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- PDB-9l8p: in situ structure of mtHsp60-Hsp10 -

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基本情報

登録情報
データベース: PDB / ID: 9l8p
タイトルin situ structure of mtHsp60-Hsp10
要素
  • 10 kDa heat shock protein, mitochondrial
  • 60 kDa heat shock protein, mitochondrial
キーワードCHAPERONE / mtHsp60-Hsp10
機能・相同性
機能・相同性情報


coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / high-density lipoprotein particle binding / migrasome / cysteine-type endopeptidase activator activity ...coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / high-density lipoprotein particle binding / migrasome / cysteine-type endopeptidase activator activity / positive regulation of T cell mediated immune response to tumor cell / chaperonin ATPase / Mitochondrial protein import / positive regulation of macrophage activation / negative regulation of execution phase of apoptosis / cellular response to interleukin-7 / MyD88-dependent toll-like receptor signaling pathway / 'de novo' protein folding / biological process involved in interaction with symbiont / sperm plasma membrane / apoptotic mitochondrial changes / B cell activation / : / B cell proliferation / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / DNA replication origin binding / apolipoprotein binding / RHOG GTPase cycle / positive regulation of execution phase of apoptosis / response to unfolded protein / Mitochondrial unfolded protein response (UPRmt) / isomerase activity / chaperone-mediated protein complex assembly / sperm midpiece / clathrin-coated pit / positive regulation of interleukin-12 production / protein folding chaperone / Mitochondrial protein degradation / intrinsic apoptotic signaling pathway / response to cold / secretory granule / T cell activation / protein maturation / ATP-dependent protein folding chaperone / lipopolysaccharide binding / positive regulation of T cell activation / positive regulation of interleukin-6 production / positive regulation of type II interferon production / osteoblast differentiation / p53 binding / unfolded protein binding / protein folding / single-stranded DNA binding / double-stranded RNA binding / protein-folding chaperone binding / protein refolding / early endosome / mitochondrial inner membrane / protein stabilization / mitochondrial matrix / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / ATP binding / metal ion binding / membrane / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / GroES-like superfamily
類似検索 - ドメイン・相同性
ADENOSINE-5'-TRIPHOSPHATE / : / 60 kDa heat shock protein, mitochondrial / 10 kDa heat shock protein, mitochondrial
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法電子顕微鏡法 / サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 7.3 Å
データ登録者Jung, M. / Roh, S.
資金援助 韓国, 5件
組織認可番号国
National Research Foundation (NRF, Korea)2019R1C1C1004598 韓国
National Research Foundation (NRF, Korea)2020R1A5A1018081 韓国
National Research Foundation (NRF, Korea)2021M3A9I4021220 韓国
National Research Foundation (NRF, Korea)2019M3E5D6063871 韓国
National Research Foundation (NRF, Korea)2020R1A6C101A183 韓国
引用ジャーナル: Sci Adv / 年: 2025
タイトル: In situ characterization of mitochondrial Hsp60-Hsp10 chaperone complex under folding stress.
著者: Mingyu Jung / Minjung Kim / Su Jin Ham / Jongkyeong Chung / Soung-Hun Roh /
要旨: Mitochondrial proteostasis is critical for maintaining mitochondrial function, and its disruption induces mitochondrial unfolded protein response, which up-regulates chaperones to alleviate protein- ...Mitochondrial proteostasis is critical for maintaining mitochondrial function, and its disruption induces mitochondrial unfolded protein response, which up-regulates chaperones to alleviate protein-folding stress. However, how these chaperones mitigate protein-folding stress remains unclear. Here, using correlated cryo-electron tomography, we show that folding stress triggers marked mitochondrial morphological changes, including the accumulation of amorphous protein aggregates and increased abundance and spatial clustering of the mitochondrial heat shock protein 60-heat shock protein 10 (mtHsp60-Hsp10) complex. Subtomogram analysis revealed the in situ architecture and conformational heterogeneity of mtHsp60-Hsp10 under stress, which retains its canonical double-ring structure while adopting distinct football, half-football, and bullet-like states. Notably, the mtHsp60-Hsp10 complex encapsulates unstructured substrates through conserved hydrophobic interactions. We further demonstrate that knockdown of the mtHsp60-Hsp10 complex exacerbates folding stress, as evidenced by elevated cellular stress responses and activation of mitophagy. Our study defines the in situ structural properties of the mtHsp60-Hsp10 complex and provides mechanistic insight into how it safeguards mitochondrial proteostasis under folding stress.
