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- PDB-6x6s: Cryo-EM Structure of the Helicobacter pylori OMC -

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基本情報

登録情報
データベース: PDB / ID: 6x6s
タイトルCryo-EM Structure of the Helicobacter pylori OMC
要素
  • (Type IV secretion system apparatus protein ...) x 4
  • Cag pathogenicity island protein (Cag7)
  • Unknown protein fragment
キーワードPROTEIN TRANSPORT / Helicobacter / T4SS / Secretion / Cag
機能・相同性
機能・相同性情報


Cag pathogenicity island protein Cag12 / Cag pathogenicity island protein Cag12 / CagY type 1 repeat / CagY type 1 repeat / DC-EC / DC-EC Repeat / Type IV secretion system CagX conjugation protein / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily ...Cag pathogenicity island protein Cag12 / Cag pathogenicity island protein Cag12 / CagY type 1 repeat / CagY type 1 repeat / DC-EC / DC-EC Repeat / Type IV secretion system CagX conjugation protein / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / Type IV secretion system, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / Prokaryotic membrane lipoprotein lipid attachment site profile.
類似検索 - ドメイン・相同性
Type IV secretion system apparatus protein Cag3 / Type IV secretion system apparatus protein CagM / Type IV secretion system apparatus protein CagX / Cag pathogenicity island protein (Cag7) / Cag pathogenicity island protein
類似検索 - 構成要素
生物種Helicobacter pylori (ピロリ菌)
手法電子顕微鏡法 / 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, M.J. / Chung, J.M. / Sawhney, N. / Durie, C.L. / Cover, T.L. / Ohi, M.D. / Lacy, D.B.
資金援助 米国, 7件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI118932 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)CA116087 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI039657 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 米国
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)2T32DK007673 米国
National Institutes of Health/Office of the DirectorS10OD020011 米国
Other government1I01BX004447 米国
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
登録2020年5月29日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年10月7日Provider: repository / タイプ: Initial release
改定 1.12021年4月14日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
改定 1.22024年3月6日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

