+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-22081 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM Structure of the Helicobacter pylori OMC | ||||||||||||||||||||||||
マップデータ | Helicobacter pylori OMC | ||||||||||||||||||||||||
試料 |
| ||||||||||||||||||||||||
キーワード | Helicobacter / T4SS / Secretion / Cag / PROTEIN TRANSPORT | ||||||||||||||||||||||||
機能・相同性 | 機能・相同性情報 | ||||||||||||||||||||||||
生物種 | Helicobacter pylori (ピロリ菌) | ||||||||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | ||||||||||||||||||||||||
データ登録者 | Sheedlo MJ / Chung JM | ||||||||||||||||||||||||
資金援助 | 米国, 7件
| ||||||||||||||||||||||||
引用 | ジャーナル: Elife / 年: 2020 タイトル: Cryo-EM reveals species-specific components within the Cag type IV secretion system core complex. 著者: Michael J Sheedlo / Jeong Min Chung / Neha Sawhney / Clarissa L Durie / Timothy L Cover / Melanie D Ohi / D Borden Lacy / 要旨: The pathogenesis of -associated gastric cancer is dependent on delivery of CagA into host cells through a type IV secretion system (T4SS). The Cag T4SS includes a large membrane-spanning core ...The pathogenesis of -associated gastric cancer is dependent on delivery of CagA into host cells through a type IV secretion system (T4SS). The Cag T4SS includes a large membrane-spanning core complex containing five proteins, organized into an outer membrane cap (OMC), a periplasmic ring (PR) and a stalk. Here, we report cryo-EM reconstructions of a core complex lacking Cag3 and an improved map of the wild-type complex. We define the structures of two unique species-specific components (Cag3 and CagM) and show that Cag3 is structurally similar to CagT. Unexpectedly, components of the OMC are organized in a 1:1:2:2:5 molar ratio (CagY:CagX:CagT:CagM:Cag3). CagX and CagY are components of both the OMC and the PR and bridge the symmetry mismatch between these regions. These results reveal that assembly of the T4SS core complex is dependent on incorporation of interwoven species-specific components. | ||||||||||||||||||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_22081.map.gz | 463.2 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-22081-v30.xml emd-22081.xml | 19.1 KB 19.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_22081_fsc.xml | 17.9 KB | 表示 | FSCデータファイル |
画像 | emd_22081.png | 139.6 KB | ||
Filedesc metadata | emd-22081.cif.gz | 7.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-22081 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22081 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_22081_validation.pdf.gz | 638.2 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_22081_full_validation.pdf.gz | 637.7 KB | 表示 | |