履歴
登録2024年12月27日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02025年10月1日Provider: repository / タイプ: Initial release
改定 1.12025年10月15日Group: Database references / カテゴリ: citation / Item: _citation.title
改定 1.22025年11月19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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: 60 kDa heat shock protein, mitochondrial
G: 60 kDa heat shock protein, mitochondrial
F: 60 kDa heat shock protein, mitochondrial
E: 60 kDa heat shock protein, mitochondrial
D: 60 kDa heat shock protein, mitochondrial
C: 60 kDa heat shock protein, mitochondrial
B: 60 kDa heat shock protein, mitochondrial
J: 60 kDa heat shock protein, mitochondrial
I: 60 kDa heat shock protein, mitochondrial
H: 60 kDa heat shock protein, mitochondrial
N: 60 kDa heat shock protein, mitochondrial
Y: 60 kDa heat shock protein, mitochondrial
L: 60 kDa heat shock protein, mitochondrial
K: 60 kDa heat shock protein, mitochondrial
O: 10 kDa heat shock protein, mitochondrial
U: 10 kDa heat shock protein, mitochondrial
T: 10 kDa heat shock protein, mitochondrial
S: 10 kDa heat shock protein, mitochondrial
R: 10 kDa heat shock protein, mitochondrial
Q: 10 kDa heat shock protein, mitochondrial
P: 10 kDa heat shock protein, mitochondrial
X: 10 kDa heat shock protein, mitochondrial
W: 10 kDa heat shock protein, mitochondrial
V: 10 kDa heat shock protein, mitochondrial
2: 10 kDa heat shock protein, mitochondrial
1: 10 kDa heat shock protein, mitochondrial
Z: 10 kDa heat shock protein, mitochondrial
M: 10 kDa heat shock protein, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,016,75756
ポリマ－1,009,10928
非ポリマー7,64828
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法, not applicable
タイプ名称対称操作数
identity operation1_5551
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1chain "Q"
d_2ens_1chain "2"
d_3ens_1chain "M"
d_4ens_1chain "O"
d_5ens_1chain "P"
d_6ens_1chain "1"
d_7ens_1chain "R"
d_8ens_1chain "S"
d_9ens_1chain "T"
d_10ens_1chain "U"
d_11ens_1chain "V"
d_12ens_1chain "W"
d_13ens_1chain "X"
d_14ens_1chain "Z"
d_1ens_2chain "F"
d_2ens_2chain "B"
d_3ens_2chain "C"
d_4ens_2chain "D"
d_5ens_2chain "E"
d_6ens_2chain "A"
d_7ens_2chain "G"
d_8ens_2chain "H"
d_9ens_2chain "I"
d_10ens_2chain "J"
d_11ens_2chain "K"
d_12ens_2chain "L"
d_13ens_2chain "N"
d_14ens_2chain "Y"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYASPASPQT3 - 1023 - 102
d_21ens_1GLYGLYASPASP2Y3 - 1023 - 102
d_31ens_1GLYGLYASPASPMBA3 - 1023 - 102
d_41ens_1GLYGLYASPASPOO3 - 1023 - 102
d_51ens_1GLYGLYASPASPPU3 - 1023 - 102
d_61ens_1GLYGLYASPASP1Z3 - 1023 - 102
d_71ens_1GLYGLYASPASPRS3 - 1023 - 102
d_81ens_1GLYGLYASPASPSR3 - 1023 - 102
d_91ens_1GLYGLYASPASPTQ3 - 1023 - 102
d_101ens_1GLYGLYASPASPUP3 - 1023 - 102
d_111ens_1GLYGLYASPASPVX3 - 1023 - 102
d_121ens_1GLYGLYASPASPWW3 - 1023 - 102
d_131ens_1GLYGLYASPASPXV3 - 1023 - 102
d_141ens_1GLYGLYASPASPZAA3 - 1023 - 102
d_11ens_2TYRTYRGLUGLUFC0 - 52626 - 552
d_12ens_2ATPATPATPATPFGA601
d_22ens_2ATPATPATPATPBOA601
d_31ens_2TYRTYRGLUGLUCF0 - 52626 - 552
d_32ens_2ATPATPATPATPCMA601
d_41ens_2TYRTYRGLUGLUDE0 - 52626 - 552
d_42ens_2ATPATPATPATPDKA601
d_51ens_2TYRTYRGLUGLUED0 - 52626 - 552
d_52ens_2ATPATPATPATPEIA601
d_61ens_2TYRTYRGLUGLUAA0 - 52626 - 552
d_62ens_2ATPATPATPATPACA601
d_71ens_2TYRTYRGLUGLUGB0 - 52626 - 552
d_72ens_2ATPATPATPATPGEA601
d_81ens_2TYRTYRGLUGLUHJ0 - 52626 - 552
d_82ens_2ATPATPATPATPHUA601
d_91ens_2TYRTYRGLUGLUII0 - 52626 - 552
d_92ens_2ATPATPATPATPISA601
d_101ens_2TYRTYRGLUGLUJH0 - 52626 - 552
d_102ens_2ATPATPATPATPJQA601
d_111ens_2TYRTYRGLUGLUKN0 - 52626 - 552
d_112ens_2ATPATPATPATPKCB601
d_121ens_2TYRTYRGLUGLULM0 - 52626 - 552
d_122ens_2ATPATPATPATPLAB601
d_131ens_2TYRTYRGLUGLUNK0 - 52626 - 552
d_132ens_2ATPATPATPATPNWA601
d_141ens_2TYRTYRGLUGLUYL0 - 52626 - 552
d_142ens_2ATPATPATPATPYYA601