ムービー
  • 登録構造単位
  • Jmolによる作画
  • ダウンロード
  • 単純化した表面モデル + あてはめた原子モデル
  • マップデータ: EMDB-22081
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-22081
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
AA: Type IV secretion system apparatus protein Cag3
AB: Type IV secretion system apparatus protein Cag3
AC: Type IV secretion system apparatus protein Cag3
AD: Type IV secretion system apparatus protein Cag3
AE: Type IV secretion system apparatus protein Cag3
AM: Type IV secretion system apparatus protein CagM
AT: Type IV secretion system apparatus protein CagT
AU: Unknown protein fragment
AX: Type IV secretion system apparatus protein CagX
AY: Cag pathogenicity island protein (Cag7)
Am: Type IV secretion system apparatus protein CagM
At: Type IV secretion system apparatus protein CagT
BA: Type IV secretion system apparatus protein Cag3
BB: Type IV secretion system apparatus protein Cag3
BC: Type IV secretion system apparatus protein Cag3
BD: Type IV secretion system apparatus protein Cag3
BE: Type IV secretion system apparatus protein Cag3
BM: Type IV secretion system apparatus protein CagM
BT: Type IV secretion system apparatus protein CagT
BU: Unknown protein fragment
BX: Type IV secretion system apparatus protein CagX
BY: Cag pathogenicity island protein (Cag7)
Bm: Type IV secretion system apparatus protein CagM
Bt: Type IV secretion system apparatus protein CagT
CA: Type IV secretion system apparatus protein Cag3
CB: Type IV secretion system apparatus protein Cag3
CC: Type IV secretion system apparatus protein Cag3
CD: Type IV secretion system apparatus protein Cag3
CE: Type IV secretion system apparatus protein Cag3
CM: Type IV secretion system apparatus protein CagM
CT: Type IV secretion system apparatus protein CagT
CU: Unknown protein fragment
CX: Type IV secretion system apparatus protein CagX
CY: Cag pathogenicity island protein (Cag7)
Cm: Type IV secretion system apparatus protein CagM
Ct: Type IV secretion system apparatus protein CagT
DA: Type IV secretion system apparatus protein Cag3
DB: Type IV secretion system apparatus protein Cag3
DC: Type IV secretion system apparatus protein Cag3
DD: Type IV secretion system apparatus protein Cag3
DE: Type IV secretion system apparatus protein Cag3
DM: Type IV secretion system apparatus protein CagM
DT: Type IV secretion system apparatus protein CagT
DU: Unknown protein fragment
DX: Type IV secretion system apparatus protein CagX
DY: Cag pathogenicity island protein (Cag7)
Dm: Type IV secretion system apparatus protein CagM
Dt: Type IV secretion system apparatus protein CagT
EA: Type IV secretion system apparatus protein Cag3
EB: Type IV secretion system apparatus protein Cag3
EC: Type IV secretion system apparatus protein Cag3
ED: Type IV secretion system apparatus protein Cag3
EE: Type IV secretion system apparatus protein Cag3
EM: Type IV secretion system apparatus protein CagM
ET: Type IV secretion system apparatus protein CagT
EU: Unknown protein fragment
EX: Type IV secretion system apparatus protein CagX
EY: Cag pathogenicity island protein (Cag7)
Em: Type IV secretion system apparatus protein CagM
Et: Type IV secretion system apparatus protein CagT
FA: Type IV secretion system apparatus protein Cag3
FB: Type IV secretion system apparatus protein Cag3
FC: Type IV secretion system apparatus protein Cag3
FD: Type IV secretion system apparatus protein Cag3
FE: Type IV secretion system apparatus protein Cag3
FM: Type IV secretion system apparatus protein CagM
FT: Type IV secretion system apparatus protein CagT
FU: Unknown protein fragment
FX: Type IV secretion system apparatus protein CagX
FY: Cag pathogenicity island protein (Cag7)
Fm: Type IV secretion system apparatus protein CagM
Ft: Type IV secretion system apparatus protein CagT
GA: Type IV secretion system apparatus protein Cag3
GB: Type IV secretion system apparatus protein Cag3
GC: Type IV secretion system apparatus protein Cag3
GD: Type IV secretion system apparatus protein Cag3
GE: Type IV secretion system apparatus protein Cag3
GM: Type IV secretion system apparatus protein CagM
GT: Type IV secretion system apparatus protein CagT
GU: Unknown protein fragment
GX: Type IV secretion system apparatus protein CagX
GY: Cag pathogenicity island protein (Cag7)
