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万見
- EMDB-53467: Composite map of proximal A-C linker of Tetrahymena centriole -

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データを開く


IDまたはキーワード:

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基本情報

登録情報
データベース: EMDB / ID: EMD-53467
タイトルComposite map of proximal A-C linker of Tetrahymena centriole
マップデータComposite map of Tetrahymena proximal A-C linker
試料
  • 細胞器官・細胞要素: proximal A-C linker of Tetrahymena thermophila basal body centriole
    • タンパク質・ペプチド: x 15種
キーワードcentriole / basal body / centrosome / STRUCTURAL PROTEIN
機能・相同性
機能・相同性情報


MWP complex / cell projection organization / centrosome cycle / microtubule organizing center / cilium assembly / centriole / centriolar satellite / ciliary basal body / centrosome
類似検索 - 分子機能
: / : / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / : / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site ...: / : / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / : / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
類似検索 - ドメイン・相同性
Uncharacterized protein / WD repeat WRAP73-like protein, putative / POC1 centriolar protein homolog / TBC1 domain family member 31 / Rab-GAP TBC domain-containing protein / Centrosomal protein, putative
類似検索 - 構成要素
生物種Tetrahymena thermophila (真核生物)
手法単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.8 Å
データ登録者Cai B / Xu JW / Luo L / Aarts E / Leitner A / Ishikawa T / Beltro P / Pilhofer M / Wieczorek M
資金援助 スイス, 3件
OrganizationGrant number国
ETH ZurichETH-22 22-1 スイス
Swiss National Science Foundation320030-231677 スイス
Swiss National Science FoundationIZLIZ3 200294 スイス
引用ジャーナル: Sci Adv / 年: 2025
タイトル: Structure and assembly of the A-C linker connecting microtubule triplets in centrioles.
著者: Bin Cai / Jingwei Xu / Erik H Collet / Ellen Aarts / Leo Luo / Alexander Leitner / Takashi Ishikawa / Pedro Beltrao / Chad G Pearson / Martin Pilhofer / Michal Wieczorek /
要旨: Centriole assembly involves the coordination of centriolar modules. One module is the A-C linker, an enigmatic protein assembly connecting the A-microtubule of one microtubule triplet to the C- ...Centriole assembly involves the coordination of centriolar modules. One module is the A-C linker, an enigmatic protein assembly connecting the A-microtubule of one microtubule triplet to the C-microtubule of the neighboring triplet. Here, we integrated biochemistry, multiscale cryo-electron microscopy, and AlphaFold modeling to investigate the architecture of the centriole. Using an improved centriole isolation method, we determined the structure of the A-C linker bound to microtubule triplets, which revealed how the A-C linker cross-links microtubules and integrates with the B-C junction. We found marked changes in the structure and composition of the A-C linker that correlate with the presence of other centriolar modules, including the pinhead, cartwheel, and inner scaffold. Our findings show that the A-C linker is a highly integrated component of the centriole whose polymorphism may orchestrate the assembly of spatially distinct centriolar modules, and provide a framework for dissecting the biology of centrioles.
履歴
登録2025年4月22日-
ヘッダ(付随情報) 公開2025年9月17日-
マップ公開2025年9月17日-
更新2025年10月22日-
現状2025年10月22日処理サイト: PDBe / 状態: 公開

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構造の表示

添付画像

emd_53467.png

ダウンロードとリンク

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マップ

ファイルダウンロード / ファイル: emd_53467.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈Composite map of Tetrahymena proximal A-C linker
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.)
1.32 Å/pix.
x 480 pix.
= 631.2 Å		1.32 Å/pix.
x 480 pix.
= 631.2 Å		1.32 Å/pix.
x 480 pix.
= 631.2 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: 1.315 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: 5.0
最小 - 最大0.0 - 13.599174
平均 (標準偏差)0.22337514 (±1.0351868)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ480480480
Spacing480480480
セルA=B=C: 631.2 Å
α=β=γ: 90.0 °

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添付データ

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試料の構成要素

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全体 : proximal A-C linker of Tetrahymena thermophila basal body centriole

