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- EMDB-8479: Cryo-EM map of the transcriptional Mediator -

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基本情報

登録情報
データベース: EMDB / ID: EMD-8479
タイトルCryo-EM map of the transcriptional Mediator
マップデータSp Mediator
試料
  • 複合体: Mediator complex
    • タンパク質・ペプチド: x 16種
キーワードtranscription / transcriptional / Mediator / Head / Middle / Tail / Srb / RNA polymerase II / Med
機能・相同性
機能・相同性情報


core mediator complex / mediator complex / termination of RNA polymerase II transcription / positive regulation of transcription initiation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / euchromatin / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II ...core mediator complex / mediator complex / termination of RNA polymerase II transcription / positive regulation of transcription initiation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / euchromatin / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleus / cytoplasm
類似検索 - 分子機能
Mediator complex, subunit Med6, fungi / Mediator complex, subunit Med27 / Mediator complex subunit 27 / Mediator complex, subunit Med31 / Mediator complex, subunit Med21 / Mediator of RNA polymerase II, subunit Med31 superfamily / Mediator complex, subunit Med7 superfmaily / SOH1 / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 ...Mediator complex, subunit Med6, fungi / Mediator complex, subunit Med27 / Mediator complex subunit 27 / Mediator complex, subunit Med31 / Mediator complex, subunit Med21 / Mediator of RNA polymerase II, subunit Med31 superfamily / Mediator complex, subunit Med7 superfmaily / SOH1 / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / MED7 protein / Mediator complex, subunit Med20 / Mediator complex, subunit Med14 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex subunit MED14 / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex protein / Mediator complex, subunit Med18 / Med18 protein
類似検索 - ドメイン・相同性
Uncharacterized protein C24C9.04 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 27 / Mediator of RNA polymerase II transcription subunit 11 ...Uncharacterized protein C24C9.04 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 27 / Mediator of RNA polymerase II transcription subunit 11 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 6 / Mediator of RNA polymerase II transcription subunit 31
類似検索 - 構成要素
生物種Schizosaccharomyces pombe (分裂酵母)
手法単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.4 Å
データ登録者Tsai K-L / Yu X
引用ジャーナル: Nature / 年: 2017
タイトル: Mediator structure and rearrangements required for holoenzyme formation.
著者: Kuang-Lei Tsai / Xiaodi Yu / Sneha Gopalan / Ti-Chun Chao / Ying Zhang / Laurence Florens / Michael P Washburn / Kenji Murakami / Ronald C Conaway / Joan W Conaway / Francisco J Asturias /
要旨: The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is ...The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is crucial for determining how the complex influences transcription initiation and conveys regulatory information to the basal transcription machinery. Here we present a 4.4 Å resolution cryo-electron microscopy map of Schizosaccharomyces pombe Mediator in which conserved Mediator subunits are individually resolved. The essential Med14 subunit works as a central backbone that connects the Mediator head, middle and tail modules. Comparison with a 7.8 Å resolution cryo-electron microscopy map of a Mediator-RNA polymerase II holoenzyme reveals that changes in the structure of Med14 facilitate a large-scale Mediator rearrangement that is essential for holoenzyme formation. Our study suggests that access to different conformations and crosstalk between structural elements are essential for the Mediator regulation mechanism, and could explain the capacity of the complex to integrate multiple regulatory signals.
履歴
登録2016年11月26日-
ヘッダ(付随情報) 公開2017年3月8日-
マップ公開2017年3月8日-
更新2024年3月13日-
現状2024年3月13日処理サイト: RCSB / 状態: 公開

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構造の表示

ムービー
  • 表面図（断面を密度値に従い着色）
  • 表面レベル: 0.016
  • UCSF Chimeraによる作画
  • ダウンロード
  • 表面図（半径に従い着色）
  • 表面レベル: 0.016
  • UCSF Chimeraによる作画
  • ダウンロード
  • あてはめたモデルとの重ね合わせ
  • 原子モデル: PDB-5u0p
  • 表面レベル: 0.016
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
構造ビューアEMマップ:
SurfViewMolmilJmol/JSmol
添付画像

emd_8479.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_8479.map.gz / 形式: CCP4 / 大きさ: 166.4 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈Sp Mediator
ボクセルのサイズX=Y=Z: 1.31 Å
密度
表面レベル登録者による: 0.016 / ムービー #1: 0.016
最小 - 最大-0.017003836 - 0.07525921
平均 (標準偏差)-0.000033825316 (±0.0022060836)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ352352352
Spacing352352352
セルA=B=C: 461.12 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z461.120461.120461.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.0170.075-0.000