Gm: Type IV secretion system apparatus protein CagM
Gt: Type IV secretion system apparatus protein CagT
HA: Type IV secretion system apparatus protein Cag3
HB: Type IV secretion system apparatus protein Cag3
HC: Type IV secretion system apparatus protein Cag3
HD: Type IV secretion system apparatus protein Cag3
HE: Type IV secretion system apparatus protein Cag3
HM: Type IV secretion system apparatus protein CagM
HT: Type IV secretion system apparatus protein CagT
HU: Unknown protein fragment
HX: Type IV secretion system apparatus protein CagX
HY: Cag pathogenicity island protein (Cag7)
Hm: Type IV secretion system apparatus protein CagM
Ht: Type IV secretion system apparatus protein CagT
IA: Type IV secretion system apparatus protein Cag3
IB: Type IV secretion system apparatus protein Cag3
IC: Type IV secretion system apparatus protein Cag3
ID: Type IV secretion system apparatus protein Cag3
IE: Type IV secretion system apparatus protein Cag3
IM: Type IV secretion system apparatus protein CagM
IT: Type IV secretion system apparatus protein CagT
IU: Unknown protein fragment
IX: Type IV secretion system apparatus protein CagX
IY: Cag pathogenicity island protein (Cag7)
Im: Type IV secretion system apparatus protein CagM
It: Type IV secretion system apparatus protein CagT
JA: Type IV secretion system apparatus protein Cag3
JB: Type IV secretion system apparatus protein Cag3
JC: Type IV secretion system apparatus protein Cag3
JD: Type IV secretion system apparatus protein Cag3
JE: Type IV secretion system apparatus protein Cag3
JM: Type IV secretion system apparatus protein CagM
JT: Type IV secretion system apparatus protein CagT
JU: Unknown protein fragment
JX: Type IV secretion system apparatus protein CagX
JY: Cag pathogenicity island protein (Cag7)
Jm: Type IV secretion system apparatus protein CagM
Jt: Type IV secretion system apparatus protein CagT
KA: Type IV secretion system apparatus protein Cag3
KB: Type IV secretion system apparatus protein Cag3
KC: Type IV secretion system apparatus protein Cag3
KD: Type IV secretion system apparatus protein Cag3
KE: Type IV secretion system apparatus protein Cag3
KM: Type IV secretion system apparatus protein CagM
KT: Type IV secretion system apparatus protein CagT
KU: Unknown protein fragment
KX: Type IV secretion system apparatus protein CagX
KY: Cag pathogenicity island protein (Cag7)
Km: Type IV secretion system apparatus protein CagM
Kt: Type IV secretion system apparatus protein CagT
LA: Type IV secretion system apparatus protein Cag3
LB: Type IV secretion system apparatus protein Cag3
LC: Type IV secretion system apparatus protein Cag3
LD: Type IV secretion system apparatus protein Cag3
LE: Type IV secretion system apparatus protein Cag3
LM: Type IV secretion system apparatus protein CagM
LT: Type IV secretion system apparatus protein CagT
LU: Unknown protein fragment
LX: Type IV secretion system apparatus protein CagX
LY: Cag pathogenicity island protein (Cag7)
Lm: Type IV secretion system apparatus protein CagM
Lt: Type IV secretion system apparatus protein CagT
MA: Type IV secretion system apparatus protein Cag3
MB: Type IV secretion system apparatus protein Cag3
MC: Type IV secretion system apparatus protein Cag3
MD: Type IV secretion system apparatus protein Cag3
ME: Type IV secretion system apparatus protein Cag3
MM: Type IV secretion system apparatus protein CagM
MT: Type IV secretion system apparatus protein CagT
MU: Unknown protein fragment
MX: Type IV secretion system apparatus protein CagX
MY: Cag pathogenicity island protein (Cag7)
Mm: Type IV secretion system apparatus protein CagM
Mt: Type IV secretion system apparatus protein CagT
NA: Type IV secretion system apparatus protein Cag3
NB: Type IV secretion system apparatus protein Cag3
NC: Type IV secretion system apparatus protein Cag3
ND: Type IV secretion system apparatus protein Cag3
NE: Type IV secretion system apparatus protein Cag3
NM: Type IV secretion system apparatus protein CagM
NT: Type IV secretion system apparatus protein CagT
NU: Unknown protein fragment
NX: Type IV secretion system apparatus protein CagX
NY: Cag pathogenicity island protein (Cag7)
Nm: Type IV secretion system apparatus protein CagM
Nt: Type IV secretion system apparatus protein CagT