全体名称: proximal A-C linker of Tetrahymena thermophila basal body centriole
要素
  • 細胞器官・細胞要素: proximal A-C linker of Tetrahymena thermophila basal body centriole
    • タンパク質・ペプチド: WD repeat WRAP73-like protein, putative
    • タンパク質・ペプチド: Centrosomal protein, putative
    • タンパク質・ペプチド: Rab-GAP TBC domain-containing protein
    • タンパク質・ペプチド: TBC1 domain family member 31
    • タンパク質・ペプチド: POC1 centriolar protein homolog
    • タンパク質・ペプチド: Unknown Protein Chain
    • タンパク質・ペプチド: Unknown Protein Chain
    • タンパク質・ペプチド: SWIM-type domain-containing protein
    • タンパク質・ペプチド: Unknown Protein Chain
    • タンパク質・ペプチド: Unknown Protein Chain
    • タンパク質・ペプチド: Unknown Protein Chain
    • タンパク質・ペプチド: Unknown Protein Chain
    • タンパク質・ペプチド: Unknown Protein Chain
    • タンパク質・ペプチド: Unknown Protein Chain
    • タンパク質・ペプチド: Unknown Protein Chain

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超分子 #1: proximal A-C linker of Tetrahymena thermophila basal body centriole

超分子名称: proximal A-C linker of Tetrahymena thermophila basal body centriole
タイプ: organelle_or_cellular_component / ID: 1 / 親要素: 0 / 含まれる分子: all
由来(天然)生物種: Tetrahymena thermophila (真核生物)

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分子 #1: WD repeat WRAP73-like protein, putative

分子名称: WD repeat WRAP73-like protein, putative / 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: Tetrahymena thermophila (真核生物)
分子量理論値: 51.977465 KDa
配列文字列: MQFSNIIQGA CSAIFSQDSS LIAISNGSKI LIKDINQELI NRNVYSFQDI ITHMEFSPDN QLILVVQSNS NTVEVKNFND EQWICKIVD QACGLLHAVW APDSRSIITF SDFQMKATIY SLTDKQQYLI KNPKYTDKGL SFSSDGKFMA LAERRDIKDY I GIYYTKDW ...文字列:
MQFSNIIQGA CSAIFSQDSS LIAISNGSKI LIKDINQELI NRNVYSFQDI ITHMEFSPDN QLILVVQSNS NTVEVKNFND EQWICKIVD QACGLLHAVW APDSRSIITF SDFQMKATIY SLTDKQQYLI KNPKYTDKGL SFSSDGKFMA LAERRDIKDY I GIYYTKDW KLVNHFQVDT MDLVDIQWSK DDGSILVWDS SINYKFLVYH PSNGLIQRIQ PYEYALGIKC VELSNTPNFV AI GSYDEKI RLVNTLTWKI ITELEHKANI KEYSNAVVYR EQNSTLLNAQ HLVDRTTTQF VIDESINKLP GAKQSTDKSQ QSG VTDVTF SFNANYIASK SASFPNAVFI WEVSLLELRY IILLQNPVKG FLWSHNSNNL IIYAGSNKIY FWSLDGASVC ELPQ YGKQF SVNKVLWNKN SKCLVLIDRR DAIIGYPPID LEYNEEHEEE QREEYEN

UniProtKB: WD repeat WRAP73-like protein, putative

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分子 #2: Centrosomal protein, putative

分子名称: Centrosomal protein, putative / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Tetrahymena thermophila (真核生物)
分子量理論値: 44.594297 KDa
配列文字列: MRNSLFNERK YLLLRKKLDE LHYTQPLQIE SAELVDKLLN DLLKTSEGFQ KLKNKNQELE QQLCIIEKSL NPLKAENQKL MRENNNLQS EIILSSENAQ QKYNLLTVRL KQLQTEAQDL KFVLQKSEER CLKLQDENSA LKNKLDTISA KVYLPSCEKG F EDLPKSYV ...文字列:
MRNSLFNERK YLLLRKKLDE LHYTQPLQIE SAELVDKLLN DLLKTSEGFQ KLKNKNQELE QQLCIIEKSL NPLKAENQKL MRENNNLQS EIILSSENAQ QKYNLLTVRL KQLQTEAQDL KFVLQKSEER CLKLQDENSA LKNKLDTISA KVYLPSCEKG F EDLPKSYV NSNYKSLTNM SIARDNREGF NVLPQDNSNQ KNSNSSKEYD IQRLQNISDS KQNYQDGYSN LISTIKELQE QL RNCKEQV HTQEAQLSYL KMQVSNRDGE INRLKTRLDV GGINMVKLVQ DYNYMQQNDK IKLLNHQIDY LNKENTEMDS ILR SKPYIA LSQANVKLLA ENSSYLEKLR KTEEILEEYE RRFQIQQQSA KYTKQLSQNA LVDN