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添付データ

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マスク #1

ファイルemd_8479_msk_1.map
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 : Mediator complex

全体名称: Mediator complex
要素
  • 複合体: Mediator complex
    • タンパク質・ペプチド: Mediator complex subunit 14
    • タンパク質・ペプチド: Mediator complex subunit 6
    • タンパク質・ペプチド: Mediator complex subunit 8
    • タンパク質・ペプチド: Mediator complex subunit 17
    • タンパク質・ペプチド: Mediator complex subunit 18
    • タンパク質・ペプチド: Mediator complex subunit 20
    • タンパク質・ペプチド: Mediator complex subunit 11
    • タンパク質・ペプチド: Mediator complex subunit 22
    • タンパク質・ペプチド: Mediator complex subunit 4
    • タンパク質・ペプチド: Mediator complex subunit 7
    • タンパク質・ペプチド: Mediator complex subunit 21
    • タンパク質・ペプチド: Mediator complex subunit 31
    • タンパク質・ペプチド: Mediator complex subunit 9
    • タンパク質・ペプチド: Mediator complex subunit 27
    • タンパク質・ペプチド: Mediator complex subunit 19
    • タンパク質・ペプチド: Mediator complex subunit 10

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超分子 #1: Mediator complex

超分子名称: Mediator complex / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all
由来(天然)生物種: Schizosaccharomyces pombe (分裂酵母)

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分子 #1: Mediator complex subunit 14

分子名称: Mediator complex subunit 14 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 105.382461 KDa
配列文字列: MEPPAIPHIT EGFYPLPEIV ETFSHHVLQE LVSLAEVLPS MSNVEKKKKI LDWLLRSRAF TMRLLVLARW VHLSPSVHRC IDVVAFLQG QKFCFQNLVH VLQDIRYQLS FARLRNSDLV TALDILSTGT SLRLANAPTS KLYMLSESPL STKQILQTLH A LNMLIRIR ...文字列:
MEPPAIPHIT EGFYPLPEIV ETFSHHVLQE LVSLAEVLPS MSNVEKKKKI LDWLLRSRAF TMRLLVLARW VHLSPSVHRC IDVVAFLQG QKFCFQNLVH VLQDIRYQLS FARLRNSDLV TALDILSTGT SLRLANAPTS KLYMLSESPL STKQILQTLH A LNMLIRIR LSLYEIIPTP FQHFTIANGR CTFTVPNEFS VSLTTNSQDP KSTGISFQWI VVDFQFHLPD FSSTPAKYRV FI ELHLNEE IAAAFVLQKP ILPLIYNILH KFCLYQRLNL LSQQTFQLSR ESWLGHLRGV YDEKPPRLRL YYWPQLNVKK EGK PGKIGH YIHIFVNTQP ISAFERTLSS KRSSCEYDHF LLLVEWHHDG IVEHVPLDDH MDAQHLLLLI TQKHAQLILE QIRK ELHPN IFSEHVGGGL KIHVFDNEII VKVNSVTGRL VLSSSASPLS PPRHLRAAEK NIALNTQPPA QILNRLYFFC IQTQL LEVA QCAELHAVQG YYSFPYLTFS KGKWRKDGDS LWVLAYNVES NSWSVRLLNA AGQTLYTQDV HTTKGTLSIE SFSRLS YLL EVQILLFNVQ TACQARGMPF EYLPIPPKAL IEDDFTTYVQ TGCLCIMMPS SNEDMLPVVF VRAHDGQLIF DSRIKGK LP YQSETETEKN CYIDWRTGRI TIRVQNFSSF EKTWIGLLKL VALSKTSAFN VDCITLKHVD FTYLDDEKFR ATIHDDNT F TLHFFNRHSP FHLISQFLQD TFSDGPSAIQ PLRVIMDRTR GVLVAQELGY VVLARSLRQY RIILSKNHGI QVLLNRHGC ILQDLSYLSA DSRYLEGTQT LTSQWEPCSW LNTVWEGDLG DDELNGQIEA APEMHLIKMN KTADLTAILK RILAISRKK (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(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: Mediator of RNA polymerase II transcription subunit 14

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分子 #2: Mediator complex subunit 6

