[日本語] English
万見
- PDB-6gb7: Structure of H-2Db with scoop loop from tapasin -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 6gb7
タイトルStructure of H-2Db with scoop loop from tapasin
要素
  • (Beta-2-microglobulin) x 2
  • GLY-GLY-LEU-SER
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • PHE-ALA-PRO-GLY-ASN-TYR-PRO
キーワードIMMUNE SYSTEM / MHC / MHC-I / H-2Kb / H-2K(b)
機能・相同性
機能・相同性情報


antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / TAP complex binding / helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / learning or memory / immune response / ribonucleoprotein complex / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / plasma membrane / cytosol
類似検索 - 分子機能
Tapasin / Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / : / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...Tapasin / Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / : / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Nucleoprotein / Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Tapasin
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Sendai virus (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.15 Å
データ登録者Hafstrand, I. / Sandalova, T. / Achour, A.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2019
タイトル: Successive crystal structure snapshots suggest the basis for MHC class I peptide loading and editing by tapasin.
著者: Hafstrand, I. / Sayitoglu, E.C. / Apavaloaei, A. / Josey, B.J. / Sun, R. / Han, X. / Pellegrino, S. / Ozkazanc, D. / Potens, R. / Janssen, L. / Nilvebrant, J. / Nygren, P.A. / Sandalova, T. / ...著者: Hafstrand, I. / Sayitoglu, E.C. / Apavaloaei, A. / Josey, B.J. / Sun, R. / Han, X. / Pellegrino, S. / Ozkazanc, D. / Potens, R. / Janssen, L. / Nilvebrant, J. / Nygren, P.A. / Sandalova, T. / Springer, S. / Georgoudaki, A.M. / Duru, A.D. / Achour, A.
履歴
登録2018年4月13日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年3月6日Provider: repository / タイプ: Initial release
改定 1.12019年3月13日Group: Data collection / Database references
カテゴリ: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22019年3月20日Group: Data collection / Database references
カテゴリ: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.32024年1月17日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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

-
集合体

登録構造単位
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: PHE-ALA-PRO-GLY-ASN-TYR-PRO
J: PHE-ALA-PRO-GLY-ASN-TYR-PRO
K: PHE-ALA-PRO-GLY-ASN-TYR-PRO
L: PHE-ALA-PRO-GLY-ASN-TYR-PRO
P: GLY-GLY-LEU-SER
R: GLY-GLY-LEU-SER
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)207,02429
ポリマ－205,62614
非ポリマー1,39715
水13,944774
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
K: PHE-ALA-PRO-GLY-ASN-TYR-PRO
P: GLY-GLY-LEU-SER
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)52,60712
ポリマ－51,8664
非ポリマー7418
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
I: PHE-ALA-PRO-GLY-ASN-TYR-PRO
R: GLY-GLY-LEU-SER
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)52,1477
ポリマ－51,8664
非ポリマー2803
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
L: PHE-ALA-PRO-GLY-ASN-TYR-PRO
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,0144
ポリマ－50,9183
非ポリマー961
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
J: PHE-ALA-PRO-GLY-ASN-TYR-PRO
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,2566
ポリマ－50,9753
非ポリマー2803
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)92.700, 123.860, 100.110
Angle α, β, γ (deg.)90.00, 103.66, 90.00
Int Tables number4
Space group name H-MP1211

-
要素

-
タンパク質 , 3種, 8分子 ACEGBDHF

#1: タンパク質
H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


分子量: 38449.129 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: H2-D1 / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: P01899
#2: タンパク質 Beta-2-microglobulin


分子量: 11761.411 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: B2m / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: P01887
#3: タンパク質 Beta-2-microglobulin


分子量: 11704.359 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: B2m / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: P01887

-
タンパク質・ペプチド , 2種, 6分子 IJKLPR

#4: タンパク質・ペプチド
PHE-ALA-PRO-GLY-ASN-TYR-PRO


分子量: 764.825 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) Sendai virus (ウイルス) / 参照: UniProt: O57286*PLUS
#5: タンパク質・ペプチド GLY-GLY-LEU-SER


分子量: 890.917 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9R233*PLUS

-
非ポリマー , 3種, 789分子

#6: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 4 / 由来タイプ: 合成 / 式: SO4
#7: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 11 / 由来タイプ: 合成 / 式: C3H8O3
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 774 / 由来タイプ: 天然 / 式: H2O