UniProtKB: Centrosomal protein, putative

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分子 #3: Rab-GAP TBC domain-containing protein

分子名称: Rab-GAP TBC domain-containing protein / 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: Tetrahymena thermophila (真核生物)
分子量理論値: 110.098609 KDa
配列文字列: MKISQQQKLS LVNRTGKLEA KKESGQDGLC DVINFKTLKK GNWHSFKLQF DSKGATYGCL DQAGNVTLFY LDKNRYTNVD VQVDSSNLT FIEKPTGYLA VSNADCSISI YSILSGKLIQ QLKWHTFKIK KLQVNHMSGY LLSVSSDNCT IWNINTYERR K SFFVKNTR ...文字列:
MKISQQQKLS LVNRTGKLEA KKESGQDGLC DVINFKTLKK GNWHSFKLQF DSKGATYGCL DQAGNVTLFY LDKNRYTNVD VQVDSSNLT FIEKPTGYLA VSNADCSISI YSILSGKLIQ QLKWHTFKIK KLQVNHMSGY LLSVSSDNCT IWNINTYERR K SFFVKNTR YAQGCLTPAG EHLITLSQNG LVECHNTDTL KIEKKEEIGL KLKQAHLDIS AEGVYIAICG DSNYCLIGRL DC QQGFDFE LYELPNNIQS VKKIKFIRNS LLTLLGSDEK IYVLSAENNM EIVLCFELPS RKGIVDYDLN IDAKYLVVIS TLG EKYVYD FHQLIANQKK HQQDVTMKKG SFSRQTLTRM DLDELKQTLF YQTKENQMKY ANSKKQKHEG KINGETNMIM LDRV GGATP EVEIFVNGKR QDQYDIQNQK SSFLDREKLR EFLSRFGYFP EKHRVVVWNY LLKLPSNYEA FDNLARKGLH PNYLN LKST FPIQSDKLYY RTQRILSCLA HYCPVFAQLD YMPAFVFPFV KLLGTNEAFC FEVILSFLVQ WGQFFFEFAP NPPVSY LKA FMELLEYHEP QLHAQLNQNI PHTQLFNTIW SSLQVVLTDV LKREDWLCFI DFLVAHSEKP DLLLHILVAY FTYFKRH II SFTTGSQLLR FFQQDHQIRI QNLLQDALEY RNRTPPRIPQ AVVLQDNLPL TSEQYPIFNF YPKFSLDQHK EIREQIIQ E ELKATEKKRT LKELNTLQQQ LNDLEKLYEE KQDALMRHER ERREIITYEQ EMRYSKLVDA ERQVREERLQ QMKKLEEES RKAIQIAENS RKADLDFIDQ ELQKKRANDN KFIASKMEEE AILNLELKTA GRINEVLNTK TKDQNIQSIT LQAEIAQKRL DMKYKQMEQ QIDQQIEEEN IRQDHILQRK ALQREIEDDV SKQREIKGQL LAEEFERE

UniProtKB: Rab-GAP TBC domain-containing protein

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分子 #4: TBC1 domain family member 31

