YFLITGGIIY DVIVEPPSVG SMTDEHGHQR PVAFLAYRVN GQYIMEGLA SSFLFTMGGL GFIILDRSNA PNIPKLNRFL LLFIGFVCVL LSFFMARVFM RMKLPGYLMG

UniProtKB: Oligosaccharyltransferase complex subunit OSTC

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

分子名称: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4
タイプ: protein_or_peptide / ID: 13 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 4.196004 KDa
配列文字列:
MITDVQLAIF ANMLGVSLFL LVVLYHYVAV NNPKKQE

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4

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

分子名称: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258
タイプ: protein_or_peptide / ID: 14 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 9.083804 KDa
配列文字列:
MELEAMSRYT SPVNPAVFPH LTVVLLAIGM FFTAWFFVYE VTSTKYTRDI YKELLISLVA SLFMGFGVLF LLLWVGIYV

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258

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

分子名称: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1
タイプ: protein_or_peptide / ID: 15 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 12.503631 KDa
配列文字列:
MSASVVSVIS RFLEEYLSST PQRLKLLDAY LLYILLTGAL QFGYCLLVGT FPFNSFLSGF ISCVGSFILA VCLRIQINPQ NKADFQGIS PERAFADFLF ASTILHLVVM NFVG

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1

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

分子名称: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2
タイプ: protein_or_peptide / ID: 16 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 14.689456 KDa
配列文字列:
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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分子 #17: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48...

分子名称: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
タイプ: protein_or_peptide / ID: 17 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 50.854578 KDa
配列文字列: MGYFRCARAG SFGRRRKMEP STAARAWALF WLLLPLLGAV CASGPRTLVL LDNLNVRETH SLFFRSLKDR GFELTFKTAD DPSLSLIKY GEFLYDNLII FSPSVEDFGG NINVETISAF IDGGGSVLVA ASSDIGDPLR ELGSECGIEF DEEKTAVIDH H NYDISDLG ...文字列:
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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分子 #18: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

分子名称: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
タイプ: protein_or_peptide / ID: 18 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 68.656156 KDa
配列文字列: MEAPAAGLFL LLLLGTWAPA PGSASSEAPP LINEDVKRTV DLSSHLAKVT AEVVLAHLGG GSTSRATSFL LALEPELEAR LAHLGVQVK GEDEEENNLE VRETKIKGKS GRFFTVKLPV ALDPGAKISV IVETVYTHVL HPYPTQITQS EKQFVVFEGN H YFYSPYPT ...文字列:
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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分子 #19: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

分子名称: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
タイプ: protein_or_peptide / ID: 19 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 69.347508 KDa
配列文字列: MAPPGSSTVF LLALTIIAST WALTPTHYLT KHDVERLKAS LDRPFTNLES AFYSIVGLSS LGAQVPDAKK ACTYIRSNLD PSNVDSLFY AAQASQALSG CEISISNETK DLLLAAVSED SSVTQIYHAV AALSGFGLPL ASQEALSALT ARLSKEETVL A TVQALQTA ...文字列:
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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分子 #20: Endoplasmin

分子名称: Endoplasmin / タイプ: protein_or_peptide / ID: 20 / コピー数: 1 / 光学異性体: LEVO
EC番号: 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 96.254234 KDa
配列文字列: MRALWVLGLC CVLLTFGSVR ADDEVDVDGT VEEDLGKSRE GSRTDDEVVQ REEEAIQLDG LNASQIRELR EKSEKFAFQA EVNRMMKLI INSLYKNKEI FLRELISNAS DALDKIRLIS LTDENALSGN EELTVKIKCD KEKNLLHVTD TGVGMTREEL V KNLGTIAK ...文字列:
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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分子 #25: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,1...

分子名称: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate
タイプ: ligand / ID: 25 / コピー数: 1 / 式: ELU
分子量理論値: 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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実験情報

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構造解析

手法クライオ電子顕微鏡法
解析単粒子再構成法
試料の集合状態particle

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試料調製

濃度0.056 mg/mL
緩衝液pH: 7.4
構成要素:
濃度式名称
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

詳細: HEPES buffer was adjusted to pH 7.4 with potassium hydroxide.
グリッドモデル: Quantifoil R1.2/1.3 / 材質: GOLD / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 2 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 25 sec.
凍結凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 295 K / 装置: FEI VITROBOT MARK IV
詳細: 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..
詳細Native ribosome-translocon complexes isolated from HEK293 microsomes by affinity purification via a Flag-tag on FKBP11

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電子顕微鏡法

顕微鏡TFS KRIOS
撮影フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)
撮影したグリッド数: 1 / 実像数: 6569 / 平均電子線量: 60.0 e/Å2
電子線加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
電子光学系照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm
最大 デフォーカス（公称値）: 1.9000000000000001 µm
最小 デフォーカス（公称値）: 0.9 µm / 倍率（公称値）: 53000
試料ステージ試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
ホルダー冷却材: NITROGEN
実験機器
モデル: Titan Krios / 画像提供: FEI Company

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画像解析

粒子像選択選択した数: 741983
CTF補正タイプ: NONE
初期モデルモデルのタイプ: OTHER / 詳細: Unpublished ribosome-translocon map
最終 再構成使用したクラス数: 1 / 解像度のタイプ: BY AUTHOR / 解像度: 4.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 5.0) / 使用した粒子像数: 55750
初期 角度割当タイプ: MAXIMUM LIKELIHOOD
最終 角度割当タイプ: MAXIMUM LIKELIHOOD
最終 3次元分類クラス数: 4

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原子モデル構築 1

詳細Tightly restrained real-space refinement in Coot and Phenix
精密化空間: REAL / プロトコル: FLEXIBLE FIT
得られたモデル

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

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る