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- PDB-7ux5: Structure of PDL1 in complex with FP28136, a Helicon Polypeptide -

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基本情報

登録情報
データベース: PDB / ID: 7ux5
タイトルStructure of PDL1 in complex with FP28136, a Helicon Polypeptide
要素
  • Helicon FP28136
  • Programmed cell death 1 ligand 1
キーワードIMMUNE SYSTEM / Complex / stapled
機能・相同性
機能・相同性情報


negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production ...negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / positive regulation of interleukin-10 production / Co-inhibition by PD-1 / positive regulation of T cell proliferation / negative regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / cellular response to lipopolysaccharide / early endosome membrane / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / immune response / positive regulation of cell migration / receptor ligand activity / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
類似検索 - 分子機能
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
N,N'-(1,4-phenylene)diacetamide / Programmed cell death 1 ligand 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.35 Å
データ登録者Agarwal, S. / Li, K. / Tokareva, O. / Thomson, T. / Travaline, T. / Wahl, S. / Verdine, G. / McGee, J.
資金援助 米国, 1件
組織認可番号国
Other private 米国
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2022
タイトル: De novo mapping of alpha-helix recognition sites on protein surfaces using unbiased libraries.
著者: Li, K. / Tokareva, O.S. / Thomson, T.M. / Wahl, S.C.T. / Travaline, T.L. / Ramirez, J.D. / Choudary, S.K. / Agarwal, S. / Walkup 4th, W.G. / Olsen, T.J. / Brennan, M.J. / Verdine, G.L. / McGee, J.H.
履歴
登録2022年5月5日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年12月28日Provider: repository / タイプ: Initial release
改定 1.12023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Programmed cell death 1 ligand 1
C: Programmed cell death 1 ligand 1
B: Helicon FP28136
D: Helicon FP28136
E: Programmed cell death 1 ligand 1
F: Helicon FP28136
G: Programmed cell death 1 ligand 1
H: Helicon FP28136
I: Programmed cell death 1 ligand 1
J: Helicon FP28136
K: Programmed cell death 1 ligand 1
L: Helicon FP28136
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)102,40518
ポリマ－101,25212
非ポリマー1,1536
水00
1
A: Programmed cell death 1 ligand 1
B: Helicon FP28136
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,0673
ポリマ－16,8752
非ポリマー1921
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Programmed cell death 1 ligand 1
D: Helicon FP28136
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,0673
ポリマ－16,8752
非ポリマー1921
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Programmed cell death 1 ligand 1
F: Helicon FP28136
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,0673
ポリマ－16,8752
非ポリマー1921
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Programmed cell death 1 ligand 1
H: Helicon FP28136
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,0673
ポリマ－16,8752
非ポリマー1921
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
I: Programmed cell death 1 ligand 1
J: Helicon FP28136
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,0673
ポリマ－16,8752
非ポリマー1921
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
6
K: Programmed cell death 1 ligand 1
L: Helicon FP28136
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,0673
ポリマ－16,8752
非ポリマー1921
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)76.477, 77.882, 127.747
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 18 through 44 or resid 48...
d_2ens_1(chain "C" and (resid 18 through 44 or resid 48...
d_3ens_1(chain "E" and (resid 18 through 44 or resid 48...
d_4ens_1(chain "G" and (resid 18 through 44 or resid 48...
d_5ens_1(chain "I" and (resid 18 through 44 or resid 48...
d_6ens_1(chain "K" and (resid 18 through 70 or resid 72...
d_1ens_2(chain "B" and (resid 1 through 16 or resid 101))
d_2ens_2(chain "D" and (resid 1 through 16 or resid 101))
d_3ens_2(chain "F" and (resid 1 through 16 or resid 101))
d_4ens_2(chain "H" and (resid 1 through 16 or resid 101))
d_5ens_2(chain "J" and (resid 1 through 16 or resid 101))
d_6ens_2(chain "L" and (resid 1 through 16 or resid 101))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAVALA1 - 27
d_12ens_1LEUGLYA31 - 53
d_13ens_1GLULEUA55 - 57
d_14ens_1VALLYSA59 - 72
d_15ens_1GLNASNA74 - 114
d_21ens_1ALAVALB1 - 27
d_22ens_1LEUGLYB31 - 53
d_23ens_1GLULEUB55 - 57
d_24ens_1VALLYSB59 - 72
d_25ens_1GLNASNB74 - 114
d_31ens_1ALAVALG1 - 27
d_32ens_1LEUGLYG31 - 53
d_33ens_1GLULEUG55 - 57
d_34ens_1VALLYSG59 - 72
d_35ens_1GLNASNG74 - 114
d_41ens_1ALAVALJ1 - 27
d_42ens_1LEUGLYJ31 - 53
d_43ens_1GLULEUJ55 - 57
d_44ens_1VALLYSJ59 - 72
d_45ens_1GLNASNJ74 - 114
d_51ens_1ALAVALM1 - 27
d_52ens_1LEUGLYM31 - 53
d_53ens_1GLULEUM55 - 57
d_54ens_1VALLYSM59 - 72
d_55ens_1GLNASNM74 - 114
d_61ens_1ALAGLYP1 - 50
d_62ens_1GLULEUP52 - 54
d_63ens_1VALLYSP56 - 69
d_64ens_1GLNASNP71 - 111
d_11ens_2ASPGLUC1 - 16
d_12ens_2WHLWHLD
d_21ens_2ASPGLUE1 - 16
d_22ens_2WHLWHLF
d_31ens_2ASPGLUH1 - 16
d_32ens_2WHLWHLI
d_41ens_2ASPGLUK1 - 16
d_42ens_2WHLWHLL
d_51ens_2ASPGLUN1 - 16
d_52ens_2WHLWHLO
d_61ens_2ASPGLUQ1 - 16
d_62ens_2WHLWHLR

