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- PDB-6z7v: Crystal structure of Mindy2 (C266A) in complex with Lys48 linked ... -

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基本情報

登録情報
データベース: PDB / ID: 6z7v
タイトルCrystal structure of Mindy2 (C266A) in complex with Lys48 linked di-ubiquitin (K48-Ub2)
要素
  • Polyubiquitin-C
  • Ubiquitin carboxyl-terminal hydrolase MINDY-2
キーワードHYDROLASE / CYSTEINE PROTEASE / ISOPEPTIDASE AND UBIQUITIN BINDING
機能・相同性
機能・相同性情報


K11-linked polyubiquitin modification-dependent protein binding / K6-linked polyubiquitin modification-dependent protein binding / cysteine-type carboxypeptidase activity / K48-linked deubiquitinase activity / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora ...K11-linked polyubiquitin modification-dependent protein binding / K6-linked polyubiquitin modification-dependent protein binding / cysteine-type carboxypeptidase activity / K48-linked deubiquitinase activity / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of AXIN / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Stabilization of p53 / Hh mutants are degraded by ERAD / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Activation of NF-kappaB in B cells / Negative regulation of FGFR1 signaling / EGFR downregulation / Degradation of GLI1 by the proteasome / Termination of translesion DNA synthesis
類似検索 - 分子機能
MINDY deubiquitinase / MINDY deubiquitinase domain / MINDY deubiquitinase / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family ...MINDY deubiquitinase / MINDY deubiquitinase domain / MINDY deubiquitinase / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
類似検索 - ドメイン・相同性
: / Polyubiquitin-C / Ubiquitin carboxyl-terminal hydrolase MINDY-2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.65 Å
データ登録者Abdul Rehman, S.A. / Lange, S.M. / Kulathu, Y.
資金援助 英国, 2件
組織認可番号国
Medical Research Council (MRC, United Kingdom)MC_UU_12016/6 英国
European Research Council (ERC)677623 英国
引用ジャーナル: Mol.Cell / 年: 2021
タイトル: Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2.
著者: Abdul Rehman, S.A. / Armstrong, L.A. / Lange, S.M. / Kristariyanto, Y.A. / Grawert, T.W. / Knebel, A. / Svergun, D.I. / Kulathu, Y.
履歴
登録2020年6月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年6月9日Provider: repository / タイプ: Initial release
改定 1.12021年10月13日Group: Data collection / Database references
カテゴリ: citation / citation_author ...citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22021年11月3日Group: Data collection / Database references
カテゴリ: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32024年1月24日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Ubiquitin carboxyl-terminal hydrolase MINDY-2
B: Ubiquitin carboxyl-terminal hydrolase MINDY-2
C: Polyubiquitin-C
D: Polyubiquitin-C
E: Polyubiquitin-C
F: Polyubiquitin-C
G: Polyubiquitin-C
H: Polyubiquitin-C
I: Polyubiquitin-C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)123,11416
ポリマ－122,3759
非ポリマー7397
水68538
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: SAXS, Mindy1 and Mindy2 both are structurally identical. The SAXS measurements for Mindy2-Lys48 linked di-ubiquitin complex show it to be a dimer which consists of one molecule of Mindy2 and ...根拠: SAXS, Mindy1 and Mindy2 both are structurally identical. The SAXS measurements for Mindy2-Lys48 linked di-ubiquitin complex show it to be a dimer which consists of one molecule of Mindy2 and one polymer of ubiquitin (the individual chain of ubiquitin are covalently linked and are considered as a single molecule). This observation from MIndy2-Lys48 linked di-ubiquitin can be extrapolated onto Mindy1-Lys48 linked di-ubiquitin complex. Moreover, the structure-based mutational studies have validated the complex observed in the crystal structure.
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16100 Å2
ΔGint-13 kcal/mol
Surface area42810 Å2
手法PISA
単位格子
Length a, b, c (Å)94.011, 117.597, 125.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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要素

#1: タンパク質 Ubiquitin carboxyl-terminal hydrolase MINDY-2 / Deubiquitinating enzyme MINDY-2 / Protein FAM63B


分子量: 31168.389 Da / 分子数: 2 / 変異: C266A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MINDY2, FAM63B, KIAA1164 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q8NBR6, ubiquitinyl hydrolase 1
#2: タンパク質
Polyubiquitin-C