分子量 (理論値)分子数
合計 (水以外)10,109,835168
ポリマ－10,109,835168
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_5551
Buried area957130 Å2
ΔGint-5215 kcal/mol
Surface area1136350 Å2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1chain "CA"
d_2ens_1chain "BA"
d_3ens_1chain "NA"
d_4ens_1chain "DA"
d_5ens_1chain "EA"
d_6ens_1chain "FA"
d_7ens_1chain "GA"
d_8ens_1chain "HA"
d_9ens_1chain "IA"
d_10ens_1chain "JA"
d_11ens_1chain "KA"
d_12ens_1chain "LA"
d_13ens_1chain "MA"
d_14ens_1chain "AA"
d_1ens_2chain "KT"
d_2ens_2chain "BT"
d_3ens_2chain "CT"
d_4ens_2chain "DT"
d_5ens_2chain "ET"
d_6ens_2chain "FT"
d_7ens_2chain "GT"
d_8ens_2chain "AT"
d_9ens_2chain "IT"
d_10ens_2chain "JT"
d_11ens_2chain "HT"
d_12ens_2chain "LT"
d_13ens_2chain "MT"
d_14ens_2chain "NT"
d_1ens_3chain "EU"
d_2ens_3chain "BU"
d_3ens_3chain "CU"
d_4ens_3chain "DU"
d_5ens_3chain "LU"
d_6ens_3chain "FU"
d_7ens_3chain "GU"
d_8ens_3chain "HU"
d_9ens_3chain "IU"
d_10ens_3chain "JU"
d_11ens_3chain "KU"
d_12ens_3chain "AU"
d_13ens_3chain "MU"
d_14ens_3chain "NU"
d_1ens_4chain "KX"
d_2ens_4chain "BX"
d_3ens_4chain "CX"
d_4ens_4chain "DX"
d_5ens_4chain "EX"
d_6ens_4chain "FX"
d_7ens_4chain "GX"
d_8ens_4chain "HX"
d_9ens_4chain "IX"
d_10ens_4chain "JX"
d_11ens_4chain "NX"
d_12ens_4chain "LX"
d_13ens_4chain "AX"
d_14ens_4chain "MX"
d_1ens_5chain "HY"
d_2ens_5chain "BY"
d_3ens_5chain "CY"
d_4ens_5chain "DY"
d_5ens_5chain "EY"
d_6ens_5chain "FY"
d_7ens_5chain "GY"
d_8ens_5chain "MY"
d_9ens_5chain "IY"
d_10ens_5chain "JY"
d_11ens_5chain "KY"
d_12ens_5chain "LY"
d_13ens_5chain "AY"
d_14ens_5chain "NY"
d_1ens_6chain "Gt"
d_2ens_6chain "Bt"
d_3ens_6chain "Ct"
d_4ens_6chain "Dt"
d_5ens_6chain "Et"
d_6ens_6chain "Ft"
d_7ens_6chain "At"
d_8ens_6chain "Ht"
d_9ens_6chain "It"
d_10ens_6chain "Jt"
d_11ens_6chain "Kt"
d_12ens_6chain "Lt"
d_13ens_6chain "Mt"
d_14ens_6chain "Nt"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSGLUY1 - 248
d_21ens_1LYSGLUM1 - 248
d_31ens_1LYSGLUAF1 - 248
d_41ens_1LYSGLUQD1 - 248
d_51ens_1LYSGLUWA1 - 248
d_61ens_1LYSGLUIB1 - 248
d_71ens_1LYSGLUUB1 - 248
d_81ens_1LYSGLUGC1 - 248
d_91ens_1LYSGLUSC1 - 248
d_101ens_1LYSGLUED1 - 248
d_111ens_1LYSGLUQD1 - 248
d_121ens_1LYSGLUCE1 - 248
d_131ens_1LYSGLUOE1 - 248
d_141ens_1LYSGLUA1 - 248
d_11ens_2LYSSERBE1 - 253
d_21ens_2LYSSERS1 - 253
d_31ens_2LYSSEREA1 - 253
d_41ens_2LYSSERQA1 - 253
d_51ens_2LYSSERCB1 - 253
d_61ens_2LYSSEROB1 - 253
d_71ens_2LYSSERAC1 - 253
d_81ens_2LYSSERG1 - 253
d_91ens_2LYSSERYC1 - 253
d_101ens_2LYSSERKD1 - 253
d_111ens_2LYSSERMC1 - 253
d_121ens_2LYSSERIE1 - 253
d_131ens_2LYSSERUE1 - 253
d_141ens_2LYSSERGF1 - 253
d_11ens_3ALAALADB1 - 160
d_21ens_3ALAALAT1 - 160
d_31ens_3ALAALAFA1 - 160
d_41ens_3ALAALARA1 - 160
d_51ens_3ALAALAJE1 - 160
d_61ens_3ALAALAPB1 - 160
d_71ens_3ALAALABC1 - 160
d_81ens_3ALAALANC1 - 160
d_91ens_3ALAALAZC1 - 160
d_101ens_3ALAALALD1 - 160
d_111ens_3ALAALAXD1 - 160
d_121ens_3ALAALAH1 - 160
d_131ens_3ALAALAVE1 - 160
d_141ens_3ALAALAHF1 - 160
d_11ens_4ALALYSYD1 - 166
d_21ens_4ALALYSU1 - 166
d_31ens_4ALALYSGA1 - 166
d_41ens_4ALALYSSA1 - 166
d_51ens_4ALALYSEB1 - 166
d_61ens_4ALALYSQB1 - 166
d_71ens_4ALALYSCC1 - 166
d_81ens_4ALALYSOC1 - 166
d_91ens_4ALALYSAD1 - 166
d_101ens_4ALALYSMD1 - 166
d_111ens_4ALALYSIF1 - 166
d_121ens_4ALALYSKE1 - 166
d_131ens_4ALALYSI1 - 166
d_141ens_4ALALYSWE1 - 166
d_11ens_5PROTHRPC - OC1 - 203
d_21ens_5PROTHRV1 - 203
d_31ens_5PROTHRHA1 - 203
d_41ens_5PROTHRTA1 - 203
d_51ens_5PROTHRFB1 - 203
d_61ens_5PROTHRRB1 - 203
d_71ens_5PROTHRDC1 - 203
d_81ens_5PROTHRXE1 - 203
d_91ens_5PROTHRBD1 - 203
d_101ens_5PROTHRND1 - 203
d_111ens_5PROTHRZD1 - 203
d_121ens_5PROTHRLE1 - 203
d_131ens_5PROTHRJ1 - 203
d_141ens_5PROTHRJF1 - 203
d_11ens_6VALILEAC1 - 192
d_21ens_6VALILES1 - 192
d_31ens_6VALILEEA1 - 192
d_41ens_6VALILEQA1 - 192
d_51ens_6VALILECB1 - 192
d_61ens_6VALILEOB1 - 192
d_71ens_6VALILEG1 - 192
d_81ens_6VALILEMC1 - 192
d_91ens_6VALILEYC1 - 192
d_101ens_6VALILEKD1 - 192
d_111ens_6VALILEWD1 - 192
d_121ens_6VALILEIE1 - 192
d_131ens_6VALILEUE1 - 192
d_141ens_6VALILEGF1 - 192