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.618407633866, -0.785756366047, -0.0126068073778), (-0.785763269098, -0.618502329541, 0.00556356799154), (-0.0121689486985, 0.00646541326053, -0.999905053052)226.106960136, 456.254102119, 382.073079874
2given(-0.908306913846, 0.418209690248, 0.00889973264098), (0.418198721371, 0.908350104724, -0.00314907788304), (-0.00940104796249, 0.000861527597594, -0.999955438041)281.312845356, -60.9776781842, 382.558766529
3given(-0.21860799098, -0.975796512408, -0.00563139877814), (0.975765132761, -0.218536662568, -0.0111414901297), (0.00964116011701, -0.00793054135015, 0.999922074237)419.461230646, 49.4965362182, -0.305346224661
4given(0.617108657112, -0.786840740807, -0.00765205357881), (0.786877174857, 0.617065237236, 0.00740301858327), (-0.00110318036931, -0.0105896931584, 0.99994331909)225.159148278, -79.4263681775, 2.58174032926
5given(-0.206597508194, -0.978402653379, -0.00676146946975), (-0.978330000798, 0.206475490594, 0.0154363636157), (-0.0137069013942, 0.00980406269031, -0.999857990521)417.649272487, 332.718166633, 381.709822239
6given(0.606424657627, 0.795039820344, -0.0126814309059), (-0.795075108141, 0.60650255973, 0.00319647553408), (0.0102326456398, 0.00814426846753, 0.99991447827)-72.2841726444, 225.808955049, -3.64785539552
7given(-0.24903608275, 0.968487719621, -0.00354491647093), (-0.968351916177, -0.248935085869, 0.0180524087145), (0.0166010820635, 0.00792842780777, 0.999830757732)55.2215530491, 416.683524614, -5.03509176251
8given(-0.90660300737, 0.421938104809, 0.00626280592258), (-0.421980149211, -0.906561656622, -0.00887222714112), (0.00193408900692, -0.0106863675859, 0.999941028685)280.68498111, 445.257691645, 1.85605060906
9given(-0.896093084851, -0.443734481132, 0.0108117314193), (0.443595142148, -0.896131295079, -0.013116853377), (0.0155091310062, -0.00695789007031, 0.999855516873)441.854142439, 280.202267735, -1.70888926281
10given(0.999848144313, -0.00524221685873, -0.0166194908347), (-0.00551707247511, -0.999848055292, -0.016535665707), (-0.0165302820455, 0.0166248456076, -0.999725144369)5.928791227, 387.000953508, 380.908848928
11given(0.624367227753, 0.781123606622, 0.00338763724918), (0.781108480702, -0.624310498458, -0.0102928562928), (-0.00592505553025, 0.00907263433407, -0.999941288788)-78.2131043486, 163.706593029, 380.159222168
12given(-0.233579224397, 0.972337306707, 0.000952846641575), (0.972306772593, 0.233579490274, -0.00775639696254), (-0.00776439956516, -0.000885273943777, -0.999969464729)49.7029881644, -36.9752294146, 382.573114049
13given(-0.889550948631, -0.456266404475, 0.0228052173322), (-0.456303312904, 0.889815921479, 0.00386167252766), (-0.0220543969145, -0.0069709417599, -0.999732468987)439.714046393, 107.206287375, 386.786466224