分子量: 8576.831 Da / 分子数: 7 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBC / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0CG48
#3: 化合物
ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 4 / 由来タイプ: 合成 / 式: K
#4: 化合物 ChemComp-PG4 / TETRAETHYLENE GLYCOL / テトラエチレングリコ-ル


分子量: 194.226 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C8H18O5 / コメント: 沈殿剤*YM
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 38 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.84 Å3/Da / 溶媒含有率: 56.74 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 50 mM potassium phosphate monobasic, 14% PEG 8000

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: ID29 / 波長: 0.97625 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2016年11月25日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97625 Å / 相対比: 1
反射解像度: 2.65→47.79 Å / Num. obs: 40463 / % possible obs: 98.4 % / 冗長度: 4.4 % / Biso Wilson estimate: 58.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.044 / Rrim(I) all: 0.094 / Net I/σ(I): 11.8 / Num. measured all: 176139 / Scaling rejects: 4
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.65-2.764.50.6412037245690.7040.3360.7282.199.6
9.55-47.793.80.02335999350.9990.0120.02643.395.3

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19rc7_4070精密化
XDSデータ削減
Aimless0.7.4データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5JKN, 1UBQ

5jkn

1ubq


解像度: 2.65→47.79 Å / SU ML: 0.3616 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 26.7096
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.2543 2094 5.18 %RANDOM
Rwork0.2127 38315 --
obs0.2148 40409 98.01 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 69.59 Å2
精密化ステップサイクル: LAST / 解像度: 2.65→47.79 Å
タンパク質核酸リガンド溶媒全体
原子数7919 0 43 38 8000
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00328092
X-RAY DIFFRACTIONf_angle_d0.581310993
X-RAY DIFFRACTIONf_chiral_restr0.04341305
X-RAY DIFFRACTIONf_plane_restr0.00471415
X-RAY DIFFRACTIONf_dihedral_angle_d5.25191104
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.710.38411320.33322542X-RAY DIFFRACTION99.48
2.71-2.780.34581250.3032590X-RAY DIFFRACTION99.16
2.78-2.850.31321520.27972529X-RAY DIFFRACTION99
2.85-2.940.35011260.28222557X-RAY DIFFRACTION98.97
2.94-3.030.35931390.27762503X-RAY DIFFRACTION97.42
3.03-3.140.31411400.28122547X-RAY DIFFRACTION98.57
3.14-3.270.34271480.2672554X-RAY DIFFRACTION99.16
3.27-3.420.26891340.23462548X-RAY DIFFRACTION98.97
3.42-3.60.3011450.22282554X-RAY DIFFRACTION98.4
3.6-3.820.26571200.20052520X-RAY DIFFRACTION96.7
3.82-4.120.22681230.19212567X-RAY DIFFRACTION98.1
4.12-4.530.19011390.15672573X-RAY DIFFRACTION97.94
4.53-5.190.18551480.16552526X-RAY DIFFRACTION96.4
5.19-6.530.23661790.20622567X-RAY DIFFRACTION97.51
6.53-47.790.23391440.19642638X-RAY DIFFRACTION94.75
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.917206753362.35624446905-1.519643662157.450854121751.208622356212.70433759493-0.03918654224880.04847109346741.137138228480.382911832724-0.03575050183230.665611936817-1.12515300952-0.765787592180.03905944288230.8677869523390.301128431568-0.1400163856180.5824339433550.04738570837590.56709379399733.7571614344-44.994041185558.8588236728
21.48488817783-1.89451543168-0.8913337369934.7104857053-0.6927466992415.751675122640.203571662740.3823614232870.73164601863-0.183084679097-0.232747670371-0.549888458597-0.828521726408-0.1266398175480.03917119964940.513354582701-0.0900489616449-0.115632544780.5207397545720.09767973861290.61390841534246.2381756279-53.530365553747.3405482135
33.2833350387-1.8824217966-0.5889477657285.38091467183-0.4885091009554.98435342207-0.276314105641-0.08530881085680.1581933073090.4278476821940.13539935641-0.0619154201584-0.161935307637-0.5466829097430.1339217452420.353995608404-0.0396201117672-0.1247408568710.384196685395-0.01113949425720.30028849587840.6944094193-66.890363593863.6014192787