分子名称: Mediator complex subunit 6 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 24.928947 KDa
配列文字列: MASGAPPSVD LTSIQWRMPE WVQSMGGLRT ENVLEYFSQS PFYSHKSNNE MLKMQSQFNA LDLGDLNSQL KRLTGIQFVI IHERPPFLW VIQKQNRLNE NEVKPLTVYF VCNENIYMAP NAYTLLATRM LNATYCFQKA LTKIEKFPQY NPQEGYTYPK L SNDNLEVD ...文字列:
MASGAPPSVD LTSIQWRMPE WVQSMGGLRT ENVLEYFSQS PFYSHKSNNE MLKMQSQFNA LDLGDLNSQL KRLTGIQFVI IHERPPFLW VIQKQNRLNE NEVKPLTVYF VCNENIYMAP NAYTLLATRM LNATYCFQKA LTKIEKFPQY NPQEGYTYPK L SNDNLEVD HSNTNEPADE NKNQSIENAD YSFSPEDFSV VRAFMQSLHS SKEAPDVK

UniProtKB: Mediator of RNA polymerase II transcription subunit 6

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分子 #3: Mediator complex subunit 8

分子名称: Mediator complex subunit 8 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 23.360068 KDa
配列文字列: MEDISTEKTV ESLEAIRHRI AQIVQSLTHF LAILHQSESL SPWPTIHKNF NILLSQIHSL SNNLAAHSHT LQTTSIYPSL EFPVKEQEP LLTTLLRTKA LPEVEEWEAN TLQEYEASIS SQPKKKEAND AYQKDQLWDQ ARIIFMEERE NYSWFDFVTR R QESEGEFV ...文字列:
MEDISTEKTV ESLEAIRHRI AQIVQSLTHF LAILHQSESL SPWPTIHKNF NILLSQIHSL SNNLAAHSHT LQTTSIYPSL EFPVKEQEP LLTTLLRTKA LPEVEEWEAN TLQEYEASIS SQPKKKEAND AYQKDQLWDQ ARIIFMEERE NYSWFDFVTR R QESEGEFV SQRQLEIDRA TEEQNANQML TDILSFMKSG KR

UniProtKB: Mediator of RNA polymerase II transcription subunit 8

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分子 #4: Mediator complex subunit 17

分子名称: Mediator complex subunit 17 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 62.55141 KDa
配列文字列: MAEEANKDAD ISSLSLSLDP EIIGGQNNFL ENNLQQIFQK IIQERGPFRD LKEEDLQKEL QKESIKDESS AKSSETENVL EFATLDSKR NVNDTEVESM DSQAYKKELI EQIMIAQTEC SLALDMTSLL LSKFKENSIE TISPFLKSTV PPSSLQFSRS Q PPESKESD ...文字列:
MAEEANKDAD ISSLSLSLDP EIIGGQNNFL ENNLQQIFQK IIQERGPFRD LKEEDLQKEL QKESIKDESS AKSSETENVL EFATLDSKR NVNDTEVESM DSQAYKKELI EQIMIAQTEC SLALDMTSLL LSKFKENSIE TISPFLKSTV PPSSLQFSRS Q PPESKESD ATLAKCWKEK SLTSSCKFLF EAKERLTSVV ETEHEYYTEL VKVKEASWPL FNSQGSNHLS VQYSCLGGIS LG LGLIRMK PESKSFEVQS SLLYSQAALK ISILNKDRDE IGSSTWSWPS QNCNSVLLKD IYKLQEILFE MDIWNSLLQE AQS CGNQGV NFTGDEILVP ISDDHVVRIT LETSSKNTES GFTEDKKSNE DTSTNFVTIK QEKELLKCLC DTLNAIAHIL FLKH CRKSD RRSQQPELYM AIDANAPLIL RPLIFYYNLN QESLEFQRWL KQRDISFKFM PNYPWEKAKD FLELENSLSI NRLSI SWRI MVSNFEPAIF IQHTPTLHGT DKSVWRCKDQ YSSNQFSSLK NVCQYIEHHI NSLSRRSKKT E

UniProtKB: Mediator of RNA polymerase II transcription subunit 17

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分子 #5: Mediator complex subunit 18