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6

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要素

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Type IV secretion system apparatus protein ... , 4種, 140分子 AAABACADAEBABBBCBDBECACBCCCDCEDADBDCDDDEEAEBECEDEEFAFBFCFDFE...

#1: タンパク質 ...
Type IV secretion system apparatus protein Cag3


分子量: 55105.828 Da / 分子数: 70 / 由来タイプ: 天然 / 由来: (天然) Helicobacter pylori (ピロリ菌) / 参照: UniProt: A0A2J9KJK3
#2: タンパク質 ...
Type IV secretion system apparatus protein CagM


分子量: 43830.027 Da / 分子数: 28 / 由来タイプ: 天然 / 由来: (天然) Helicobacter pylori (ピロリ菌) / 参照: UniProt: A0A2J9KJL4
#3: タンパク質 ...
Type IV secretion system apparatus protein CagT / Cag12 / Cag pathogenicity island protein


分子量: 32418.971 Da / 分子数: 28 / 由来タイプ: 天然 / 由来: (天然) Helicobacter pylori (ピロリ菌) / 参照: UniProt: Q6VRP0
#5: タンパク質
Type IV secretion system apparatus protein CagX


分子量: 60720.480 Da / 分子数: 14 / 由来タイプ: 天然 / 由来: (天然) Helicobacter pylori (ピロリ菌) / 参照: UniProt: A0A2J9KJM4

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タンパク質 , 2種, 28分子 AUBUCUDUEUFUGUHUIUJUKULUMUNUAYBYCYDYEYFYGYHYIYJYKYLYMYNY

#4: タンパク質
Unknown protein fragment


分子量: 13634.798 Da / 分子数: 14 / 由来タイプ: 天然 / 由来: (天然) Helicobacter pylori (ピロリ菌)
#6: タンパク質
Cag pathogenicity island protein (Cag7)


分子量: 219748.641 Da / 分子数: 14 / 由来タイプ: 天然 / 由来: (天然) Helicobacter pylori (ピロリ菌) / 参照: UniProt: O25262