44.669312061691.42929158261-2.519501952428.76446357793.251234342935.448076257980.509374602366-0.507801220850.3364699852510.747005374762-0.572202023345-0.632639597272-0.5809220935010.3190657352020.05378367176760.70302368957-0.112030035878-0.2235303155360.4089718002580.034037247870.40040645409660.8013701236-62.877211896198.3718961374
58.566826189254.15666867142-2.119158193163.65842115408-1.608404947623.596599600930.441429257601-1.159569122690.9087806426991.24143670625-0.3885141181540.556868171196-0.728318941595-0.17536335601-0.01693873520491.0020734519-0.09404009231220.1190966805660.591903722017-0.04635305532060.53171246444347.0744820349-70.4064976308108.424693486
64.45194253973.088357473350.01110647314436.35689567321-0.8441149906992.50466387956-0.1473775703830.149403543588-0.029967597078-0.1579193621850.08498477629310.06404992276320.0404435229993-0.1586530864430.04798514448140.2930497195450.0591805265134-0.05508430802970.233705099064-0.03648291384120.28165127259848.6078663126-74.890696372583.6369223412
75.64776783565-0.9265341800852.327932160042.011326749074.877352812298.84779717532-0.130473518570.17771271452-0.7088935307490.784934406201-0.016662560899-1.449217463760.2733604309880.8279748897120.09732296244750.733153660721-0.0296176661630.02266213135030.3877745696290.07561152280410.91784994608556.8941032237-102.94342686892.7599449445
88.113758334274.182677473431.390142729759.55400182568-0.1273291349586.803903842960.135280368528-0.110753140832-0.5693596326680.349508189846-0.570746836011-0.6289230657030.2864381721710.3375201493460.4125708734640.5533710255610.0512226930760.03122978894690.2492949732340.01969977687530.55839064200552.9182646032-93.178114652594.4186059325
99.86384822515-2.604005853387.217753119534.02862910703-3.701408959342.003085305990.405360275599-0.60050813864-0.4579144376762.007812269570.2968177824670.8266991177490.358049757181-0.207136555766-0.7113789408651.316049195550.003732991365620.1029620870720.4094954139250.07149534466340.74589231088845.0433327925-101.81377433896.7581097285
102.42629183744-0.113715927715-0.4039987168631.9354203257-1.684955473622.75891816237-0.026527108539-0.346030791199-1.25536160662-0.586578635692-0.197160096919-0.4774313114810.886070418564-0.2450797530820.2164723597360.5874518268830.0037090871115-0.01783170105890.340159303473-0.03522797361240.89563306323249.1674819699-100.07427661992.183492874
117.357640874581.662225728652.625726407617.18252719470.3325599337114.02810341740.211702588949-0.0288659603763-0.1843554445980.1166152339920.0392517784990.7398085182360.505501144814-0.720499176225-0.2335873622040.854334333624-0.4985759090940.06072503835180.961327663283-0.05902874771820.51719539574128.4483668764-83.696561103640.2018676461
122.000668094681.599722371261.999486666839.69983981579-4.130611730652.00036385409-0.3312863530831.372847762060.0757794253781-2.770265262580.3892133081330.266477578214-0.391458213797-0.201652876496-0.05316130728521.29345208576-0.4682120225770.007905478710011.33709580954-0.03683174674780.56256783333731.5653476873-78.713757282926.3320204338
135.01544533927-1.923947051931.878434871872.012984732014.825167569136.20199989340.2349739090970.778715403311-0.131563262881-0.687672415471-0.6021040771190.8360852702370.0417886201976-1.142423687150.3454128454050.574734238542-0.147496314575-0.1186883030280.7043594003550.01762934595190.53745145733731.5817412627-72.720701074338.8493139987
142.0156719372.505115235973.276634244767.98447307897-4.433187407098.26672737543-0.5557846828591.09916539977-0.418620102105-1.482885346460.254887414301-0.3929523525781.036194405620.1318392319410.2774569726220.742744939275-0.1753365285750.19100250220.60240141751-0.1358212884640.58466374094939.8312284694-80.773656848632.2249527293