分子名称: Mediator complex subunit 18 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 24.056377 KDa
配列文字列: MQELYLLGVV PSRRFEAVVN SLSKTLDGPK TILEFWVVYR PKDVPPNLPR QPDSWLRLCS NIESHDETDT EWSKNTQWSM YLEGNSEPK REDKCGIRPV NRAKLTNGSV TEFVEKMGYE FSHEYIIQGL EYFFFDTTVR IYQTLIPSQQ RSIKPPFHPM N EEQPWILH ...文字列:
MQELYLLGVV PSRRFEAVVN SLSKTLDGPK TILEFWVVYR PKDVPPNLPR QPDSWLRLCS NIESHDETDT EWSKNTQWSM YLEGNSEPK REDKCGIRPV NRAKLTNGSV TEFVEKMGYE FSHEYIIQGL EYFFFDTTVR IYQTLIPSQQ RSIKPPFHPM N EEQPWILH VYTHVADASN QVAMAKAEAN LTKVKTLLSA FCDLKNVRL

UniProtKB: Mediator of RNA polymerase II transcription subunit 18

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分子 #6: Mediator complex subunit 20

分子名称: Mediator complex subunit 20 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 22.374775 KDa
配列文字列: MPVHGVIYYS SPSMATFLSP AQDNLVRTYF AQHLKKWVVQ YKLYRNAVTP KTLEFLKQNI NPSMLACVDE ATMIDAEPEL EDIIVRTKL WNFRQSFTIE GSIYEVGSFK VAIANVLQKS VWKGILFHVT YDGTESVDLA RPIIQEFFLK CFLQNNKSVT P VYESFFNQ ...文字列:
MPVHGVIYYS SPSMATFLSP AQDNLVRTYF AQHLKKWVVQ YKLYRNAVTP KTLEFLKQNI NPSMLACVDE ATMIDAEPEL EDIIVRTKL WNFRQSFTIE GSIYEVGSFK VAIANVLQKS VWKGILFHVT YDGTESVDLA RPIIQEFFLK CFLQNNKSVT P VYESFFNQ PRHSLDSKLL LQLFKQRIDT VSQRT

UniProtKB: Mediator of RNA polymerase II transcription subunit 20

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分子 #7: Mediator complex subunit 11

分子名称: Mediator complex subunit 11 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 13.1188 KDa
配列文字列:
MTNSDDDLFS EKSTSSDTQQ VQNILELEAK IPDILSSAGK CIEAIQLNNS LEDFRKYSKE FLETVEFIST GLRRQALELE KAEVPVVSL QPKKRYASTP LSNLIFDQSS KLIPKYC

UniProtKB: Mediator of RNA polymerase II transcription subunit 11

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分子 #8: Mediator complex subunit 22

分子名称: Mediator complex subunit 22 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 15.396165 KDa
配列文字列:
MSSDSFQRQL VQRTNTLNSS IDNATLTILS RFQDILDIAI NEGKDKYTVA PEVYQIECHT VSMVRAVEQL LDVSRQIKSY WLTNSLSTS FPTVDYSEPD LEKVKRTLTK LQNHLLEVSL IEPEASETTE APTVSDT

UniProtKB: Mediator of RNA polymerase II transcription subunit 22

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分子 #9: Mediator complex subunit 4

分子名称: Mediator complex subunit 4 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 20.35801 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)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(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: Mediator complex subunit 7

分子名称: Mediator complex subunit 7 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 43.573094 KDa
配列文字列: MEPNEGVQLF SAFPPPPPYY KLFTRENIEK VISNMEKEAK HEDDANTLQP KTEEEIESLA KLFKKPSCLT SGTYQMFGDT WRLDEAIPS LKEFGIPELY KDIKDGEDEI EVVEYDPKSN AIVGTSFTRV HDYDKNSPIE NEKILEDDQH TAMKEKDNES D KTMKDVEE ...文字列:
MEPNEGVQLF SAFPPPPPYY KLFTRENIEK VISNMEKEAK HEDDANTLQP KTEEEIESLA KLFKKPSCLT SGTYQMFGDT WRLDEAIPS LKEFGIPELY KDIKDGEDEI EVVEYDPKSN AIVGTSFTRV HDYDKNSPIE NEKILEDDQH TAMKEKDNES D KTMKDVEE KTEPSLKKEE EDIQMKEPLD SQDTGAVSAS SVNEGFRADQ KSKDGETSDL IKIPRRAYEL RFLSRSLMLN FL ELLGIMA KAPEQFPSKV ENIRVLLLNL HHLINDYRPH QSRESLIMLL EKQLKHEESQ VELLRTHNRQ MTETLEKYKS LDF NMEKEG DVIQQLKSSI KKPLSGAEDE QKSRSMFSKN DEKLKKSLEL MEDVIKRDLS