分子名称: TBC1 domain family member 31 / タイプ: protein_or_peptide / ID: 4 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Tetrahymena thermophila (真核生物)
分子量理論値: 141.643859 KDa
配列文字列: MNNIHTSTHV STYFNEALVD RIDTQKYLKS NGKIKKVVSD PDNHYTAAID DSGNITVIVH KLNRFVSIKP SSPATHLVFI RNGNLLVAQ QNGHISQYLA SNGKLTSVIK HHNSKLLALE YNPVTKQILT IANDQCTLWD AQSFNKIKTL FAKASYFATG S LTPNGQSL ...文字列:
MNNIHTSTHV STYFNEALVD RIDTQKYLKS NGKIKKVVSD PDNHYTAAID DSGNITVIVH KLNRFVSIKP SSPATHLVFI RNGNLLVAQ QNGHISQYLA SNGKLTSVIK HHNSKLLALE YNPVTKQILT IANDQCTLWD AQSFNKIKTL FAKASYFATG S LTPNGQSL ITSFQDGNVY VWNLNNFEVT AKSEVEENMK NQKISVSADS SRFVIGGSTA YLYYCDISHS PLCISSFALP SG STSVKKI KFTHGNYLGI ITDNQVFYAI DSSTNQIALE FRLPKNKGIT DFDINPNNLE ILIVSGNGEI FKYDLQKLFI MEM NQQQRL LERGIESSLV YNVLKPGNQN HSLKFESHVD FVSHGKENVI INGESKLVND PDDLMKANTQ RETNIIQLCT FPKH TLEKM FKSALINVNS LPNMSVHKLR QFLQKHKVYP DKHRAFIYKQ LLELPLNVDN FATLVQKGLY PSFKDLYRKY PISDS KLYQ KMQTILSCLA NFCDLFGESD QFIQIAFPFV KLFGQEELLA FEIVLCFAHQ ILQNYFVDFP HPPLDLLQNI DEIIKY NDP ILHQHLKQHN FKFVDYIWPF LSGFFTSALD KESWLQLIDY LITYNDTPEL FMFITAAFII YFKHPLMKLK SKDELEI FI SRQNPVSVNH IIESGFSLLK RTPIDKIFVK FSKILPLSKT SYNQFTNYNV FNVAHSRLTR QQETEAEAKL EESKHKIR Q MQSLTDQILS VEQRYKEKQE NLIRSEQIRR EEVIYNAEQK LSRQMKLEES IKQTRLQQLN KIQTLTRANL QAQEELRQK ELDLLEAELQ YQQQADGQQM QNRKEEIQIL EMEAQAAARL RQVMELREKE DRQRMVRMDM DIHRQQEEDR DNALIQQWRV EDTEMRLRR ETLKQKKLQD LYKYEEENEK KLIEAKMLET EILKEQQMRD IERERKLRQI AEQELDQNER YAEYVKQLEQ E QLKTQIHK LQETLNHHRQ KALNFSQARL NQAEEEKNRL LNEIQIHKNM LSAKQKTLQT GEIESQIAQK RREAEQSIIE HE KKLQSIL LDIENEKRLM YELQSQILQR EKDIKEQEGF YDVLKENEQR AINENRYQTA LQQQRFEEDL NRQTMQKSYQ QQQ RLQEQM QLREQQLIQE TDQMRETIQQ ENMKRLEEAV NNNTLLRNTN SNNQSQDYSP ANNFQRNHYK MPSEINEEEG EQDE EQ

UniProtKB: TBC1 domain family member 31

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分子 #5: POC1 centriolar protein homolog

分子名称: POC1 centriolar protein homolog / タイプ: protein_or_peptide / ID: 5 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Tetrahymena thermophila (真核生物)
分子量理論値: 71.408133 KDa
配列文字列: MKKTTIASSA VASQKQTQSK LGNTSSKITE QQTTHDPALS RSFRGHEDII TCADFDPKMR QVASCSKDSI VYVWNFKPQQ RPFKFVGHK GAVYCVKYSP DGETIASCGQ DRQIRLWQNT VQSKCSIIKA HCGAIRSMSF SADGGYLLSS SDDKTLKLWR L QDKKFMCS ...文字列:
MKKTTIASSA VASQKQTQSK LGNTSSKITE QQTTHDPALS RSFRGHEDII TCADFDPKMR QVASCSKDSI VYVWNFKPQQ RPFKFVGHK GAVYCVKYSP DGETIASCGQ DRQIRLWQNT VQSKCSIIKA HCGAIRSMSF SADGGYLLSS SDDKTLKLWR L QDKKFMCS FAGHKNWVRS GVISPDMRLV ASGSDDKTVM LWDLNFQKIV SKYSTLDDNV KISQINSYSD HMDTVSQVLF HP DGTCLIS SSFDHKIKIT DIRSNKLIQH YNAHDAQVNS ISIHPTGYFL ASAGSDSKIK IWDLRQGRQI YTLYSNDKDI TTV QFNQSG DYFATGGSQN LCMVWKTNFD QNIQNIEQVQ RSTVRQNDVE YSSGGLYAQT LFKTNKTASL SPSKKTISII PPQQ LQDTF NNRGDDELNN GRVHENKQSN SPTFSQQQQQ QQLNLSENQY PGLEIVGNQF NLQQSTLSNN NNQNNLIKSQ NDSIV SNKN AIPFHPSSEF QQSAVQQQFS QQPKLVVNNG TATYPSNFVP KVEEENIMTE AIAASMQQIY SRLDTMFQYM TNLENR VVQ SEQLQKSFVS QNHQNTLDPK QQTMNFGYSN IQDHSLSASL NDRNVVNIFQ AGALANTGSI EASLINKQQE E