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.375700324402, 0.179660712287, -0.909159664033), (0.196239672495, -0.974205036856, -0.111420541655), (-0.905725817885, -0.136552461071, -0.40126570772)-15.1273950397, -9.41534241741, -25.3657835081
2given(-0.534470599955, -0.281758083762, -0.796839732957), (-0.453172211049, -0.700284483516, 0.551576458235), (-0.713425626759, 0.65590702419, 0.246596534245)22.9465706958, -8.71977870723, -28.0436376011
3given(0.584561943154, -0.34618883027, 0.73378513777), (0.263768024292, -0.77418765244, -0.575378056734), (0.767276849629, 0.529893170937, -0.361247094684)7.20329250665, -13.6514894891, -69.9731882209
4given(-0.436514163763, -0.289777353043, -0.851753761657), (-0.778186940852, 0.596731838927, 0.195796316358), (0.451531250216, 0.748291519446, -0.485982851553)22.2323658635, 29.0514059448, -34.4519483454
5given(0.51252990679, -0.377657539518, 0.771160085515), (0.460041635369, 0.879088632294, 0.124759249348), (-0.725034335996, 0.290822900432, 0.624297406859)16.6899558268, -33.6711912412, 13.9680539479
6given(0.535018293854, 0.295809596174, 0.791360921485), (-0.362984365531, -0.765349544388, 0.531490757479), (0.762887787045, -0.571608920257, -0.302101748855)54.8526537699, 29.2326356197, -34.1216924057
7given(-0.795853482844, 0.501604876966, -0.339130920514), (0.433923202054, 0.0818637461227, -0.897222927588), (-0.422288868625, -0.861214766754, -0.282809541849)12.1162021965, -73.0929076656, -56.0805002319
8given(-0.528730283442, 0.461642169892, 0.712271573453), (0.361036017528, 0.881781528898, -0.303503425586), (-0.768177896986, 0.0966842400423, -0.632894048249)44.6112217222, -21.5236936391, -62.6448765548
9given(-0.796930785293, 0.568365726268, -0.204601379899), (-0.470613760392, -0.796513856648, -0.379589732074), (-0.378713627933, -0.206218518496, 0.902247144993)21.5586250371, -4.37212752112, 28.9740630099
10given(0.996468947605, -0.03730409518, -0.0752199504177), (0.0354393302906, -0.625294645743, 0.779583645207), (-0.0761162947508, -0.779496639177, -0.621764665437)4.00612335215, 11.8022532442, -39.6791758266

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要素

#1: タンパク質
Programmed cell death 1 ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


分子量: 14809.955 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9NZQ7
#2: タンパク質・ペプチド
Helicon FP28136


分子量: 2065.307 Da / 分子数: 6 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: 化合物
ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide / N,N′-(1,4-フェニレン)ビスアセトアミド


分子量: 192.214 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C10H12N2O2 / 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 modificationY

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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: 1.88 Å3/Da / 溶媒含有率: 34.43 %
結晶化温度: 291.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.1 M TRIS pH 8, 25% v/v PEG 350 MME.