152.862795132411.524623745131.885500299331.001993965680.6078402155532.082165995790.01432877024710.321141490397-0.3451641428280.009560336840670.0298185024623-0.0663591189360.557555688676-0.507640170127-0.02060241987320.738455361565-0.382402555601-0.03956968663680.592470936918-0.07034262610450.42030402016835.9663758505-74.232166278545.5374639732
167.879707667882.19390671094-0.7177795082366.93759972356-3.711606705843.98094652695-0.247346030570.379907027847-0.658414093153-0.925710343576-0.208766949222-1.272161497890.5735294273941.023676362410.4325057988540.4329311004110.08457481236270.1228546201870.615943198141-0.03312817904350.62034952550271.1146413727-79.757007132375.0845394831
174.670238319070.623822172962-0.5426934007245.988042846460.9529076081037.408552939340.17092279197-0.0492583321103-0.1234781236610.151282353034-0.245479425585-1.032102096230.2933029092320.8040666375560.06563414336280.3712083522360.0897175988173-0.0495662129370.346500804006-0.01262530871940.62689204895666.5871975534-79.978779208282.741384616
182.007751234366.349017577912.675555068467.931703812589.187140934862.005647914830.140554053757-0.692329561807-1.217096564710.5967526774420.77156415765-1.04887671082-0.1182744699570.579685104082-0.9266602939420.505632927954-0.007303467537530.09623775189460.708158638821-0.09714994553190.5227479417970.6830816212-72.569554930982.8824701963
194.680210095050.3557509575590.8340353585480.193968122604-1.011147515377.014778637120.882977699376-0.2412233533710.2069832583510.890479898952-0.06618590758360.534860286379-0.0384329470944-2.11010044897-0.7783205064770.861299915482-0.1820833104880.4107521497650.7946999648830.03744885241561.1700849597324.6615764936-88.9107952388103.775563794
208.41776905486-7.20586158786-8.080607789562.002366567846.361175956522.00312194620.1032602027530.8109052334991.5250810865-0.604287800484-0.2076657935781.75475493997-1.1142930211-1.247516470720.09209473283990.6633849935720.132366635817-0.008393213487240.6110797806970.0207141415991.1942826086626.4790956774-84.915599461695.3403875526
212.00653073856-1.575708793283.841000810632.00865998899-8.898960947786.87135071053-0.173343623070.244188116252-0.7381643051650.914955594530.2329981868251.2072311916-0.864099595138-0.103999787379-0.03102761014850.6981992765520.04502876130040.1676196284650.737724917734-0.01032324381310.71668739129931.0576083665-79.318538801699.1175888798
227.98934985275-5.03823633546-1.014348779354.555221478634.319476272699.91310595879-0.325889154677-0.250685920598-0.6946055715120.9055363799780.3404341129080.6914040148090.307073705073-0.412662825329-0.003169943015960.700403710747-0.0817983613350.05452550050590.4005457672930.1138964710880.57795705298334.6279826123-93.1534744458102.062314366
236.625039492375.25525584844-7.21376877947.49551195332-3.523836894342.007542369910.456721480387-1.065979360390.2451760832461.85316352982-0.5446982074541.47865337763-0.4348029435520.04383773807960.08941783730270.886753572635-0.1044201753030.2525362610850.712143408258-0.03766183693730.64124919179931.7625015127-80.406129763105.153938955
245.51845170033-2.46364682169-6.275385788372.000743358474.618205925549.11707926642-0.8127631026810.132204187222-0.903798767286-0.311844848370.175763290517-0.07175416013270.6019367952540.6596386355530.6610934973570.617858626038-0.1167157679660.1755819875820.6357676735010.081057515360.85992527742263.7447550716-69.184171600532.7840220671
252.61823363915-1.79960514092-0.7188523480614.78885324135.023374361235.961895561630.1014352079320.3612018356760.1852671472590.2439335526270.206151302763-0.3607970206270.05520843351860.164671889739-0.2597580192820.621927781032-0.04617336490450.1746107826970.5555375054810.1572464271630.74224947939662.9929572768-70.547490604636.1777366232