XML形式データ | emd_22081_validation.xml.gz | 15.9 KB | 表示 | |
CIF形式データ | emd_22081_validation.cif.gz | 22.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22081 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22081 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_22081.map.gz / 形式: CCP4 / 大きさ: 506 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Helicobacter pylori OMC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.64 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
-全体 : Helicobacter pylori Cag T4SS OMC
全体 | 名称: Helicobacter pylori Cag T4SS OMC |
---|---|
要素 |
|
-超分子 #1: Helicobacter pylori Cag T4SS OMC
超分子 | 名称: Helicobacter pylori Cag T4SS OMC / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
---|---|
由来(天然) | 生物種: Helicobacter pylori (ピロリ菌) |
-分子 #1: Type IV secretion system apparatus protein Cag3
分子 | 名称: Type IV secretion system apparatus protein Cag3 / タイプ: protein_or_peptide / ID: 1 / コピー数: 70 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Helicobacter pylori (ピロリ菌) |
分子量 | 理論値: 55.105828 KDa |
配列 | 文字列: MFRKLATAVS LIGLLTSNTL YAKEISEADK VIKATKETKE TKKEAKRLKK EAKQRQQIPD HKKPQYVSVD DTKTQALFDI YDTLNVNDK SFGDWFGNSA LKDKTYLYAM DLLDYNNYLS IENPIIKTRA MGTYADLIII TGSLEQVNGY YNILKALNKR N AKFVLKIN ...文字列: MFRKLATAVS LIGLLTSNTL YAKEISEADK VIKATKETKE TKKEAKRLKK EAKQRQQIPD HKKPQYVSVD DTKTQALFDI YDTLNVNDK SFGDWFGNSA LKDKTYLYAM DLLDYNNYLS IENPIIKTRA MGTYADLIII TGSLEQVNGY YNILKALNKR N AKFVLKIN ENMPYAQATF LRVPKRSDPN AHTLDKGASI DENKLFEQQK KMYFNYANDV ICRPDDEVCS PLRDEMVAMP TS DSVTQKP NIIAPYSLYR LKETNNANEA QPSPYATATA PENSKEKLIE ELIANSQLVA NEEEREKKLL AEKEKQEAEL AKY KLKDLE NQKKLKALEA ELKKKNAKKP RVVEVPVSPQ TSNSDETMRV VKEKENYNGL LVDKETTIKR SYEGTLISEN SYSK KTPLN PNDLRSLEEE IKSYYIKSNG LCYTNGINLY VKIKNDPYKE GMLCGYESVQ NLLSPLKDKL KYDKQKLQKA LLKDS K UniProtKB: Type IV secretion system apparatus protein Cag3 |
-分子 #2: Type IV secretion system apparatus protein CagM
分子 | 名称: Type IV secretion system apparatus protein CagM / タイプ: protein_or_peptide / ID: 2 / コピー数: 28 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Helicobacter pylori (ピロリ菌) |
分子量 | 理論値: 43.830027 KDa |
配列 | 文字列: MLAKIVFSSL VAFGVLSANV EQFGSFFNEI KKEQEEVAAK EDALKARKKL LNNTHDFLED LIFRKQKIKE LMDHRAKVLS DLENKYKKE KEALEKETRG KILTAKSKAY GDLEQALKDN PLYRKLLPNP YAYVLNQETF TKEDRERLSY YYPQVKTSSI F KKTTATTK ...文字列: MLAKIVFSSL VAFGVLSANV EQFGSFFNEI KKEQEEVAAK EDALKARKKL LNNTHDFLED LIFRKQKIKE LMDHRAKVLS DLENKYKKE KEALEKETRG KILTAKSKAY GDLEQALKDN PLYRKLLPNP YAYVLNQETF TKEDRERLSY YYPQVKTSSI F KKTTATTK DKAQALLQMG VFSLDEEQNK KASRLALSYK QAIEEYSNNV SNLLSRKELD NIDYYLQLER NKFDSKAKDI AQ KATNTLI FNSERLAFSM AIDKINEKYL RGYEAFSNLL KNVKDDVELN TLTKNFTNQK LSFAQKQKLC LLVLDSFNFD TQS KKSILK KTNEYNIFVD SDPMMSDKTT MQKEHYKIFN FFKTVVSAYR NNVAKNNPFE UniProtKB: Type IV secretion system apparatus protein CagM |