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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: NSRRC / ビームライン: TPS 05A / 波長: 0.99984 Å
検出器タイプ: RAYONIX MX300-HS / 検出器: CCD / 日付: 2021年6月11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: 0.99984 Å / 相対比: 1
反射解像度: 3.35→49.02 Å / Num. obs: 11440 / % possible obs: 99.64 % / 冗長度: 10.8 % / Biso Wilson estimate: 84.48 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.199 / Net I/σ(I): 9.9
反射 シェル解像度: 3.35→3.47 Å / Rmerge(I) obs: 0.75 / Num. unique obs: 25562 / CC1/2: 0.949

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20_4444精密化
XSCALEデータスケーリング
PHASER位相決定
Aimlessデータスケーリング
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 5C3T

5c3t


解像度: 3.35→49.02 Å / SU ML: 0.511 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 29.5823
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.3007 550 4.81 %
Rwork0.2332 10887 -
obs0.2365 11437 99.66 %
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: 83.62 Å2
精密化ステップサイクル: LAST / 解像度: 3.35→49.02 Å
タンパク質核酸リガンド溶媒全体
原子数6417 0 84 0 6501
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00586627
X-RAY DIFFRACTIONf_angle_d1.04578961
X-RAY DIFFRACTIONf_chiral_restr0.0619981
X-RAY DIFFRACTIONf_plane_restr0.00631135
X-RAY DIFFRACTIONf_dihedral_angle_d16.83942413
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.400500517692
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.478242121953
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.392318831841
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.481185632814
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.444302257466
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.218465458371
ens_2d_3CX-RAY DIFFRACTIONTorsion NCS0.216905558896
ens_2d_4CX-RAY DIFFRACTIONTorsion NCS0.215707317337
ens_2d_5CX-RAY DIFFRACTIONTorsion NCS0.210308759941
ens_2d_6CX-RAY DIFFRACTIONTorsion NCS0.206678679007
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.690.36151150.28412667X-RAY DIFFRACTION99.53
3.69-4.220.31831740.25662654X-RAY DIFFRACTION99.96
4.22-5.310.28081180.20882734X-RAY DIFFRACTION99.79
5.32-49.020.28251430.21992832X-RAY DIFFRACTION99.37
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)
17.91563065838-3.328713116310.2794459699159.44875074090.7095719511438.456185679680.651082122382-0.242582896153-1.426941314220.12119834348-0.410188906146-0.64612803562-0.008071312894940.82436973816-0.1947309141570.309864760006-0.0676211719687-0.0708197589370.7428887715230.008101302103380.85269968078918.97526826871.47543734953-14.5170028744
24.03011865628-1.109464618681.576349309732.510520931263.225284302836.51620339181-0.467683032015-0.787822308642-0.2362171492060.525277492268-0.641380608871.49358806912-0.6408787453531.151496317151.105012693730.772998032018-0.0576031575680.170818976270.836269728564-0.1160244330630.5367596349289.5734774905218.0339196661-5.27576846075
37.844657696250.9610982493842.949605937789.26824278756-1.966337953815.444396656710.217099725205-0.89524644401-0.6514059317191.020647177530.02680655677250.51231535037-0.726207876568-0.117569205753-0.186617703330.6194422711430.08123877624450.04055893187110.5593567668570.09403068638820.3983658458875.02847472724-0.511580765734-6.76897110915
42.044762201297.019411188757.695477178532.006549729169.909734130737.735443280990.915566455334-1.863276353060.3250435577382.46060421159-0.006684726111081.563893248454.58346901951-0.523145444826-0.7053435781621.11800317030.2068093206520.1401096882291.096303640230.1836399321980.67753831249810.6780723433-10.3651821374-3.9079727242
57.168841818722.01351687637-0.02651265990252.03668978457-6.795553424883.63083912321.89150208806-0.8104523821970.219570503188-0.189615612827-2.681753371072.36975396980.5859954138240.5198995304720.9036021584670.6206730910830.0861625131167-0.1876410931190.64181445944-0.0698147667730.67782178497115.56761729696.50175647858-2.72658069086