268.44221831163-3.5310630311-2.855050258369.886726296196.932393865679.42160557472-0.3771709352330.792365279004-0.2958327118861.59754291612-0.144983858533-1.50908907960.03887301703690.795556581050.5115917804540.622229393768-0.210248154447-0.1170178794120.5445639997140.2345454642160.9799197389662.7628382035-70.48301829244.0324521721
276.48812227405-6.603958830897.388808216929.81488965569-4.987087403382.00478202433-0.458398935448-0.2568600399640.2127864225741.157559882160.114921337465-0.700880482973-1.158907862520.7598787819710.3654420481940.597347783774-0.217444806282-0.09597518437770.5952060413430.1240664457090.47989057736258.0834427435-63.8113553545.166582602
289.16378675166-0.725275408084-4.957497355342.001616862790.3367852647862.00081537619-0.09523612221550.2084861827490.337617959553-0.321490186689-0.4391834270330.632666324240.5286628039120.7146137815750.5245492631540.80274155658-0.05237859204490.03703144322870.42910445570.008102844851730.42287891583650.127516486-65.576670858833.7209624637
296.725932937961.97761826597-4.725485688557.6840827051-0.228104278965.43983754824-0.6589933445840.228267734837-0.0350586235983-0.8305440198710.1876873232920.2189550316530.4390823315470.2424454081220.4935154343070.686022466351-0.0242055551115-0.04381673625870.4142651683470.0594304737840.43293594232750.6615698831-73.994971046938.6076924775
309.14115353365-8.29420627967-8.802335077487.526096378847.95357762212.001731885290.04087755224631.33827228075-0.676947933149-1.213247834050.339010328192-1.362920339470.2988542622190.573242536977-0.3834164018070.7410623941850.01221637252530.1678302278140.758923626068-0.05346278539080.63725946095858.1730044118-74.180428429127.9371003511
312.01591434342-2.44012613366-7.930489858898.96005391563-1.760121591119.43007041371-0.167325177050.06483107593790.717655708474-0.2070740416240.257130363129-0.910552509351-0.9733840937080.764018469456-0.06840654755890.389904347862-0.114254567508-0.06486214642980.5331955453970.05313814802910.5344024684158.0769786975-60.966699076639.7732039847
329.95041248689-2.08236206162-1.524018149172.00679955899-2.769513474683.38896294653-0.440518739081-0.539594326184-1.138886017851.026128274650.3235293543181.06538379027-0.285253133797-1.426114653850.1077137116840.5798837763410.08960166239830.01425202459241.031757068210.1938312627710.64325784155320.9310112826-70.493402056669.9872915828
339.243309846463.87726414773-0.3376515251156.296483834381.097226308485.11751676226-0.0485236742995-0.105597353007-0.21650624173-0.0121737764373-0.2755842161291.7560295714-0.458352194262-2.690420782410.3279986791070.5428821919510.0614946976535-0.06625104515181.67631583550.0755240310330.97623361787314.1844750144-65.61413757765.2446849062
341.956667138161.5995551346-1.802656676179.081197591444.95807510336.97363963079-0.4950289759450.2635557284740.592601912248-0.6767712886290.1818459010741.04677932393-0.355456145579-1.287023866710.3123613391330.482855452840.108268309682-0.08330941221961.096298608270.147194747530.66521147224324.319189164-64.712657629258.1691568439
355.35979212449-4.67489243094-0.8163764842529.285073026061.476152054555.08519570999-0.3532654868940.0468502919529-0.5002869776040.05352208740420.5261831635870.974510735693-0.272339379092-0.531347808881-0.168173288420.365339014654-0.07377750476170.01190561202970.9400741578170.06968676143440.5251016113225.4184159391-68.153895426264.5614105894
360.01454679296860.208389997503-0.2279273043552.73943795816-3.028650793593.349718071650.1350105509860.4022753176130.01617321834-0.2344057437870.179355570311-0.111289415773-0.248405543678-0.55053655456-0.3055470228541.53444909623-0.1568389746540.3178684978652.117928959530.2667863126750.7218389759140.6962579165-43.563539530126.7292952426