UniProtKB: Mediator of RNA polymerase II transcription subunit 7

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分子 #11: Mediator complex subunit 21

分子名称: Mediator complex subunit 21 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 15.821031 KDa
配列文字列:
MACRCTQLQD TIDEVATQFY SSIHYLSSHH DFVPLPGQEK VSDSKVNPIS AEELQFAQRD LAKDLVTKFM QIDTLINQLP GISTAPKHQ LEKIKKLQNS IEEKQLERKS LESENEDLKL QLAKRIETFG RLSCVLFQP

UniProtKB: Mediator of RNA polymerase II transcription subunit 21

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分子 #12: Mediator complex subunit 31

分子名称: Mediator complex subunit 31 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 16.913975 KDa
配列文字列:
METKWLLSKV PDDKSRFEIE LEFVQMLSNP WYLNFLAQHK YFEDEAFLQY LEYMEYWREP EYVKFIIYPT CLHMLTLLKN PQFRNDISR ADLSKQVNDE IYYEWLGKGL QQYGSADDAT LSQPQQEEDE KKVDVKKENE

UniProtKB: Mediator of RNA polymerase II transcription subunit 31

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分子 #13: Mediator complex subunit 9

分子名称: Mediator complex subunit 9 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 13.810964 KDa
配列文字列:
MDPAHHIKDT SAELLSQQDF SILQSRLLEF LASQEARETV TASKELTLLR QGIRQLKEKV SKMEPEEMTV KEKKSIIEIL KARIALKKA FLKMALSESN DTVVKKEDVR ESPVDTFMEN AT

UniProtKB: Uncharacterized protein C24C9.04

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分子 #14: Mediator complex subunit 27

分子名称: Mediator complex subunit 27 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 31.132693 KDa
配列文字列: MSLEEQRTRD ELKHKLLDLN QLHEQLAELR TICPSLLKLL HPETGTSRKF EKSAQEAIEK VNSFYTHLKS SQNVFDYAEK SLQADSSNL LPTYLYNSED LSNDTENNET KSINGKSALD LKEPHHSELH DNDNFQNSDI NIESFKGDIE ASGSILTTHE N KSFTLKLA ...文字列:
MSLEEQRTRD ELKHKLLDLN QLHEQLAELR TICPSLLKLL HPETGTSRKF EKSAQEAIEK VNSFYTHLKS SQNVFDYAEK SLQADSSNL LPTYLYNSED LSNDTENNET KSINGKSALD LKEPHHSELH DNDNFQNSDI NIESFKGDIE ASGSILTTHE N KSFTLKLA NELEFIFFHD TRGKFSVYCS SSKDDAITFS INRNNNFLGN LWSLMPKILD YQHLYSKPCD FCKSLISPVY LE LPSVRRN ANSTVKPTSK DILALHAECV PAQSDL

UniProtKB: Mediator of RNA polymerase II transcription subunit 27

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分子 #15: Mediator complex subunit 19

分子名称: Mediator complex subunit 19 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 11.847596 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)

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分子 #16: Mediator complex subunit 10

分子名称: Mediator complex subunit 10 / 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: Schizosaccharomyces pombe (分裂酵母)
分子量理論値: 11.251861 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)

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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1 mg/mL
緩衝液pH: 7.4
詳細: 20 mM HEPES, pH 7.4, 200 mM potassium acetate, 5 mM b-Mercaptoethanol, 0.01% NP-40
凍結凍結剤: ETHANE

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電子顕微鏡法

顕微鏡FEI TITAN KRIOS
撮影フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
検出モード: COUNTING / 実像数: 11181 / 平均露光時間: 7.0 sec. / 平均電子線量: 9.6 e/Å2
電子線加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
電子光学系C2レンズ絞り径: 100.0 µm / 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）: 4.0 µm / 最小 デフォーカス（公称値）: 1.0 µm / 倍率（公称値）: 22500
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

初期モデルモデルのタイプ: NONE
最終 再構成想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 1.4) / 使用した粒子像数: 42484
初期 角度割当タイプ: ANGULAR RECONSTITUTION / ソフトウェア - 名称: RELION (ver. 1.4)
最終 角度割当タイプ: ANGULAR RECONSTITUTION / ソフトウェア - 名称: RELION (ver. 1.4)
FSC曲線 (解像度の算出)

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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://pdbjlvh1.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