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.72 Å3/Da / 溶媒含有率: 54.71 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8
詳細: 1.8M ammonium sulfate, 0.1M Tris-HCl (pH 8) and 0.5M NaCl

-
データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: BESSY / ビームライン: 14.1 / 波長: 0.97625 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2016年2月7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: 2.15→97.28 Å / Num. obs: 117221 / % possible obs: 98.4 % / 冗長度: 3.1 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 5.8
反射 シェル解像度: 2.15→2.19 Å / 冗長度: 3.1 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2 / Num. unique obs: 5702 / % possible all: 97.9

-
解析

ソフトウェア
名称バージョン分類
PHENIX(1.11.1_2575: ???)精密化
XDSデータ削減
Aimless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: 1s7u

1s7u


解像度: 2.15→52.242 Å / SU ML: 0.28 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 27.91
Rfactor反射数%反射
Rfree0.2659 5813 4.97 %
Rwork0.2391 --
obs0.2404 117037 98.19 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 2.15→52.242 Å
タンパク質核酸リガンド溶媒全体
原子数12379 0 86 774 13239
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00412881
X-RAY DIFFRACTIONf_angle_d0.65817495
X-RAY DIFFRACTIONf_dihedral_angle_d15.7157611
X-RAY DIFFRACTIONf_chiral_restr0.0441736
X-RAY DIFFRACTIONf_plane_restr0.0032286
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.17440.32552190.29693666X-RAY DIFFRACTION98
2.1744-2.20.33811850.28523645X-RAY DIFFRACTION98
2.2-2.22680.33051960.28043615X-RAY DIFFRACTION97
2.2268-2.2550.33891680.27933669X-RAY DIFFRACTION96
2.255-2.28470.28982170.27763489X-RAY DIFFRACTION94
2.2847-2.3160.27871750.25893678X-RAY DIFFRACTION98
2.316-2.34910.28151860.26693757X-RAY DIFFRACTION99
2.3491-2.38420.27412060.26423775X-RAY DIFFRACTION99
2.3842-2.42140.31442050.27073695X-RAY DIFFRACTION99
2.4214-2.46110.28772020.2573712X-RAY DIFFRACTION99
2.4611-2.50350.26741860.25853793X-RAY DIFFRACTION99
2.5035-2.54910.26851840.26243690X-RAY DIFFRACTION99
2.5491-2.59810.3072030.25783747X-RAY DIFFRACTION99
2.5981-2.65110.30281900.26263799X-RAY DIFFRACTION100
2.6511-2.70880.29022010.25913710X-RAY DIFFRACTION99
2.7088-2.77180.3211680.27263691X-RAY DIFFRACTION98
2.7718-2.84110.28281880.26063670X-RAY DIFFRACTION97
2.8411-2.91790.2871650.24823636X-RAY DIFFRACTION96
2.9179-3.00380.28411590.24273638X-RAY DIFFRACTION95
3.0038-3.10070.28762130.24553765X-RAY DIFFRACTION100
3.1007-3.21150.28612050.23783743X-RAY DIFFRACTION100
3.2115-3.34010.27092030.23453754X-RAY DIFFRACTION100
3.3401-3.4920.24912300.23213711X-RAY DIFFRACTION99
3.492-3.67610.24072180.2153727X-RAY DIFFRACTION99
3.6761-3.90640.21391940.2063749X-RAY DIFFRACTION99
3.9064-4.20790.22391800.20813722X-RAY DIFFRACTION97
4.2079-4.63110.21952080.19563638X-RAY DIFFRACTION97
4.6311-5.30060.24191940.20593793X-RAY DIFFRACTION100
5.3006-6.67610.26062060.24673780X-RAY DIFFRACTION99
6.6761-52.25710.2961590.26933767X-RAY DIFFRACTION96
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)
14.1274-0.6455-0.31093.65120.35532.3432-0.02990.06070.30430.12090.0396-0.3078-0.16660.33590.01260.2095-0.08960.0160.39230.0090.1953-25.86675.4644115.0049
23.7552-0.3441-0.77221.75070.01581.3977-0.10490.4433-0.1001-0.11010.02990.07860.02960.06260.06250.1813-0.02590.01290.2305-0.00060.1517-39.4096-1.6123111.1846