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: Helicobacter pylori Cag T4SS OMC / タイプ: COMPLEX / Entity ID: all / 由来: NATURAL
分子量実験値: NO
由来(天然)生物種: Helicobacter pylori (ピロリ菌)
緩衝液pH: 7
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: ETHANE

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD
撮影
IDImaging-ID電子線照射量 (e/Å2)フィルム・検出器のモデル
1159.2GATAN K2 SUMMIT (4k x 4k)
2159GATAN K2 SUMMIT (4k x 4k)

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解析

ソフトウェア
名称バージョン分類
phenix.real_space_refine1.18.2_3874精密化
PHENIX1.18.2_3874精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: C14 (14回回転対称)
3次元再構成解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 47440 / 対称性のタイプ: POINT
精密化交差検証法: NONE
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
原子変位パラメータBiso mean: 127.49 Å2
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.0113219310
ELECTRON MICROSCOPYf_angle_d1.4773296212
ELECTRON MICROSCOPYf_chiral_restr0.075533698
ELECTRON MICROSCOPYf_plane_restr0.008138164
ELECTRON MICROSCOPYf_dihedral_angle_d19.008229568
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2BAELECTRON MICROSCOPYNCS constraints0.000704586526381
ens_1d_3NAELECTRON MICROSCOPYNCS constraints0.000707093479802
ens_1d_4DAELECTRON MICROSCOPYNCS constraints0.000691927279386
ens_1d_5EAELECTRON MICROSCOPYNCS constraints0.000699629173395
ens_1d_6FAELECTRON MICROSCOPYNCS constraints0.000701411187048
ens_1d_7GAELECTRON MICROSCOPYNCS constraints0.00070893724952
ens_1d_8HAELECTRON MICROSCOPYNCS constraints0.000714582529589
ens_1d_9IAELECTRON MICROSCOPYNCS constraints0.000697900856266
ens_1d_10JAELECTRON MICROSCOPYNCS constraints0.000704661590852
ens_1d_11KAELECTRON MICROSCOPYNCS constraints0.000701372907024
ens_1d_12LAELECTRON MICROSCOPYNCS constraints0.000708709213723
ens_1d_13MAELECTRON MICROSCOPYNCS constraints0.000711164687446
ens_1d_14AAELECTRON MICROSCOPYNCS constraints0.000701543600352
ens_2d_2BTELECTRON MICROSCOPYNCS constraints0.000710277598301
ens_2d_3CTELECTRON MICROSCOPYNCS constraints0.000714645151627
ens_2d_4DTELECTRON MICROSCOPYNCS constraints0.0695275491073
ens_2d_5ETELECTRON MICROSCOPYNCS constraints0.0695397256021
ens_2d_6FTELECTRON MICROSCOPYNCS constraints0.000706823246061
ens_2d_7GTELECTRON MICROSCOPYNCS constraints0.000751853398245
ens_2d_8ATELECTRON MICROSCOPYNCS constraints0.0007037723033
ens_2d_9ITELECTRON MICROSCOPYNCS constraints0.000710767076385
ens_2d_10JTELECTRON MICROSCOPYNCS constraints0.000700518855955
ens_2d_11HTELECTRON MICROSCOPYNCS constraints0.00070842423214
ens_2d_12LTELECTRON MICROSCOPYNCS constraints0.0695311696874
ens_2d_13MTELECTRON MICROSCOPYNCS constraints0.000706984631973
ens_2d_14NTELECTRON MICROSCOPYNCS constraints0.000706856553451
ens_3d_2BUELECTRON MICROSCOPYNCS constraints0.00071441389846
ens_3d_3CUELECTRON MICROSCOPYNCS constraints0.000713012108859
ens_3d_4DUELECTRON MICROSCOPYNCS constraints0.000706526548465
ens_3d_5LUELECTRON MICROSCOPYNCS constraints0.000707267208104
ens_3d_6FUELECTRON MICROSCOPYNCS constraints0.000697526778077