-分子 #3: Type IV secretion system apparatus protein CagT
分子 | 名称: Type IV secretion system apparatus protein CagT / タイプ: protein_or_peptide / ID: 3 / コピー数: 28 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Helicobacter pylori (ピロリ菌) |
分子量 | 理論値: 32.418971 KDa |
配列 | 文字列: MKLRASVLIG ATILCLILSA CSNYAKKVVK QKNHVYTPVY NELIEKYSEI PLNDKLKDTP FMVQVKLPNY KDYLLDNKQV VLTFKLVHH SKKITLIGDA NKILQYKNYF QANGARSDID FYLQPTLNQK GVVMIASNYN DNPNSKEKPQ TFDVLQGSQP M LGANTKNL ...文字列: MKLRASVLIG ATILCLILSA CSNYAKKVVK QKNHVYTPVY NELIEKYSEI PLNDKLKDTP FMVQVKLPNY KDYLLDNKQV VLTFKLVHH SKKITLIGDA NKILQYKNYF QANGARSDID FYLQPTLNQK GVVMIASNYN DNPNSKEKPQ TFDVLQGSQP M LGANTKNL HGYDVSGANN KQVINEVARE KAQLEKINQY YKTLLQDKEQ EYTTRKNNQR EILETLSNRA GYQMRQNVIS SE IFKNGNL NMQAKEEEVR EKLQEERENE YLRNQIRSLL SGK UniProtKB: Cag pathogenicity island protein |
-分子 #4: Unknown protein fragment
分子 | 名称: Unknown protein fragment / タイプ: protein_or_peptide / ID: 4 / コピー数: 14 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Helicobacter pylori (ピロリ菌) |
分子量 | 理論値: 13.634798 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) |
-分子 #5: Type IV secretion system apparatus protein CagX
分子 | 名称: Type IV secretion system apparatus protein CagX / タイプ: protein_or_peptide / ID: 5 / コピー数: 14 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Helicobacter pylori (ピロリ菌) |
分子量 | 理論値: 60.72048 KDa |
配列 | 文字列: MGQAFFKKIV GCFCLGYLFL SSAIEAAALD IKNFNRGRVK VVNKKIAYLG DEKPITIWTS LDNVTVIQLE KDETISYITT GFNKGWSIV PNSNHIFIQP KSVKSNLMFE KEAVNFALMT RDYQEFLKTK KLIVDAPDPK ELEEQKKALE KEKEAKEQAQ K AQKDKREK ...文字列: MGQAFFKKIV GCFCLGYLFL SSAIEAAALD IKNFNRGRVK VVNKKIAYLG DEKPITIWTS LDNVTVIQLE KDETISYITT GFNKGWSIV PNSNHIFIQP KSVKSNLMFE KEAVNFALMT RDYQEFLKTK KLIVDAPDPK ELEEQKKALE KEKEAKEQAQ K AQKDKREK RKEERAKNRA NLENLTNAMS NPQNLSNNKN LSEFIKQQRE NELDQMERLE DMQEQAQANA LKQIEELNKK QA EETIKQR AKDKINIKTD KPQKSPEDNS IELSPSDSAW RTNLVVRTNK ALYQFILRIA QKDNFASAYL TVKLEYPQRH EVS SVIEEE LKKREEAKRQ KELIKQENLN TTAYINRVMM ASNEQIINKE KIREEKQKII LDQAKALETQ YVHNALKRNP VPRN YNYYQ APEKRSKHIM PSEIFDDGTF TYFGFKNITL QPAIFVVQPD GKLSMTDAAI DPNMTNSGLR WYRVNEIAEK FKLIK DKAL VTVINKGYGK NPLTKNYNIK NYGELERVIK KLPLVRDK UniProtKB: Type IV secretion system apparatus protein CagX |
-分子 #6: Cag pathogenicity island protein (Cag7)
分子 | 名称: Cag pathogenicity island protein (Cag7) / タイプ: protein_or_peptide / ID: 6 / コピー数: 14 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Helicobacter pylori (ピロリ菌) |
分子量 | 理論値: 219.748641 KDa |