UniProtKB: POC1 centriolar protein homolog

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分子 #6: Unknown Protein Chain

分子名称: Unknown Protein Chain / 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: Tetrahymena thermophila (真核生物)
分子量理論値: 2.74137 KDa
配列文字列:
(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)

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分子 #7: Unknown Protein Chain

分子名称: Unknown Protein Chain / 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: Tetrahymena thermophila (真核生物)
分子量理論値: 13.039064 KDa
配列文字列: (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) ...文字列:
(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)(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)(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)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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分子 #8: SWIM-type domain-containing protein

分子名称: SWIM-type domain-containing protein / タイプ: protein_or_peptide / ID: 8 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Tetrahymena thermophila (真核生物)
分子量理論値: 26.274373 KDa
配列文字列: MFSKAPRPAS CKPLSSKEVI SIQKGATDLG KALFYAIKHQ DYKHASELVA LGAPIERCYE VEKDVYRTTC SLLVGMICTA RIAKGHREI SYRIPDRILD TFIQLGVDLR CHCSNKFEHR CPLFVALKIL NVQNEQELFK DKNQIVQKLI INGATIKNHI Q PHKTFHNI ...文字列:
MFSKAPRPAS CKPLSSKEVI SIQKGATDLG KALFYAIKHQ DYKHASELVA LGAPIERCYE VEKDVYRTTC SLLVGMICTA RIAKGHREI SYRIPDRILD TFIQLGVDLR CHCSNKFEHR CPLFVALKIL NVQNEQELFK DKNQIVQKLI INGATIKNHI Q PHKTFHNI PHFDIEGIRS YLISKSQLAS VKKSGSLQTA TSNYHDNCKN PLPYKHNSEF SKTGYNFTFQ YK

UniProtKB: Uncharacterized protein

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分子 #9: Unknown Protein Chain

分子名称: Unknown Protein Chain / 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: Tetrahymena thermophila (真核生物)
分子量理論値: 12.868854 KDa
配列文字列: (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) ...文字列:
(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)(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)(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)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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分子 #10: Unknown Protein Chain

分子名称: Unknown Protein Chain / 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: Tetrahymena thermophila (真核生物)
分子量理論値: 13.975214 KDa
配列文字列: (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) ...文字列:
(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)(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)(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)(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)

+
分子 #11: Unknown Protein Chain

分子名称: Unknown Protein Chain / タイプ: protein_or_peptide / ID: 11 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Tetrahymena thermophila (真核生物)
分子量理論値: 14.230525 KDa
配列文字列: (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) ...文字列:
(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)(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)(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)(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)

+
分子 #12: Unknown Protein Chain

分子名称: Unknown Protein Chain / 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: Tetrahymena thermophila (真核生物)
分子量理論値: 13.719902 KDa
配列文字列: (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) ...文字列:
(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)(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)(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)(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)

+
分子 #13: Unknown Protein Chain

分子名称: Unknown Protein Chain / 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: Tetrahymena thermophila (真核生物)
分子量理論値: 8.954028 KDa
配列文字列: (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) ...文字列:
(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)(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)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

+
分子 #14: Unknown Protein Chain

分子名称: Unknown Protein Chain / 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: Tetrahymena thermophila (真核生物)
分子量理論値: 10.826337 KDa
配列文字列: (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) ...文字列:
(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)(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)(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)

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分子 #15: Unknown Protein Chain

分子名称: Unknown Protein Chain / 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: Tetrahymena thermophila (真核生物)
分子量理論値: 8.698714 KDa
配列文字列: (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) ...文字列:
(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)(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)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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実験情報

-
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filament

-
試料調製

緩衝液pH: 7.5
凍結凍結剤: ETHANE-PROPANE

-
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)
平均電子線量: 35.0 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 / 最大 デフォーカス（公称値）: 3.0 µm / 最小 デフォーカス（公称値）: 0.8 µm
実験機器
モデル: Titan Krios / 画像提供: FEI Company

+
画像解析

CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
初期モデルモデルのタイプ: OTHER
最終 再構成解像度のタイプ: BY AUTHOR / 解像度: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION / 使用した粒子像数: 155485
初期 角度割当タイプ: MAXIMUM LIKELIHOOD
最終 角度割当タイプ: MAXIMUM LIKELIHOOD

+
万見について

-
お知らせ

-
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