ens_3d_7GUELECTRON MICROSCOPYNCS constraints0.000708018000025
ens_3d_8HUELECTRON MICROSCOPYNCS constraints0.000699717945465
ens_3d_9IUELECTRON MICROSCOPYNCS constraints0.000711449145856
ens_3d_10JUELECTRON MICROSCOPYNCS constraints0.000700874802489
ens_3d_11KUELECTRON MICROSCOPYNCS constraints0.000709001718641
ens_3d_12AUELECTRON MICROSCOPYNCS constraints0.0007054505678
ens_3d_13MUELECTRON MICROSCOPYNCS constraints0.000719579551828
ens_3d_14NUELECTRON MICROSCOPYNCS constraints0.000720798906273
ens_4d_2BXELECTRON MICROSCOPYNCS constraints0.0857813359145
ens_4d_3CXELECTRON MICROSCOPYNCS constraints0.000704487217357
ens_4d_4DXELECTRON MICROSCOPYNCS constraints0.000715197651169
ens_4d_5EXELECTRON MICROSCOPYNCS constraints0.00070217129114
ens_4d_6FXELECTRON MICROSCOPYNCS constraints0.000707144244901
ens_4d_7GXELECTRON MICROSCOPYNCS constraints0.000705628604566
ens_4d_8HXELECTRON MICROSCOPYNCS constraints0.000705988378526
ens_4d_9IXELECTRON MICROSCOPYNCS constraints0.00070450520392
ens_4d_10JXELECTRON MICROSCOPYNCS constraints0.000694457813643
ens_4d_11NXELECTRON MICROSCOPYNCS constraints0.000706827310327
ens_4d_12LXELECTRON MICROSCOPYNCS constraints0.0857810575492
ens_4d_13AXELECTRON MICROSCOPYNCS constraints0.000703143165663
ens_4d_14MXELECTRON MICROSCOPYNCS constraints0.000692837508237
ens_5d_2BYELECTRON MICROSCOPYNCS constraints0.000706648262848
ens_5d_3CYELECTRON MICROSCOPYNCS constraints0.000701975929972
ens_5d_4DYELECTRON MICROSCOPYNCS constraints0.000694958971493
ens_5d_5EYELECTRON MICROSCOPYNCS constraints0.000705813605196
ens_5d_6FYELECTRON MICROSCOPYNCS constraints0.000706722721898
ens_5d_7GYELECTRON MICROSCOPYNCS constraints0.000710266219748
ens_5d_8MYELECTRON MICROSCOPYNCS constraints0.000710356905054
ens_5d_9IYELECTRON MICROSCOPYNCS constraints0.000711784275729
ens_5d_10JYELECTRON MICROSCOPYNCS constraints0.000707157615857
ens_5d_11KYELECTRON MICROSCOPYNCS constraints0.000702159711151
ens_5d_12LYELECTRON MICROSCOPYNCS constraints0.000707819260128
ens_5d_13AYELECTRON MICROSCOPYNCS constraints0.000701747109157
ens_5d_14NYELECTRON MICROSCOPYNCS constraints0.000706070951768
ens_6d_2BtELECTRON MICROSCOPYNCS constraints0.000710433077196
ens_6d_3CtELECTRON MICROSCOPYNCS constraints0.000705404445246
ens_6d_4DtELECTRON MICROSCOPYNCS constraints0.000702463628965
ens_6d_5EtELECTRON MICROSCOPYNCS constraints0.000698946546712
ens_6d_6FtELECTRON MICROSCOPYNCS constraints0.000703107167529
ens_6d_7AtELECTRON MICROSCOPYNCS constraints0.000707372445488
ens_6d_8HtELECTRON MICROSCOPYNCS constraints0.000716120556358
ens_6d_9ItELECTRON MICROSCOPYNCS constraints0.000715656685103
ens_6d_10JtELECTRON MICROSCOPYNCS constraints0.000727383274857
ens_6d_11KtELECTRON MICROSCOPYNCS constraints0.000762761393543
ens_6d_12LtELECTRON MICROSCOPYNCS constraints0.000710217360804
ens_6d_13MtELECTRON MICROSCOPYNCS constraints0.000710867132807
ens_6d_14NtELECTRON MICROSCOPYNCS constraints0.000708778371202

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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