31.3341-0.23791.52242.2545-0.52817.14940.08270.1971-0.08250.27820.109-0.4959-0.04610.6905-0.19970.29610.0553-0.00590.34110.00320.441-17.9232-8.4967127.2823
43.4368-0.64330.85345.66360.1174.2766-0.2722-0.2236-0.70271.23410.4210.27960.54830.0545-0.17160.50870.1213-00.32670.03530.4097-21.2355-11.972144.6329
55.63320.17335.59036.1349-0.02795.6006-0.215-0.4749-0.0317-0.57980.81670.9334-0.2178-0.7974-0.47460.3454-0.0293-0.0280.6276-0.07690.4322-42.24756.2756132.6358
63.83140.4492.81342.97751.56445.15710.3675-0.2374-0.16480.31870.2161-0.3603-0.14170.4951-0.47970.2445-0.0278-0.02130.3092-0.04530.2434-17.16155.2004142.4688
77.5473-1.23463.82221.44160.4024.68510.0334-0.4560.12270.08080.1142-0.1056-0.03920.0426-0.12380.2696-0.05640.020.2599-0.01570.185-23.92926.6404136.3689
86.78262.63246.70242.76292.73136.9503-0.7224-0.08340.6465-0.24980.19750.5247-0.9414-0.00860.480.4102-0.0506-0.05980.2838-0.00370.2674-30.84814.4062134.3489
90.15170.26010.40292.41762.77493.23320.6018-0.10920.58330.0663-0.0326-0.5235-1.3560.8385-0.32790.838-0.22380.17140.474-0.06380.4277-20.890618.9931137.9227
103.8532.15211.63763.3490.70471.7504-0.55360.4465-0.3491-0.62050.1339-0.27130.13520.46770.34220.2682-0.09370.01690.2791-0.06180.1789-28.61687.0492123.981
113.98860.5273.83811.47231.21875.9498-0.09040.26070.09220.07390.1127-0.1458-0.16070.76560.0070.2259-0.02390.05330.2450.00910.2174-26.1985.7481131.3051
129.3333-1.42031.76514.53171.16493.84560.065-0.7710.17910.33720.4079-0.5163-0.35780.5354-0.31090.4105-0.00050.01930.4706-0.0850.306-15.498313.802152.0827
136.5013-0.0415.34431.12670.5516.4768-0.4050.26940.91580.3599-0.0247-0.2796-0.70340.0150.38180.4678-0.02790.04350.1973-0.02150.346-28.209414.6924141.6221
148.0862.9123.19385.51323.25082.2575-0.1139-0.80250.6289-0.5608-0.05010.1091-1.212-1.2070.20170.44040.07550.01060.41610.02290.3556-40.118813.889137.6923
157.7608-3.58993.0765.6887-1.62525.17520.023-0.4846-0.284-0.0990.35620.30430.2899-0.2756-0.26010.3324-0.00730.06250.3046-0.01030.2035-24.42397.2388147.8036
163.84040.25130.21021.69010.51122.4238-0.0132-0.13750.42760.0280.02510.2522-0.2924-0.3697-0.00840.24380.04410.04540.22930.0020.204414.52375.0592130.2052
174.05231.0691-0.8243.3576-0.95442.0202-0.0345-0.2981-0.25270.10820.0389-0.2159-0.01730.04790.00340.21330.05040.04330.20010.00140.191727.5314-5.7938129.9788
180.74490.23340.18612.0671-0.49294.06360.02140.0724-0.1138-0.58930.2270.30610.3371-0.2698-0.20670.3733-0.0369-0.05630.31890.12140.49787.5074-12.8027102.2086
195.91562.5878-1.4566.072-0.72874.88570.06550.2230.14980.45980.0023-1.7641-0.82080.79950.02760.469-0.0351-0.06560.37050.08880.634828.28225.3465109.9191
201.1798-1.00951.95243.8137-1.19463.52370.61360.4697-0.0411-0.1878-0.11550.5110.3961-0.2471-0.34150.3927-0.08460.08350.40360.06040.279612.17622.8411102.1744
212.3838-1.4720.83613.4546-0.97562.5320.06530.41520.1039-0.3244-0.09970.78530.6962-0.675-0.17080.3057-0.0635-0.0880.67760.17340.37742.54264.1775101.4345
223.8531-2.27424.38172.2647-2.8955.0127-0.2726-0.23060.3731-0.05010.072-0.20710.0515-0.44480.16540.3748-0.00860.09230.44260.03560.264817.307111.4932108.6796
230.3781-0.91671.25342.3355-3.06885.5005-0.1714-0.07780.53140.0756-0.1363-0.0621-0.5002-0.79470.09660.4470.20580.05780.72250.09870.45736.281317.0727104.5038