14given(-0.907027751872, 0.421046322396, -0.00454441757435), (-0.421043242853, -0.907039044838, -0.00166095956815), (-0.0048213050938, 0.00040685988933, 0.999988294673)283.956204804, 444.31842389, 0.51949917651
15given(-0.886036305622, -0.463454893195, -0.0122158541472), (0.463397883611, -0.886120131962, 0.00731527141738), (-0.0142150126224, 0.000820795102961, 0.999898624717)451.25586108, 270.094801044, 1.7851004513
16given(-0.201043340751, -0.979571241158, -0.00466461538229), (0.979551509393, -0.201072516533, 0.00697735911338), (-0.00777274628027, -0.00316647945269, 0.999964778291)417.063444385, 40.3250587503, 1.7738041913
17given(0.630257485872, -0.776377515886, 0.00366801423618), (0.776362288818, 0.630268121047, 0.00486745245471), (-0.0060908130861, -0.000220040418892, 0.999981426617)217.449550823, -78.8249155639, 0.828507129154
18given(-0.23800414238, 0.971244454756, 0.00618363284), (-0.971245356656, -0.237955122358, -0.00773413975134), (-0.00604031323673, -0.00784658198169, 0.999950971682)48.8693767541, 422.845563336, 2.50211998877
19given(0.614726831882, 0.788720282066, -0.0055891700683), (-0.7887148912, 0.614748400367, 0.0036365705906), (0.00630417034083, 0.00217276414424, 0.999977768019)-76.2207283993, 222.790810658, -1.34364698024
20given(-0.897979245763, -0.440016825173, -0.00429741119508), (-0.440022273834, 0.897986783899, 0.000366704095328), (0.00369766248636, 0.0022202493126, -0.999990698849)446.337977911, 103.049128804, 379.795596208
21given(-0.203758153449, -0.979014933582, -0.00351777286465), (-0.978981490094, 0.203780946552, -0.00828057223064), (0.00882365895652, 0.00175660041363, -0.99995952788)417.245787787, 340.176329182, 379.244458735
22given(0.645944038428, -0.763324840433, 0.00956489395994), (-0.763291783786, -0.646010215183, -0.00751363323579), (0.011914362096, -0.00244741837681, -0.999926026324)211.136938762, 461.626479683, 379.66236782
23given(0.999881390483, 0.0147899619363, 0.00429674209051), (0.0147968853315, -0.999889265409, -0.00158401504184), (0.00427283877036, 0.0016474055626, -0.999989514397)-4.1767378379, 378.791841276, 379.922656483
24given(0.615234804462, 0.788306229642, -0.00770867607868), (0.788306667164, -0.615271378815, -0.00370525507669), (-0.00766380341914, -0.00379719886525, -0.99996342303)-75.620256939, 158.164865432, 382.718832234
25given(-0.905633567908, 0.424023685914, 0.00563510980952), (0.424008668322, 0.905650594063, -0.00369468007753), (-0.00667007241135, -0.000956690894711, -0.999977297181)281.040737634, -62.5621955235, 381.99605892
26given(-0.222061657265, 0.975032590973, 0.000258677123082), (0.975032547551, 0.222061737685, -0.000340401239334), (-0.000389344593809, 0.00017662855097, -0.999999908607)47.1373184611, -37.4944666247, 380.818108596