66.0447547638-6.92455661234-2.93716441412.02445271654.033570814471.28471487143-1.36144512555-0.571864117362-0.7414219449231.606682030441.75510477380.0118583683290.8351322933680.144747027027-0.5228627107520.6613368687020.228491821914-0.2427916205131.056346961420.025486573750.85087265882817.2127374077-5.84640646357-9.11309705374
78.96509726606-3.58931749784-1.166914000067.240501575731.907506181554.2453892105-0.609011494532-0.683676043845-1.34948492657-0.1347489485990.429824310590.1155560378930.2801537803771.143337581010.1310069173150.3410408198610.02695041667890.09773161266130.6811766202530.0005178470630070.59660507576412.00300849421.07599254742-16.3725510366
83.968983367943.634387259761.013632680957.03414714958-2.80144829288.01047302609-1.0859728880.265576270726-0.0244412371356-0.4542011130390.932737450399-1.76437979097-0.0660460785720.3688048948980.1524762881460.507566458950.00383402207440.07491057291310.5802802625940.003522733353090.6627027942125.47358282399-5.46615191077-36.9440554296
92.032563928423.00053659962-3.504523008092.88514404711-3.518978382017.18687046401-0.2025369846780.359464711847-2.62715623175-2.51572387777-0.663569793951-0.6597828074272.536119428431.140537866340.8609966392772.016617677430.065531109829-0.5572656212350.8130134823750.2425259153541.33683385225-3.86973777784-24.1208000416-34.697474546
106.892279153354.64261892663-5.367349134247.994148725741.770985316636.360859549360.02415281629540.2192905972220.0675081822837-0.963969567863-0.2853499164081.25558362587-0.0769820989763-0.9749729108630.3474368412210.6651451429990.0110674239285-0.2562595043540.7211164291770.0412499425530.746618779885-7.26930437654-6.67239638167-30.5634416339
118.033675324431.599861101493.121410160182.16652017939-7.945791252728.25327141393-1.034200655880.005648420965591.02009914335-0.6901586593850.6757739228190.2024800146670.0337653936141-0.939388273210.2319249783310.7254522673240.0307338600728-0.1218700369260.6040712562620.009526738392310.656545529199-0.249459647275-4.18580761865-32.7877912666
122.65419685928-2.34414061845-0.8115053705099.16641211329-2.421650513219.79056993031-0.06776944783020.09730225089220.5876014218212.0774838252-0.0253226332662-0.964418450609-0.841085187296-0.1859193430910.1723948777040.417886183472-0.058885285988-0.1072996921530.54585387053-0.09092805198120.5544015222157.37500391118-1.10781552769-32.313051895
139.282050570737.998614362840.4976204504269.19456752102-3.068678393769.545713318150.750617021224-1.184366052750.1352114313950.751344319048-0.1916271270190.383302670570.06248808206410.187575305349-0.5810998539620.3822598507350.03170225860190.06518476850150.686844986773-0.03239485600690.448065366008-2.33051680402-3.41747844634-10.2955182596
145.98332287456-2.817991139465.157288422888.68118147181-5.240780630812.58550399207-0.482423927034-0.839568476169-0.0374612634147-1.026766222691.433179984790.6022390436020.247771133574-1.33862279021-0.7840797571120.6780292534550.0511307242502-0.01942233152820.624865124417-0.05662509274320.604462180871-7.38490802955-5.52045897872-18.5164563805
154.245541636352.00401723287-2.367916873416.67264227969-0.4968585543474.60030231747-0.0681597219697-0.00810035151001-0.03721603540440.286394276956-0.09532791608050.980671204094-0.000353116376201-1.058847469130.1252770339610.4955326777270.01503012905190.03600823065850.966208081114-0.03427640589730.80655688678823.0825193939-20.1730788135-37.726800332
164.187364580940.855828341568-1.796818609963.341228419330.04717122091265.79419832784-0.01796560886450.333508084129-0.135458900727-0.3729962133890.3631832869630.458658921581-0.1653582661471.10446665093-0.3755895596250.712250840849-0.03716395190820.1291337037560.621551109553-0.1176294175860.79037496132728.9715658754-24.3652568617-46.3110507062
175.267742305533.06823338467-1.782882587253.81263629557-2.719936283968.047598911130.844810420598-0.8218320377210.7995200027470.262545606959-0.7899522971930.626559653288-1.01989783432-1.07341463191-0.2816542937850.9013154614760.1032582174540.05972443139611.32015335843-0.3712640812490.83288883502633.5353459102-11.1103914139-31.1659023715
187.744408830526.82922560927.30146062881.997820987768.139045020047.097274160410.737669654668-1.53732726768-0.2682709154250.806438636629-1.067650451980.310450998-0.18207573245-0.5518792083630.4098543074710.693690316521-0.274844666490.2079516632220.728875569707-0.09508515214830.639521451149-0.86062534903-7.09102789701-47.1718586899
196.892717667571.97066839101-2.31351935767.25023930684-3.952156468612.11112663031-1.560478594920.604894223917-0.545283406908-0.02387178335190.263416926435-1.33393376741-2.327030768782.242201116331.212305516271.02976306476-0.319499783361-0.1311865396261.361360161890.2552020519561.0316322136313.86033347766.11486933375-50.9742204187
200.433378201963-0.5368011173861.516507083627.365259906720.3386222487154.86977541923-0.38603018161-0.695226428779-0.1499859992270.4320187487620.356627968436-0.8625313422870.1073839209810.4878876114090.02074589565490.3554584258150.0597410289907-0.1230086329590.9187404750640.100041665930.878107058495.0227699206-15.4683259416-50.6669334654
219.277276454960.606277330513.186588471789.070404630172.192860528929.603572199340.09208830438332.1224267850.404651489838-0.6485709341320.0785870084796-0.260319439708-0.7104236247291.48811919385-0.07576400796660.455996711472-0.09918427099150.09680130134010.7443315247620.02796209637150.5260328273163.69342217906-6.21865756125-62.0133467877
225.13150490197-2.675502972221.584845099762.09344515002-8.687516896436.184916274160.8303722883681.51459081693-0.745837449021-0.0223298959443-2.08569349726-0.17711474064-0.2878057623330.9999081106741.327931088430.8662374087710.04575362975320.05208546892360.926344832506-0.07233048272450.7216591327458.50147547048-10.9328218362-67.1387667658
231.92411983146-3.501545687810.5291202607136.71893579914-2.173637868147.56434669209-0.999033257330.210028186547-0.741258644537-0.2956388353290.228563365309-4.970691913371.06375437547-1.370155887690.5522317700031.12834339189-0.442438240736-0.1434543212311.224237284280.7248543954412.3100998043313.70167141-0.922808195432-65.5571079116
240.545363434083-0.7683980857942.075645346352.121360411382.356825541381.955029562470.327038092369-1.399919891911.159626859110.4072101423580.205013255943-3.816896869750.215678539333.77536279079-0.3063682277710.6196821169550.202167604071-0.01137313152591.081276873330.2181503512081.5720634457512.0901010833-12.9043008545-53.7726510072
258.03910511387-1.439568142663.299152892119.229216649322.463792975077.489611837421.477198311740.545357972632.032986373730.6217232914370.130507233742-0.362170155624-0.9705486347031.52261065569-1.71889707720.723647193151-0.04188154708240.06661672203790.547503501876-0.1074593727241.2303822884210.5766603137-7.00130224871-53.2377545447
263.143329137982.52784986901-2.608621377893.139896813270.2212433196057.34239787471.55030894519-0.352923360957-1.85292261874-1.5745482951-0.444939373044-0.313776876241-1.034654458491.32740782615-0.7225403897231.0594152164-0.527483159576-0.2638341163071.082027669921.416318233862.0916536931414.16910822286.45950546431-59.0609622154
279.30285660984-3.541117096752.962854216626.57828926944.293755218166.05691117548-0.5645240892271.396113390450.422958600117-0.7903828266470.6986306703660.814244611128-0.5273685321960.609966238398-0.1204416702160.573814444134-0.1303348819560.01078107008480.4198951469410.0701653733080.4149168687490.678721622443-2.99612964162-54.46198493
286.202826878883.98353915815-7.175171079126.09897436585-7.042848188212.26955665356-0.3107083305920.174182305939-0.123036860968-0.08148645068430.236463810578-0.3987688905720.8163873620640.5532511207280.2237209307760.816658114003-0.1256445476220.05762441052570.674054201916-0.05847751099710.493123872837-0.628636568569-5.66337203713-69.916774505
298.548705253113.880430475-3.464007591068.6740732673-4.021493547432.001303479510.07444191549730.0741492865685-0.9236100303430.801511394346-0.2431011158-0.829977099984-0.132183831983-0.1463522564840.11154400490.6771449135040.04290829290940.002594919952521.15562184870.1465594452170.60276521145725.892838409512.2730603685-17.7583991018
304.969710360822.193848274740.813296391892.929198917690.7727180627930.1416392258620.850613457627-1.18016710028-0.143182988008-0.2313691111240.417422075461-1.88047695496-1.69783469615-0.633175271611-0.8388756438110.8488718093310.3126508274990.3056138459141.38986626256-0.002335980625230.89304475159117.07717189230.6471801439-14.2081922637
315.26313366715-4.01854066449-3.884797072788.80500645536-0.1162915106545.313105411480.1586812184690.3958088726770.256142080635-1.206544812150.391899545080.2819150108530.0907777853044-0.260473200366-0.511889774370.674283894027-0.179280444376-0.1320015359110.9515380853880.02821990962860.6993749564627.968473663722.2885721874-27.2065649423
327.8303646369-0.32833019772-1.479087559047.84722119397-5.153220070564.01623869976-0.04944729973240.9482796522090.151425080306-0.6072800570060.9960938441780.253202902943-0.135695623982-1.87125770311-0.9412060039110.776245333853-0.03753012816-0.2680566250251.150792147470.07571834739330.79784522694622.941559576620.6707566147-33.9941051912
339.490703670351.53424926084-5.815773615187.515028461472.712280137052.0883849850.6906391065110.5894109019660.0682081183711-0.2329237301360.1655037102111.05705780988-0.132669673989-2.58796473215-0.8253291738330.486343544931-0.094235277806-0.03184523239540.8064826499940.1607054884950.87443938114717.64014732718.8682999552-21.4156829403
349.270090746423.09192657118-1.593131695974.436870274891.625831268848.176880094060.0848634564942-0.204461105362-0.1786582885060.212468444105-0.610047622328-0.2602668109230.950041901808-0.02676296325560.4454539971260.6017032080810.08687047375130.2188261982770.5905039673940.1732183708460.73570212529629.832957263214.3357451886-22.834491581
355.680738408323.816080333313.407860809662.558820757692.965191474062.14227605033-0.90890129941-0.395648869328-0.637606426771-0.755487062852-0.004363464817240.364163763349-0.914671210495-0.8714563955690.9288398078440.8071852567330.1611582576240.09556509116140.7710726374170.3362951514651.2479582545533.105571140126.9940376384-32.6689414427
366.20711053361-0.977737714529-1.789308986362.760691255864.253204419085.389106225610.183598096380.7768890776720.616817682782-0.589575620432-0.160006575242-0.725361079914-0.6759509780720.211537297495-0.1066964461710.866668017957-0.0970916805645-0.02851197070140.7111828514950.2214149717650.7689573668114.7546140178-25.4571318549-8.52574273432
372.001312892418.187138073562.956578207852.01207176609-4.144967026696.773207556082.4043661285-2.994346219733.131392574270.615998102344-0.6673950403782.38572717860.582879056284.27761468342-1.652161038760.748559020826-0.05031490961890.09487149981562.18373178784-0.09724682792491.043192319110.9094148507-16.84223457318.95921608076
381.91390944663-8.8383113556-5.554137447329.657212559591.940814975085.692756825730.4176831816870.4363090888040.5720171716380.644786117236-2.38413286389-0.553152455912-0.456751333042-1.549026032112.014778689060.654466628263-0.105200626097-0.1320051439180.836743490676-0.1824872535680.95448365736912.392988177-32.39292064223.44119482246