246.5085-0.72313.33133.2017-3.13355.09050.11-0.03280.3324-0.18470.1680.18310.2389-0.7506-0.29460.31620.00180.05730.31010.00930.235618.13731.752117.4279
257.1255-2.18622.186.9075-1.66556.0631-0.3245-0.24190.3298-0.33730.41680.84060.0698-0.896-0.17690.4010.03670.02110.45580.09320.36083.80169.287105.555
265.0009-0.74831.29534.3672-1.30536.465-0.07830.2119-0.1925-0.9690.49550.9175-0.1438-1.0245-0.30080.7039-0.0343-0.06360.60920.19710.55551.524311.456290.1637
272.62792.35922.09812.20731.93318.7949-0.1605-0.51640.73260.1164-0.11520.0552-0.8554-0.16330.16150.39830.01190.01160.37320.04760.259113.930213.272101.1094
282.0887-2.45581.61479.7247-2.07132.08140.01320.97311.1405-0.68740.1715-1.0771-1.14310.4266-0.08980.4536-0.0329-0.05860.51720.08870.513825.691913.3005104.9872
295.51771.81651.53885.990.14284.2902-0.19590.3026-0.3073-1.1451-0.071-0.18550.87210.25530.27970.550.06970.04960.53090.15630.300310.8755.474294.7286
304.96920.38310.5682.62290.00043.31520.06180.0535-0.28140.1608-0.1226-0.42790.18810.33480.05860.2930.08610.00420.24710.03920.2954-24.7154-46.4225130.6328
319.01960.96682.93591.6822-0.39072.65750.0531-0.43150.03480.2321-0.1202-0.13340.14250.14330.02170.3470.02890.04970.26080.01890.2219-33.8905-48.6037137.913
325.35562.11241.68483.71191.06991.8085-0.0710.0830.16290.2433-0.0155-0.2013-0.0550.16310.06160.30590.03620.01470.19680.05620.1735-36.0137-37.8236128.4645
334.56950.3871.43252.1842-0.63932.5091-0.2381-0.42340.35320.33210.0025-0.0318-0.2117-0.04990.24040.32950.0561-0.00040.2001-0.01860.2304-39.1441-34.1714134.454
341.91890.9453-1.1863.395-1.69341.1784-0.49440.4996-0.3284-0.44210.0197-0.6220.03960.37520.33480.34310.003-0.00690.7317-0.17870.7086-12.3735-32.0857109.4062
354.68260.17831.02315.1505-0.3124.48730.05371.18190.1062-1.33030.54630.9506-0.78550.6266-0.33160.9814-0.00160.04150.63220.12220.6522-18.2626-34.875291.8123
363.64180.6549-0.47946.4995-0.8344.7885-0.04740.190.7038-0.97190.1899-0.3044-0.26220.1435-0.16670.36520.01150.05770.3695-0.05320.5039-19.2893-28.8804101.6731
373.8529-1.0302-0.50453.07750.46272.8927-0.33720.1378-0.16790.05080.4429-0.2691-0.06660.279-0.10960.3240.0310.00680.324-0.07340.2061-19.6267-47.1954106.6372
387.0741-2.4752-5.44712.71752.38524.46-0.18930.1997-0.42550.40420.0735-0.01030.0261-0.19180.14190.35690.0525-0.00880.3082-0.02670.2329-28.3553-54.4211112.2165
392.7587-0.8846-2.40845.71953.2534.9196-0.4172-0.2677-0.68690.71890.4878-0.78661.40410.45020.07060.48550.17460.05090.5363-0.01810.4726-16.8302-60.0514109.701
407.8332-1.2049-3.19512.39792.65424.2583-0.2293-0.6933-0.43260.10450.38180.24310.19820.685-0.12240.32250.06290.02270.26150.0470.1848-30.3382-44.1669120.1599
416.6906-2.3671-4.76264.24911.92185.13360.1025-0.3688-0.45110.45370.3521-0.3722-0.07060.7819-0.41010.31260.1696-0.03240.6038-0.10110.276-14.6069-51.9044110.259
427.894-1.8155-4.86482.70511.33676.3313-0.7739-0.5177-0.2447-0.0730.48020.1070.40540.77870.16730.36180.0513-0.00170.3584-0.07870.2562-17.6515-56.264100.9191
437.2366-2.2689-1.66764.40894.54438.4842-0.04490.3904-0.2440.27740.13620.19180.6113-0.66690.14890.4046-0.03890.15420.38910.06090.4542-36.3143-57.0167107.8139