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要素

#1: タンパク質
60 kDa heat shock protein, mitochondrial / 60 kDa chaperonin / Chaperonin 60 / CPN60 / Heat shock protein 60 / HSP-60 / Hsp60 / Heat shock ...60 kDa chaperonin / Chaperonin 60 / CPN60 / Heat shock protein 60 / HSP-60 / Hsp60 / Heat shock protein family D member 1 / HuCHA60 / Mitochondrial matrix protein P1 / P60 lymphocyte protein


分子量: 61132.523 Da / 分子数: 14 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P10809, chaperonin ATPase
#2: タンパク質
10 kDa heat shock protein, mitochondrial / Hsp10 / 10 kDa chaperonin / Chaperonin 10 / CPN10 / Early-pregnancy factor / EPF / Heat shock ...Hsp10 / 10 kDa chaperonin / Chaperonin 10 / CPN10 / Early-pregnancy factor / EPF / Heat shock protein family E member 1


分子量: 10946.674 Da / 分子数: 14 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P61604
#3: 化合物
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


分子量: 507.181 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / タイプ: SUBJECT OF INVESTIGATION / コメント: ATP, エネルギー貯蔵分子*YM
#4: 化合物
ChemComp-K / POTASSIUM ION


分子量: 39.098 Da / 分子数: 14 / 由来タイプ: 合成 / 式: K / タイプ: SUBJECT OF INVESTIGATION
研究の焦点であるリガンドがあるかY
Has protein modificationN

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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: CELL / ３次元再構成法: サブトモグラム平均法

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試料調製

構成要素名称: in situ human mtHsp60-Hsp10 football complex / タイプ: CELL / Entity ID: #1-#2 / 由来: NATURAL
由来(天然)生物種: Homo sapiens (ヒト)
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: TFS KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: OTHER
電子レンズモード: OTHER / 最大 デフォーカス（公称値）: 4800 nm / 最小 デフォーカス（公称値）: 3000 nm
撮影電子線照射量: 3.2 e/Å2 / Avg electron dose per subtomogram: 131 e/Å2
フィルム・検出器のモデル: FEI FALCON IV (4k x 4k)

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解析

CTF補正タイプ: NONE
対称性点対称性: D7 (2回x7回 2面回転対称)
3次元再構成解像度: 7.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 6735 / 対称性のタイプ: POINT
EM volume selectionNum. of tomograms: 169 / Num. of volumes extracted: 43800
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: 61.24 Å2
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.003766696
ELECTRON MICROSCOPYf_angle_d0.870190020
ELECTRON MICROSCOPYf_chiral_restr0.054810850
ELECTRON MICROSCOPYf_plane_restr0.005311522
ELECTRON MICROSCOPYf_dihedral_angle_d4.90739408
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2TQELECTRON MICROSCOPYNCS constraints2.41817005239E-13
ens_1d_3TQELECTRON MICROSCOPYNCS constraints3.57647122727E-11
ens_1d_4TQELECTRON MICROSCOPYNCS constraints7.33651641082E-12
ens_1d_5TQELECTRON MICROSCOPYNCS constraints2.07692963174E-10
ens_1d_6TQELECTRON MICROSCOPYNCS constraints3.02588940917E-10
ens_1d_7TQELECTRON MICROSCOPYNCS constraints4.41007073642E-13
ens_1d_8TQELECTRON MICROSCOPYNCS constraints2.91106213108E-12
ens_1d_9TQELECTRON MICROSCOPYNCS constraints3.17064973662E-12
ens_1d_10TQELECTRON MICROSCOPYNCS constraints1.25019165638E-13
ens_1d_11TQELECTRON MICROSCOPYNCS constraints1.292329628E-13
ens_1d_12TQELECTRON MICROSCOPYNCS constraints1.56005575974E-12
ens_1d_13TQELECTRON MICROSCOPYNCS constraints3.06525212788E-11
ens_1d_14TQELECTRON MICROSCOPYNCS constraints3.69315426538E-12
ens_2d_2CFELECTRON MICROSCOPYNCS constraints5.7377765134E-11
ens_2d_3CFELECTRON MICROSCOPYNCS constraints2.88825651968E-10
ens_2d_4CFELECTRON MICROSCOPYNCS constraints2.16876712979E-11
ens_2d_5CFELECTRON MICROSCOPYNCS constraints4.82749963276E-13
ens_2d_6CFELECTRON MICROSCOPYNCS constraints4.68623488158E-13
ens_2d_7CFELECTRON MICROSCOPYNCS constraints1.94193457323E-12
ens_2d_8CFELECTRON MICROSCOPYNCS constraints4.38328455942E-13
ens_2d_9CFELECTRON MICROSCOPYNCS constraints4.35301740607E-13
ens_2d_10CFELECTRON MICROSCOPYNCS constraints3.17814389114E-13
ens_2d_11CFELECTRON MICROSCOPYNCS constraints3.04415501023E-11
ens_2d_12CFELECTRON MICROSCOPYNCS constraints5.85324999798E-12
ens_2d_13CFELECTRON MICROSCOPYNCS constraints3.62713345758E-13
ens_2d_14CFELECTRON MICROSCOPYNCS constraints1.67591694929E-13

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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