375.44089483153-1.135692204880.8109511718825.27323569318-4.458372033167.50382475612-0.3593711782250.8090062014070.686355956092-0.6590970188870.618702635791-0.1437255037030.967824522803-1.99136477859-0.2297245563610.98546054539-0.09168821793260.09408757796481.403100409050.302644676841.0124707523440.9416877639-36.801144397129.1501109886
388.16639724351-3.30820269438-0.697374170722.88054642438-0.4224524261480.381858168290.7909535998951.476937073361.29235982317-0.356987026438-1.54113993836-0.5324603627690.6984583218860.05238125713850.7340703756021.00413011484-0.002018631283110.0273763985761.017889696530.2023156569830.62113791156141.4002480561-35.000867556138.0293217738
398.731011730315.30778311827-2.444223065268.41368717799-4.818130436948.101367640150.2583008190131.911885714321.38682352943-0.831392072738-0.213303874881-0.610609978453-1.32481893605-0.218692719352-0.0574660325991.039989117360.1661980841130.01180036696740.9581096009860.3056982378230.93502426941852.6000575226-39.14587271632.2141849378
408.495752063251.50862401251-7.704195011069.16401916402-1.737188397017.01670509880.4091460119650.962876342293-0.01008421184080.6409804831890.100293007773-0.08813056546850.173451866057-1.91800655075-0.5152488085720.871905945363-0.101692508432-0.1533202954121.30890288570.09393960645260.65729458079543.6890628721-42.351224389634.1823572071
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 240 through 288 )AA240 - 2881 - 49
22chain 'A' and (resid 289 through 360 )AA289 - 36050 - 121
33chain 'A' and (resid 361 through 499 )AA361 - 499122 - 260
44chain 'B' and (resid 241 through 288 )BB241 - 2881 - 48
55chain 'B' and (resid 289 through 334 )BB289 - 33449 - 94
66chain 'B' and (resid 335 through 499 )BB335 - 49995 - 259
77chain 'C' and (resid 1 through 34 )CC1 - 341 - 34
88chain 'C' and (resid 35 through 44 )CC35 - 4435 - 44
99chain 'C' and (resid 45 through 56 )CC45 - 5645 - 56
1010chain 'C' and (resid 57 through 76 )CC57 - 7657 - 76
1111chain 'D' and (resid 1 through 16 )DD1 - 161 - 16
1212chain 'D' and (resid 17 through 22 )DD17 - 2217 - 22
1313chain 'D' and (resid 23 through 44 )DD23 - 4423 - 44
1414chain 'D' and (resid 45 through 65 )DD45 - 6545 - 65
1515chain 'D' and (resid 66 through 76 )DD66 - 7666 - 76
1616chain 'E' and (resid 1 through 34 )EE1 - 341 - 34
1717chain 'E' and (resid 35 through 65 )EE35 - 6535 - 65
1818chain 'E' and (resid 66 through 73 )EE66 - 7366 - 73
1919chain 'F' and (resid 1 through 22 )FF1 - 221 - 22
2020chain 'F' and (resid 23 through 33 )FF23 - 3323 - 33
2121chain 'F' and (resid 34 through 44 )FF34 - 4434 - 44
2222chain 'F' and (resid 45 through 65 )FF45 - 6545 - 65
2323chain 'F' and (resid 66 through 73 )FF66 - 7366 - 73
2424chain 'G' and (resid 1 through 7 )GG1 - 71 - 7
2525chain 'G' and (resid 8 through 22 )GG8 - 228 - 22
2626chain 'G' and (resid 23 through 34 )GG23 - 3423 - 34
2727chain 'G' and (resid 35 through 44 )GG35 - 4435 - 44
2828chain 'G' and (resid 45 through 49 )GG45 - 4945 - 49
2929chain 'G' and (resid 50 through 59 )GG50 - 5950 - 59
3030chain 'G' and (resid 60 through 65 )GG60 - 6560 - 65
3131chain 'G' and (resid 66 through 73 )GG66 - 7366 - 73
3232chain 'H' and (resid 1 through 22 )HH1 - 221 - 22
3333chain 'H' and (resid 23 through 44 )HH23 - 4423 - 44
3434chain 'H' and (resid 45 through 55 )HH45 - 5545 - 55
3535chain 'H' and (resid 56 through 72 )HH56 - 7256 - 72
3636chain 'I' and (resid 1 through 7 )II1 - 71 - 7
3737chain 'I' and (resid 8 through 34 )II8 - 348 - 34
3838chain 'I' and (resid 35 through 44 )II35 - 4435 - 44
3939chain 'I' and (resid 45 through 59 )II45 - 5945 - 59
4040chain 'I' and (resid 60 through 74 )II60 - 7460 - 74

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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