443.15033.1982-3.44335.9918-1.39225.3349-0.22010.63540.4152-0.77890.42830.12320.1422-0.0851-0.22310.27460.05660.00570.41120.00990.2853-20.4357-49.598898.8363
452.8922-1.01750.40083.4517-0.45621.3985-0.0040.2862-0.128-0.74380.06250.46030.1286-0.2197-0.03760.3843-0.0717-0.08080.29660.00330.223122.0491-42.5302110.9645
463.8693-0.5447-0.56757.2939-0.63364.5089-0.2403-0.4570.50770.84050.42730.1824-0.3332-0.0408-0.18480.37380.03550.01160.3510.04640.43255.6046-31.1587142.1663
476.5245-1.6135-5.48723.71541.30948.8948-0.2816-0.0349-0.2494-0.70520.3795-0.7149-0.21960.7428-0.0550.3595-0.07510.09820.35140.07440.394328.4767-48.6149132.1776
483.39730.7491-1.35212.8398-0.9463.6894-0.1702-0.12050.2844-0.06820.37120.4752-0.0135-0.3388-0.16890.2228-0.0051-0.05240.24190.05330.2762.5135-47.6459138.9926
492.48221.0313-2.81521.5165-0.98293.1284-0.2723-0.00740.2665-0.34170.21570.102-0.0003-0.13710.05530.2317-0.017-0.01340.19980.05340.22089.9345-49.0297133.6529
504.66782.9522-5.74373.2171-3.04776.7887-0.76210.1083-1.2151-0.49650.063-0.19830.72360.12190.50430.31520.00230.06290.28830.06320.309317.0424-56.9819132.2436
513.59610.7972-1.73033.2928-2.77139.60020.0910.5694-0.2616-0.80010.35410.54231.1971-0.1724-0.14440.5233-0.1251-0.03380.3083-0.02220.31067.0221-61.4649134.6601
525.7121.9322-3.93911.2339-1.97412.78390.02760.2773-0.0768-0.16690.07310.0706-0.0351-0.2345-0.06660.3072-0.0237-0.01790.24060.02920.230313.7889-48.5565127.0021
537.5691.31650.392.4895-2.60695.1316-0.2621-0.8049-0.42650.77710.090.5460.6399-0.00930.18840.3325-0.02190.04450.31420.04130.2627-0.4673-56.485147.6173
544.61710.6044-6.42470.6954-0.70848.8643-0.2086-0.7034-1.172-0.2994-0.2117-0.09370.32560.45210.30.2569-0.0089-0.03140.25520.09760.299414.6115-57.5737138.4508
557.47680.57241.50047.2159-3.98159.93720.1101-0.4466-1.3076-0.4808-0.02-0.29490.55311.0071-0.05910.34810.11380.0640.3810.05370.389425.6634-56.8024136.7061
566.6855-1.2175-1.71294.5271-0.10444.0181-0.1056-0.35450.04630.12910.13330.1656-0.6380.521-0.08190.3251-0.06370.00840.37670.05640.20398.9594-50.0253144.8769
573.4899-0.4343-0.91526.2114-0.70076.65240.2405-0.4839-0.20910.5578-0.2947-0.16570.4504-0.66680.07760.3195-0.02480.06960.28320.02250.3320.4699-1.4682138.3224
582.88192.8441-0.03275.5369-1.76613.919-0.24150.0845-0.0675-0.39760.50870.07480.1721-0.2277-0.30370.7513-0.174-0.11210.41580.08040.384123.5477-41.6068103.2767
596.4040.0799-1.9236.29030.61074.57950.54670.64870.2250.1198-0.03480.2048-0.6552-0.0251-0.62240.3736-0.01370.00440.39010.04440.1769-34.7026-0.5496104.4058
600.5951-1.567-1.516.65660.66327.8566-0.194-0.21410.3648-0.13990.7972-0.09-0.02870.9166-0.47540.30280.0001-0.07640.4398-0.01350.2753-34.4506-40.2972140.3299
612.3023-0.15140.98081.8209-1.71656.6390.14960.28570.1401-0.0981-0.46330.2499-0.09820.01690.2110.5180.2076-0.0420.70560.04291.1035-45.98093.9605107.1172
620.89180.14612.40280.01790.39286.41140.2061-0.25460.0220.2480.2502-0.35910.14320.4039-0.33930.5404-0.0626-0.08010.6825-0.05480.722133.71653.279137.2005
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 198 )
4X-RAY DIFFRACTION4chain 'A' and (resid 199 through 275 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 5 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 19 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 30 )
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 41 )