配列 | 文字列: MNEENDKLET SKKAQQDSPQ DLSNEEATEA NHFENLLKES KESSDHHLDN PTETQTHFDG DKSEETQTQM DSEGNETSES SNGSLADKL FKKARKLVDN KKPFTQQKNL DEETQELNEE DDQENNEYQE ETQTDLIDDE TSKKTQQHSP QDLSNEEATE A NHFENLLK ...文字列: MNEENDKLET SKKAQQDSPQ DLSNEEATEA NHFENLLKES KESSDHHLDN PTETQTHFDG DKSEETQTQM DSEGNETSES SNGSLADKL FKKARKLVDN KKPFTQQKNL DEETQELNEE DDQENNEYQE ETQTDLIDDE TSKKTQQHSP QDLSNEEATE A NHFENLLK ESKESSDHHL DNPTETQTNF DGDKSEETQT QMDSEGNETS ESSNGSLADK LFKKARKLVD NKKPFTQQKN LD EETQELN EEDDQENNEY QEETQTDLID DETSKKTQQH SPQDLSNEEA TEANHFENLL KESKESSDHH LDNPTETQTN FDG DKSEEI TDDSNDQEII KGSKKKYIIG GIVVAVLIVI ILFSRSIFHY FMPLEDKSSR FSKDRNLYVN DEIQIRQEYN RLLK ERNEK GNMIDKNLFF NDDPNRTLYN YLNIAEIEDK NPLRAFYECI SNGGNYEECL KLIKDKKLQD QMKKTLEAYN DCIKN AKTE EERIKCLDLI KDENLKKSLL NQQKVQVALD CLKNAKTDEE RNECLKLIND PEIREKFRKE LELQKELQEY KDCIKN AKT EAEKNKCLKG LSKEAIERLK QQALDCLKNA KTDEERNECL KNIPQDLQKE LLADMSVKAY KDCVSKARNE KEKQECE KL LTPEARKKLE QQVLDCLKNA KTDEERKKCL KDLPKDLQSD ILAKESLKAY KDCVSQAKTE AEKKECEKLL TPEAKKLL E EEAKESVKAY LDCVSQAKTE AEKKECEKLL TPEAKKKLEE AKKSVKAYLD CVSRARNEKE KKECEKLLTP EAKKLLEQQ ALDCLKNAKT DKERKKCLKD LPKDLQKKVL AKESVKAYLD CVSQAKTEAE KKECEKLLTP EARKLLEEAK KSVKAYLDCV SQAKTEAEK KECEKLLTPE ARKLLEE(UNK)AK ESVKAYLDCV SQAKNEAEKK ECEKLLTLES KKKLEEAKKS VKAYLDC VS QAKTEAEKKE CEKLLTPEAK KLLEQQALDC LKNAKTEADK KRCVKDLPKD LQKKVLAKES LKAYKDCVSK ARNEKEKK E CEKLLTPEAK KLLEEAKKSV KAYLDCVSQA KTEAEKKECE KLLTPEARKL LEEAKESVKA YKDCVSKARN EKEKKECEK LLTPEAKKLL EQQVLDCLKN AKTEADKKRC VKDLPKDLQK KVLAKESVKA YLDCVSRARN EKEKKECEKL LTPEAKKLLE EAKESLKAY KDCLSQARNE EERRACEKLL TPEARKLLEQ EVKKSIKAYL DCVSRARNEK EKKECEKLLT PEARKFLAKQ V LNCLEKAG NEEERKACLK NLPKDLQENI LAKESLKAYK DCLSQARNEE ERRACEKLLT PEARKLLEQE VKKSVKAYLD CV SRARNEK EKKECEKLLT PEARKFLAKE LQQKDKAIKD CLKNADPNDR AAIMKCLDGL SDEEKLKYLQ EAREKAVADC LAM AKTDEE KRKCQNLYSD LIQEIQNKRT QNKQNQLSKT ERLHQASECL DNLDDPTDQE AIEQCLEGLS DSERALILGI KRQA DEVDL IYSDLRNRKT FDNMAAKGYP LLPMDFKNGG DIATINATNV DADKIASDNP IYASIEPDIA KQYETEKTIK DKNLE AKLA KALGGNKKDD DKEKSKKSTA EAKAENNKID KDVAETAKNI SEIALKNKKE KSGEFVDENG NPIDDKKKAE KQDETS PVK QAFIGKSDPT FVLAQYTPIE ITLTSKVDAT LTGIVSGVVA KDVWNMNGTM ILLDKGTKVY GNYQSVKGGT PIMTRLM IV FTKAITPDGV IIPLANAQAA GMLGEAGVDG YVNNHFMKRI GFAVIASVVN SFLQTAPIIA LDKLIGLGKG RSERTPEF N YALGQAINGS MQSSAQMSNQ ILGQLMNIPP SFYKNEGDSI KILTMDDIDF SGVYDVKITN KSVVDEIIKQ STKTLSREH EEITTSPKGG N UniProtKB: Cag pathogenicity island protein (Cag7) |
-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 | particle |
-試料調製
緩衝液 | pH: 7 |
---|---|
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | #0 - Image recording ID: 1 #0 - フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) #0 - 平均電子線量: 59.2 e/Å2 / #1 - Image recording ID: 2 #1 - フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) #1 - 平均電子線量: 59.0 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |