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- PDB-9b7b: Crystal structure of humanized 44H10 Fab Version 22 in complex wi... -

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基本情報

登録情報
データベース: PDB / ID: 9b7b
タイトルCrystal structure of humanized 44H10 Fab Version 22 in complex with HLA-DR (HLA-DRA*01:01/HLA-DRB1*04:01)
要素
  • (h44H10-V22 Antibody, ...) x 2
  • HLA class II histocompatibility antigen, DR alpha chain
  • Hemagglutinin HA1 chain, HLA class II histocompatibility antigen DR beta chain
キーワードIMMUNE SYSTEM / Antibody / Humanized / MHC class II
機能・相同性
機能・相同性情報


myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane ...myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / early endosome membrane / adaptive immune response / lysosome / immune response / Golgi membrane / lysosomal membrane / cell surface / extracellular exosome / plasma membrane
類似検索 - 分子機能
MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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
HLA class II histocompatibility antigen, DR alpha chain
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: 3.08 Å
データ登録者Kassardjian, A. / Julien, J.P.
資金援助 カナダ, 1件
組織認可番号国
Canadian Institutes of Health Research (CIHR)PJT-148811 カナダ
引用ジャーナル: Antibodies / 年: 2024
タイトル: Humanization of Pan-HLA-DR mAb 44H10 Hinges on Critical Residues in the Antibody Framework.
著者: Kassardjian, A. / Ivanochko, D. / Barber, B. / Jetha, A. / Julien, J.P.
履歴
登録2024年3月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年8月7日Provider: repository / タイプ: Initial release
改定 1.12024年10月30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

ダウンロードとリンク

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集合体

登録構造単位
A: HLA class II histocompatibility antigen, DR alpha chain
B: Hemagglutinin HA1 chain, HLA class II histocompatibility antigen DR beta chain
C: h44H10-V22 Antibody, heavy chain
D: h44H10-V22 Antibody, light chain
E: HLA class II histocompatibility antigen, DR alpha chain
F: Hemagglutinin HA1 chain, HLA class II histocompatibility antigen DR beta chain
G: h44H10-V22 Antibody, heavy chain
H: h44H10-V22 Antibody, light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)191,26214
ポリマ－190,1858
非ポリマー1,0776
水00
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: Hemagglutinin HA1 chain, HLA class II histocompatibility antigen DR beta chain
C: h44H10-V22 Antibody, heavy chain
D: h44H10-V22 Antibody, light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)95,6317
ポリマ－95,0924
非ポリマー5383
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
E: HLA class II histocompatibility antigen, DR alpha chain
F: Hemagglutinin HA1 chain, HLA class II histocompatibility antigen DR beta chain
G: h44H10-V22 Antibody, heavy chain
H: h44H10-V22 Antibody, light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)95,6317
ポリマ－95,0924
非ポリマー5383
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)169.586, 178.801, 178.359
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,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 4 through 32 or resid 34 through 188))
d_2ens_1(chain "E" and (resid 4 through 32 or resid 34 through 188))
d_1ens_2(chain "B" and (resid 2 through 3 or resid 5...
d_2ens_2(chain "F" and (resid 2 through 3 or resid 5...
d_1ens_3(chain "C" and (resid 1 through 200 or resid 202 through 214))
d_2ens_3(chain "G" and (resid 1 through 200 or resid 202 through 214))
d_1ens_4(chain "D" and (resid 1 through 121 or resid 123 through 301))
d_2ens_4(chain "H" and (resid 1 through 121 or resid 123 through 301))

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_1GLUGLUPHEPHEAA4 - 324 - 32
d_12ens_1VALVALLEULEUAA34 - 18734 - 187
d_13ens_1NAGNAGNAGNAGAI201
d_21ens_1GLUGLUPHEPHEEE4 - 324 - 32
d_22ens_1VALVALLEULEUEE34 - 18734 - 187
d_23ens_1NAGNAGNAGNAGEL201
d_11ens_2ALAALAPROPROBB2 - 32 - 3
d_12ens_2TYRTYRARGARGBB5 - 505 - 50
d_13ens_2ARGARGLYSLYSBB52 - 9852 - 98
d_14ens_2ALAALAALAALABB100 - 131100 - 131
d_15ens_2LEULEUALAALABB141 - 217141 - 217
d_21ens_2ALAALAPROPROFF2 - 32 - 3
d_22ens_2TYRTYRARGARGFF5 - 505 - 50
d_23ens_2ARGARGLYSLYSFF52 - 9852 - 98
d_24ens_2ALAALAALAALAFF100 - 217100 - 217
d_11ens_3GLNGLNHISHISCC1 - 2001 - 207
d_12ens_3PROPROLYSLYSCC202 - 214209 - 221
d_21ens_3GLNGLNHISHISGG1 - 2001 - 207
d_22ens_3PROPROLYSLYSGG202 - 214209 - 221
d_11ens_4ASPASPSERSERDD1 - 1211 - 121
d_12ens_4GLUGLUARGARGDD123 - 211123 - 211
d_13ens_4SO4SO4SO4SO4DK301
d_21ens_4ASPASPSERSERHH1 - 1211 - 121
d_22ens_4GLUGLUARGARGHH123 - 211123 - 211
d_23ens_4SO4SO4SO4SO4HN301

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixベクター
1given(-0.550368892344, -0.834736731646, 0.0175690404026), (-0.834640336488, 0.55060781814, 0.0143714755377), (-0.0216700495222, -0.00675421672039, -0.999742361566)-0.668216954045, 0.0477591877442, 60.5270202025
2given(-0.555980761855, -0.831079747103, 0.0138508628655), (-0.830842234528, 0.556153075521, 0.0198730449016), (-0.0242192851123, -0.000458851208513, -0.99970656479)-0.549601479216, -0.286054146138, 60.4897124942
3given(-0.540943321253, -0.841011180664, -0.00897313710651), (-0.840727557775, 0.540399830708, 0.0338407530837), (-0.0236113699322, 0.0258498930119, -0.999386955209)0.408221710381, -0.076860993307, 58.7983014766
4given(-0.546926885484, -0.837170943994, 0.00397397381696), (-0.836166443141, 0.546491884921, 0.0466079293738), (-0.0411905486733, 0.0221682260996, -0.998905355102)-0.465315248243, -0.819124707614, 58.8580988195

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要素

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タンパク質 , 2種, 4分子 AEBF

#1: タンパク質 HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


分子量: 22124.912 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-DRA, HLA-DRA1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P01903
#2: タンパク質 Hemagglutinin HA1 chain, HLA class II histocompatibility antigen DR beta chain


分子量: 25935.773 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-DRB1 / 発現宿主: Homo sapiens (ヒト)

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抗体 , 2種, 4分子 CGDH

#3: 抗体 h44H10-V22 Antibody, heavy chain


分子量: 23537.508 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#4: 抗体 h44H10-V22 Antibody, light chain


分子量: 23494.213 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

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糖 / 非ポリマー , 2種, 6分子

#5: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 2 / 由来タイプ: 合成 / 式: SO4

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詳細

研究の焦点であるリガンドがあるかN
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: 3.55 Å3/Da / 溶媒含有率: 65.4 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 20% (w/v) PEG 6000, 0.1 M citric acid, pH 4.0

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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: CLSI / ビームライン: 08ID-1 / 波長: 0.95357 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2023年11月1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: 0.95357 Å / 相対比: 1
反射解像度: 3.08→47.6 Å / Num. obs: 29589 / % possible obs: 93 % / 冗長度: 13.6 % / Biso Wilson estimate: 72.25 Å2 / CC1/2: 0.977 / Net I/σ(I): 7.8
反射 シェル解像度: 3.08→3.36 Å / Num. unique obs: 1974 / CC1/2: 0.47

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
autoPROCdata processing
XSCALE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 / 解像度: 3.08→47.56 Å / SU ML: 0.3748 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 26.5787
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2368 1495 5.06 %
Rwork0.1997 28065 -
obs0.2017 29560 58.84 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 77.03 Å2
精密化ステップサイクル: LAST / 解像度: 3.08→47.56 Å
タンパク質核酸リガンド溶媒全体
原子数12812 0 66 0 12878
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003713198
X-RAY DIFFRACTIONf_angle_d0.805817966
X-RAY DIFFRACTIONf_chiral_restr0.05312014
X-RAY DIFFRACTIONf_plane_restr0.00882298
X-RAY DIFFRACTIONf_dihedral_angle_d5.62391783
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.477062042869
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.783794898021
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.570316590701
ens_4d_2DDX-RAY DIFFRACTIONTorsion NCS0.545242942909
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.180.3384120.338213X-RAY DIFFRACTION5.02
3.18-3.30.4183470.3218897X-RAY DIFFRACTION20.96
3.3-3.430.3321840.29181564X-RAY DIFFRACTION36.28
3.43-3.580.301940.24961890X-RAY DIFFRACTION44.14
3.58-3.770.27811280.23532264X-RAY DIFFRACTION52.64
3.77-4.010.28291410.21882594X-RAY DIFFRACTION60.3
4.01-4.320.23341740.1822938X-RAY DIFFRACTION68.38
4.32-4.750.17821550.16513343X-RAY DIFFRACTION76.33
4.75-5.440.2071960.17073683X-RAY DIFFRACTION84.88
5.44-6.850.24542260.2174155X-RAY DIFFRACTION94.77
6.85-47.560.22822380.19484524X-RAY DIFFRACTION99.77
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)
13.4070706048-1.968694930131.647632723632.809874521351.742099903274.338862335680.1941159395870.4400358122170.8592651629340.2776629527540.436679591491-0.9834693217460.5420949742780.748778555685-0.1208713916060.443160617776-0.1161487389870.04423213786380.5718395801940.3167887699470.080993317155219.8538.36613.575
26.450987039082.85157241337-0.1832851719295.52422385087-1.198975891482.529706340740.277608186447-0.07518492525080.2114114119240.256350312843-0.337723610106-0.6742235936620.589082368480.4449175843210.06978644065950.9199007220480.08326553352020.078524880580.654333014460.1541878079320.3367479576422.99226.76910.118
30.386163878526-0.826189633792-0.2148246461121.56185436150.2025850969274.677575727230.4050998703360.3837141572590.315659704357-0.573080029121-0.213659531144-0.715748871088-1.27492302404-0.373124297134-0.3088401988640.47049880017-0.1362465637410.1096105836340.7269741373760.2112899653880.54663607438124.35550.2813.97
44.50287805122-5.216901281870.4829724158822.00310945185-2.146763444010.66913511675-0.1408553815780.3943351132341.07431096014-1.290278335130.487842304246-0.6837426217151.065729506730.3683862332240.03896035995590.8731655952220.042581191303-0.1115602168490.490450710219-0.2197429095450.45606298124920.2319.53236.161
50.1711551093590.642040931775-0.212281146653.54346163323-1.663320244111.57937863408-0.07471223543580.0323593606581-0.148441537040.156940206881-0.429401694165-0.862544269621-0.07361839778550.6126425572580.4096788875340.3027126796070.06343200821860.0159057760110.50287022780.03746861640280.66268674935524.63832.21928.253
64.409790751781.606485007721.763727054696.87649590494-2.116042402114.650653594040.245471158034-0.162662622487-0.3944267631090.0989141215643-0.0286959119418-0.8297140580870.4507897605630.750575028486-0.07706720489210.3224069032750.0886426948326-0.06282813676630.494319326870.1159950453590.62307743474127.85624.5935.253
72.75697561233-2.298920493170.7921404437549.28407825361-2.877763083264.81985084131-0.707980123672-0.0512223329608-0.00012033196470.4967751589350.843253692863-1.738094945050.427652254153-0.795558289082-0.4617727732520.595262472840.0795103405598-0.1021926368270.6764370719180.03395447345550.66064270611823.27932.05240.168
81.585127752981.72784437912-0.1882627367425.850543851081.321373648661.913966650010.09127157886390.3390906003830.367725799421-0.372264481499-0.06689484809010.0142620082721-0.2646722535740.7462049131120.02373719971750.387692271349-0.06789654017760.0340983524440.6595575687080.138777499910.45932188476822.68245.36210.553
93.513905948340.07727401115-0.5389083055980.5867699548710.8284318070134.29770588006-0.6256902570480.5279421281040.859167824101-1.219239586210.4282927012160.572482861539-0.4436965981070.2873450209140.2109797839640.771555614349-0.0857601944895-0.1513482650240.6247961291420.2509170736570.5160703219518.546.5866.619
103.627297281340.6893265793510.7217934731254.5600941618-3.139265751942.74635417552-0.177383742001-0.16959347711-1.44750905547-0.203662468584-0.4226693668670.1124747330130.771449352663-0.609217149204-0.1232581942010.820823165648-0.0973427518524-0.1055359810550.4494874916640.0936091476540.2838737278278.07519.55723.462
112.50721528492-1.445905800723.460603125272.45648991211-2.763308296135.383720365370.288243804913-1.20001352311-0.3724344362920.2857095320850.6375849071590.1538784698850.962320386883-1.32638341613-0.5800040304610.653953507814-0.219681169153-0.0007217245584590.9246579980750.2397366505910.8905699060781.30916.56235.138
122.414503891390.455951917151-0.4009197626721.142496194190.9589582775983.81372162716-0.314844761412-0.340102511785-0.04717461130940.6524619540860.4136561999380.23482780194-0.328757162578-0.0521634600945-0.09348771465670.711919891730.210717672291-0.1208879186090.6229008494650.01006317585790.4241479811958.25948.3350.297
134.187090142961.013177600650.6697522788151.454390200581.993809836313.12731495458-0.0466194860749-0.428361658532-0.4129319457540.6855581163620.08967095590580.1773358567060.8932882463160.05340259275-0.09804792158350.7996532250650.1630305995230.11380535520.5606052131110.05026044243240.64146115902-23.38155.81949.302
146.27359151925-2.41714836636-0.2096404587547.38869465883-0.7706415308732.850195684780.04281117033610.452279149490.732209042652-0.3998376432140.0149971209125-0.592009567602-0.269765428298-0.0990921639553-0.1000358953430.3560478471810.0227184772134-0.003570974948570.3960414928340.04457877591640.3229808619537.72658.60529.747
158.75337226858-0.3855771854511.33866673943.37617620443-0.692746730229-0.0830052423075-0.3183067908220.275192438991-0.08220414598240.3305250531330.321294929582-0.24288282592-0.0958661929558-0.196014636452-0.03290189574650.4577663533060.0454615883228-0.115748969940.586915406158-0.02096204221090.630421906034-0.02260.85532.86
163.04338124306-1.39591654223-0.08516755034153.959945217590.7683591612914.03288154267-0.092039582250.1122379283680.1192641845710.001226006205630.0715002686862-0.0594055310011-0.01421073470060.03964180004630.05065838261670.3842442569580.04756110493310.05538364817350.3584317695280.06631194209530.458005021179-26.22570.75644.986
177.893872556322.563173265460.2149589895067.058627681190.3241248197842.6328052628-0.159536945968-0.148412346365-0.5477112580150.448022795580.121086797665-0.3574282677560.5112874669840.521684518927-0.07229413544740.5408465833310.112283454101-0.01210686376110.488443934234-0.2030108546890.436485508384-38.865-0.2248.174
182.33203734682-2.912045899062.033527710466.36872312014-0.3330852776555.1599481710.3866425969050.100585300513-0.988511401154-0.1134702892940.9252158493650.856635219443-0.217922094299-0.256527858256-1.351200327770.3915281962110.113327516288-0.01732632671160.5288577224460.2254700164221.02709593939-55.186.33951.2
199.01967119033-4.14645046924-4.048675819082.387982571750.8130915002393.408446991230.288358152935-1.468188093251.334922043690.055672550530.37101882085-0.446085858413-0.3447392163790.538248565607-0.616192886440.431017805419-0.107558787064-0.0393705336290.428328010292-0.1645455521170.656707903676-39.7130.98128.13
205.09655234864-2.84614347506-1.570926668071.692403817631.084278113652.61606594860.04429544557540.292888838607-0.02554573428340.05342287880560.0454956252825-0.1282981236480.307435562794-0.1732767982590.05706418412790.378086911537-0.0178161495727-0.02917252553540.339880741118-0.05619370222860.707235939206-40.351-6.40928.84
215.11538556219-2.02349875776-1.588305547562.780801764460.9138539275813.374392051340.137795952815-0.1951786127020.0486570783016-0.7436551708470.09119033957050.370735142726-0.1629284222150.207645326921-0.2349213962550.4362706456070.02333322620450.002397088758590.250848927987-0.04291274694240.341678346068-38.043-2.94929.568
220.43885471835-0.9810470613150.9762956075995.6582623718-0.4654667976535.56093863606-0.03001158046930.666139500993-0.582855792388-0.940919412451-0.275351690307-0.186954699410.2028496701380.2744244011410.09822858588090.5538991660240.0430982350594-0.03334441449650.524327892436-0.006864082469340.468740606004-39.579-1.17919.815
238.47931504198-3.075633100271.099491995712.40806125391-2.307401865642.73160914544-0.073448732662-0.71999983971-0.2437433653090.4999774202090.4020391054050.1542693329830.1583821567540.114052482785-0.2281608129480.590646650761-0.05358858483580.1235590018950.271737439033-0.006380924578870.43724088564-50.6986.3849.337
243.35358752913-1.05924135618-1.168199052986.211166396562.042769998534.66832745943-0.302893702469-0.8642888940780.8510459471160.2231738445940.07118691321670.441215169009-0.289589144344-0.2472998059950.04455248213940.635932408660.134288649548-0.01594003428760.449348204523-0.1163817264370.598786629387-43.78718.63753.541
254.85244684109-1.041582558-2.734834876992.247183271582.14757930017.722759640860.0291033020459-0.3445725782590.222339646658-0.368927207970.413298816151-0.862031542486-0.4216471412231.51782362063-0.5042010031160.499605490988-0.0670653395307-0.04406974471920.796386749521-0.2444663818660.631622670894-19.0745.75135.555
261.64902420668-2.31056133289-0.07583869763624.525363026362.20483234033.252736361480.5438766886450.5313266466570.745142829908-1.059784596830.451712108827-0.37663070659-0.8244279436851.69694707825-1.005166877910.649337722707-0.2416967941680.02989807833251.16306867609-0.1906637336350.722339061595-15.3817.96525.936
272.542093136710.906302305157-0.3599928091764.08700549936-1.326826582194.34285374114-0.04713741315950.619327263240.0665421765871-0.8735426533330.1476302748050.0744115286305-0.381953107880.178635921142-0.03734259870590.748053087708-0.0113229440461-0.01504246311260.565945191906-0.1195429780030.42845428085-45.09620.7089.622
282.71389256305-0.03826196497261.539776723581.12940220714-0.8679439735612.10352588877-0.154269222855-0.3604729260881.260031474370.3234059569760.764867112882-0.2842605985380.174412327019-0.1366694969380.8983634914991.38099279283-0.1243549969180.04261333866461.029718005560.501805119812-0.126017402695-37.83752.1139.316
292.15387940981.05666307892.683010290014.123013727041.342254333682.59776270262-0.1527848693020.5540181970370.0256073873505-0.5440686416940.32291744354-0.4094306396130.1868861135050.220160559767-0.1441661966690.763573609136-0.07344357378840.1750572983310.6823393506430.09488357868950.481309941807-33.36950.80312.138
303.59757102783-2.217147459510.2285980962614.89542634605-0.6279817299743.08661204835-0.16406826867-0.173134216989-0.6865193869890.2104366494180.3112916445930.446089304538-0.480637218794-0.0241614880504-0.198255087460.495610026671-0.042589756370.1899738200910.4484935836310.0806074976750.605745192328-53.69826.12130.152
314.160192575491.801286917280.5162467430368.349735714262.28665370564.988929459880.332722319146-0.01041556015850.264122363214-0.664383620325-0.420218475960.0980924271061-0.568035163482-0.549615537603-0.2942812237020.345092476970.05871487305420.05152760337450.357929635907-0.01065071495930.487135675578-52.22127.42925.379
322.270012282574.126442790150.05849455741958.003850608920.339816199657-0.0119676795012-0.112967926577-0.9512897975390.8300231281170.535432148791-0.04842099610611.4698467931-0.2807423966730.2200699155860.02755937894510.807910484752-0.01200372759440.335850988860.2784047124520.2072638284720.958189205166-49.42447.02932.216
333.74392892345-0.0535291522750.4804569650656.779595932850.7039878433454.7728300502-0.1173016858241.014699848970.430176043225-0.487562452716-0.1156202738410.800536387551-0.9742647669110.02912053754970.3899462114220.768752747503-0.04456857159710.02055298181890.6659019417130.1142508288660.713096257896-44.78858.63217.444
341.75236513286-0.977775551875-2.485962356881.161701285220.9010413833793.41740270641-0.3990563925450.9885404141641.67658385109-1.31229327589-0.6239115885731.21552681734-0.45544999724-0.657578456139-0.7769095688121.19628685057-0.158360822975-0.5469498116280.7040835926310.5582985184681.25838704314-44.6564.6896.815
353.65150331665-0.5192626607760.380242531262.949653697820.8569825598823.630472002060.08324196799711.107944507480.864203213782-0.45406826440.4723065491880.492919683439-1.19521930126-0.4780042756650.1983576857831.079497981240.0580153004317-0.09358268795510.5722756973740.1063456021921.2935092631-46.30368.76819.652
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:26 )A4 - 26
2X-RAY DIFFRACTION2( CHAIN A AND RESID 27:55 )A27 - 55
3X-RAY DIFFRACTION3( CHAIN A AND RESID 56:87 )A56 - 87
4X-RAY DIFFRACTION4( CHAIN A AND RESID 88:101 )A88 - 101
5X-RAY DIFFRACTION5( CHAIN A AND RESID 102:146 )A102 - 146
6X-RAY DIFFRACTION6( CHAIN A AND RESID 147:166 )A147 - 166
7X-RAY DIFFRACTION7( CHAIN A AND RESID 167:187 )A167 - 187
8X-RAY DIFFRACTION8( CHAIN B AND RESID 2:37 )B2 - 37
9X-RAY DIFFRACTION9( CHAIN B AND RESID 38:106 )B38 - 106
10X-RAY DIFFRACTION10( CHAIN B AND RESID 107:155 )B107 - 155
11X-RAY DIFFRACTION11( CHAIN B AND ( RESID 156:217 OR RESID 301:301 ) )B156 - 217
12X-RAY DIFFRACTION11( CHAIN B AND ( RESID 156:217 OR RESID 301:301 ) )B301
13X-RAY DIFFRACTION12( CHAIN C AND RESID 1:106 )C1 - 106
14X-RAY DIFFRACTION13( CHAIN C AND RESID 107:216 )C107 - 216
15X-RAY DIFFRACTION14( CHAIN D AND RESID 1:75 )D1 - 75
16X-RAY DIFFRACTION15( CHAIN D AND RESID 76:114 )D76 - 114
17X-RAY DIFFRACTION16( CHAIN D AND RESID 115:211 )D115 - 211
18X-RAY DIFFRACTION17( CHAIN E AND RESID 4:55 )E4 - 55
19X-RAY DIFFRACTION18( CHAIN E AND RESID 56:77 )E56 - 77
20X-RAY DIFFRACTION19( CHAIN E AND RESID 78:101 )E78 - 101
21X-RAY DIFFRACTION20( CHAIN E AND RESID 102:134 )E102 - 134
22X-RAY DIFFRACTION21( CHAIN E AND RESID 135:166 )E135 - 166
23X-RAY DIFFRACTION22( CHAIN E AND RESID 167:187 )E167 - 187
24X-RAY DIFFRACTION23( CHAIN F AND RESID 2:37 )F2 - 37
25X-RAY DIFFRACTION24( CHAIN F AND RESID 38:106 )F38 - 106
26X-RAY DIFFRACTION25( CHAIN F AND RESID 107:162 )F107 - 162
27X-RAY DIFFRACTION26( CHAIN F AND ( RESID 163:217 OR RESID 301:301 ) )F163 - 217
28X-RAY DIFFRACTION26( CHAIN F AND ( RESID 163:217 OR RESID 301:301 ) )F301
29X-RAY DIFFRACTION27( CHAIN G AND RESID 1:106 )G1 - 106
30X-RAY DIFFRACTION28( CHAIN G AND RESID 107:135 )G107 - 135
31X-RAY DIFFRACTION29( CHAIN G AND RESID 136:214 )G136 - 214
32X-RAY DIFFRACTION30( CHAIN H AND RESID 1:75 )H1 - 75
33X-RAY DIFFRACTION31( CHAIN H AND RESID 76:101 )H76 - 101
34X-RAY DIFFRACTION32( CHAIN H AND RESID 102:113 )H102 - 113
35X-RAY DIFFRACTION33( CHAIN H AND RESID 114:174 )H114 - 174
36X-RAY DIFFRACTION34( CHAIN H AND RESID 175:187 )H175 - 187
37X-RAY DIFFRACTION35( CHAIN H AND RESID 188:211 )H188 - 211

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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