399.962749192610.7463950474524.508935406637.85127426617-5.324925383096.11072275359-1.413485203480.8580602516042.058520142011.33392354649-1.983601752170.837650251089-4.400499405752.224920708312.950944528911.4150138289-0.275106013306-0.384770403441.046203443710.07180265736031.1943777406117.4671480518-33.35957986310.0337254743
400.689787605337-3.179829979910.05273727758452.0770814417-1.189311449355.62008803077-0.4577054050690.370052890976-0.07308298527830.4778961032090.349395023011-2.51786137319-0.5716652666440.7706948705880.1805809016350.643350611754-0.2675086290520.06003781811441.07601350878-0.1365884101491.0847065947920.5778168685-27.3118490341.01766992361
416.25726054794-1.20458642605-5.385297361454.182767034510.4288722760297.250568317320.13175771102-0.164911821055-0.03925976312950.4898723006640.227160253188-0.661337690822-0.2477369626490.437918674956-0.5529899989770.548311425141-0.247802448278-0.04106033326710.680433091734-0.05864939175430.62351087893612.8901076986-31.3418380803-5.72046221567
422.27029870081-5.641729685282.246947187588.76562581315-4.365953117116.85278893492-0.566550265384-2.564521053280.1929608135280.830034011520.824677807144-0.720765876667-1.586357646710.851374863502-0.2471356983990.981913563238-0.2571938765310.1310704838521.0894579928-0.08710565222810.7344845750638.81867587435-39.19081306788.2530688356
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 18 through 41 )AA18 - 411 - 24
22chain 'A' and (resid 42 through 52 )AA42 - 5225 - 35
33chain 'A' and (resid 53 through 78 )AA53 - 7836 - 61
44chain 'A' and (resid 79 through 84 )AA79 - 8462 - 67
55chain 'A' and (resid 85 through 94 )AA85 - 9468 - 77
66chain 'A' and (resid 95 through 109 )AA95 - 10978 - 92
77chain 'A' and (resid 110 through 133 )AA110 - 13393 - 116
88chain 'C' and (resid 18 through 41 )CB18 - 411 - 24
99chain 'C' and (resid 42 through 52 )CB42 - 5225 - 35
1010chain 'C' and (resid 53 through 94 )CB53 - 9436 - 77
1111chain 'C' and (resid 95 through 119 )CB95 - 11978 - 102
1212chain 'C' and (resid 120 through 134 )CB120 - 134103 - 117
1313chain 'B' and (resid 1 through 17 )BC1 - 171 - 17
1414chain 'D' and (resid 1 through 17 )DE1 - 171 - 17
1515chain 'E' and (resid 18 through 119 )EG18 - 1191 - 102
1616chain 'E' and (resid 120 through 134 )EG120 - 134103 - 117
1717chain 'F' and (resid 1 through 17 )FH1 - 171 - 17
1818chain 'G' and (resid 18 through 26 )GJ18 - 261 - 9
1919chain 'G' and (resid 27 through 35 )GJ27 - 3510 - 18
2020chain 'G' and (resid 36 through 52 )GJ36 - 5219 - 35
2121chain 'G' and (resid 53 through 68 )GJ53 - 6836 - 51
2222chain 'G' and (resid 69 through 78 )GJ69 - 7852 - 61
2323chain 'G' and (resid 79 through 84 )GJ79 - 8462 - 67
2424chain 'G' and (resid 85 through 94 )GJ85 - 9468 - 77
2525chain 'G' and (resid 95 through 101 )GJ95 - 10178 - 84
2626chain 'G' and (resid 102 through 109 )GJ102 - 10985 - 92
2727chain 'G' and (resid 110 through 131 )GJ110 - 13193 - 114
2828chain 'H' and (resid 1 through 17 )HK1 - 171 - 17
2929chain 'I' and (resid 18 through 41 )IM18 - 411 - 24
3030chain 'I' and (resid 42 through 52 )IM42 - 5225 - 35
3131chain 'I' and (resid 53 through 68 )IM53 - 6836 - 51
3232chain 'I' and (resid 69 through 84 )IM69 - 8452 - 67
3333chain 'I' and (resid 85 through 101 )IM85 - 10168 - 84
3434chain 'I' and (resid 102 through 133 )IM102 - 13385 - 116
3535chain 'J' and (resid 1 through 17 )JN1 - 171 - 17
3636chain 'K' and (resid 18 through 41 )KP18 - 411 - 24
3737chain 'K' and (resid 42 through 52 )KP42 - 5225 - 32
3838chain 'K' and (resid 53 through 68 )KP53 - 6833 - 48
3939chain 'K' and (resid 69 through 78 )KP69 - 7849 - 58
4040chain 'K' and (resid 79 through 101 )KP79 - 10159 - 81
4141chain 'K' and (resid 102 through 133 )KP102 - 13382 - 113
4242chain 'L' and (resid 1 through 17 )LQ1 - 171 - 17

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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