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 51 )
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 56 )
11X-RAY DIFFRACTION11chain 'B' and (resid 57 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 77 )
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 83 )
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 90 )
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 99 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 84 )
17X-RAY DIFFRACTION17chain 'C' and (resid 85 through 162 )
18X-RAY DIFFRACTION18chain 'C' and (resid 163 through 276 )
19X-RAY DIFFRACTION19chain 'D' and (resid 0 through 5 )
20X-RAY DIFFRACTION20chain 'D' and (resid 6 through 11 )
21X-RAY DIFFRACTION21chain 'D' and (resid 12 through 28 )
22X-RAY DIFFRACTION22chain 'D' and (resid 29 through 41 )
23X-RAY DIFFRACTION23chain 'D' and (resid 42 through 51 )
24X-RAY DIFFRACTION24chain 'D' and (resid 52 through 63 )
25X-RAY DIFFRACTION25chain 'D' and (resid 64 through 71 )
26X-RAY DIFFRACTION26chain 'D' and (resid 72 through 77 )
27X-RAY DIFFRACTION27chain 'D' and (resid 78 through 83 )
28X-RAY DIFFRACTION28chain 'D' and (resid 84 through 90 )
29X-RAY DIFFRACTION29chain 'D' and (resid 91 through 99 )
30X-RAY DIFFRACTION30chain 'E' and (resid 1 through 56 )
31X-RAY DIFFRACTION31chain 'E' and (resid 57 through 84 )
32X-RAY DIFFRACTION32chain 'E' and (resid 85 through 118 )
33X-RAY DIFFRACTION33chain 'E' and (resid 119 through 173 )
34X-RAY DIFFRACTION34chain 'E' and (resid 174 through 193 )
35X-RAY DIFFRACTION35chain 'E' and (resid 194 through 206 )
36X-RAY DIFFRACTION36chain 'E' and (resid 207 through 276 )
37X-RAY DIFFRACTION37chain 'F' and (resid 1 through 28 )
38X-RAY DIFFRACTION38chain 'F' and (resid 29 through 41 )
39X-RAY DIFFRACTION39chain 'F' and (resid 42 through 51 )
40X-RAY DIFFRACTION40chain 'F' and (resid 52 through 63 )
41X-RAY DIFFRACTION41chain 'F' and (resid 64 through 71 )
42X-RAY DIFFRACTION42chain 'F' and (resid 72 through 83 )
43X-RAY DIFFRACTION43chain 'F' and (resid 84 through 90 )
44X-RAY DIFFRACTION44chain 'F' and (resid 91 through 99 )
45X-RAY DIFFRACTION45chain 'G' and (resid 1 through 174 )
46X-RAY DIFFRACTION46chain 'G' and (resid 175 through 276 )
47X-RAY DIFFRACTION47chain 'H' and (resid 0 through 5 )
48X-RAY DIFFRACTION48chain 'H' and (resid 6 through 19 )
49X-RAY DIFFRACTION49chain 'H' and (resid 20 through 30 )
50X-RAY DIFFRACTION50chain 'H' and (resid 31 through 41 )
51X-RAY DIFFRACTION51chain 'H' and (resid 42 through 51 )
52X-RAY DIFFRACTION52chain 'H' and (resid 52 through 71 )
53X-RAY DIFFRACTION53chain 'H' and (resid 72 through 77 )
54X-RAY DIFFRACTION54chain 'H' and (resid 78 through 83 )
55X-RAY DIFFRACTION55chain 'H' and (resid 84 through 90 )
56X-RAY DIFFRACTION56chain 'H' and (resid 91 through 99 )
57X-RAY DIFFRACTION57chain 'I' and (resid 1 through 7 )
58X-RAY DIFFRACTION58chain 'J' and (resid 1 through 7 )
59X-RAY DIFFRACTION59chain 'K' and (resid 1 through 7 )
60X-RAY DIFFRACTION60chain 'L' and (resid 1 through 7 )
61X-RAY DIFFRACTION61chain 'P' and (resid 0 through 3 )
62X-RAY DIFFRACTION62chain 'R' and (resid 0 through 4 )

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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