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- PDB-5e9d: RD-1 Mart-1 High bound to Mart-1 decameric peptide (ELA) in compl... -

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基本情報

登録情報
データベース: PDB / ID: 5e9d
タイトルRD-1 Mart-1 High bound to Mart-1 decameric peptide (ELA) in complex with HLA-A2
要素
  • A6-TCR Valpha
  • A6-TCR Vbeta
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Melanoma derived Mart-1 peptide
キーワードPROTEIN BINDING / single chain TCR-pMHC Complex
機能・相同性
機能・相同性情報


melanosome membrane / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell receptor complex / CD8 receptor binding ...melanosome membrane / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell receptor complex / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / Regulation of MITF-M-dependent genes involved in pigmentation / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / trans-Golgi network / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / melanosome / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion
類似検索 - 分子機能
Protein melan-A / Protein melan-A / : / : / 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 ...Protein melan-A / Protein melan-A / : / : / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
T cell receptor alpha variable 12-2 / T cell receptor beta variable 6-5 / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Melanoma antigen recognized by T-cells 1
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: 2.51 Å
データ登録者Singh, N.K. / Baker, B.M.
引用ジャーナル: Structure / 年: 2016
タイトル: An Engineered Switch in T Cell Receptor Specificity Leads to an Unusual but Functional Binding Geometry.
著者: Harris, D.T. / Singh, N.K. / Cai, Q. / Smith, S.N. / Vander Kooi, C.W. / Procko, E. / Kranz, D.M. / Baker, B.M.
履歴
登録2015年10月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年6月8日Provider: repository / タイプ: Initial release
改定 1.12016年7月20日Group: Database references
改定 1.22023年9月27日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
改定 1.32024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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 I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Melanoma derived Mart-1 peptide
D: A6-TCR Valpha
E: A6-TCR Vbeta
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Melanoma derived Mart-1 peptide
I: A6-TCR Valpha
J: A6-TCR Vbeta


分子量 (理論値)分子数
合計 (水以外)151,79110
ポリマ－151,79110
非ポリマー00
水1,31573
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Melanoma derived Mart-1 peptide
D: A6-TCR Valpha
E: A6-TCR Vbeta


分子量 (理論値)分子数
合計 (水以外)75,8955
ポリマ－75,8955
非ポリマー00
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-42 kcal/mol
Surface area27970 Å2
手法PISA
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Melanoma derived Mart-1 peptide
I: A6-TCR Valpha
J: A6-TCR Vbeta


分子量 (理論値)分子数
合計 (水以外)75,8955
ポリマ－75,8955
非ポリマー00
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-41 kcal/mol
Surface area27800 Å2
手法PISA
単位格子
Length a, b, c (Å)50.438, 164.484, 95.201
Angle α, β, γ (deg.)90.00, 100.56, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 4種, 8分子 AFBGDIEJ

#1: タンパク質 HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


分子量: 31854.203 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-A, HLAA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01892, UniProt: P04439*PLUS
#2: タンパク質 Beta-2-microglobulin


分子量: 11879.356 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: B2M, CDABP0092, HDCMA22P / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61769
#4: タンパク質 A6-TCR Valpha


分子量: 14256.660 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: TRAV12-2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A075B6T6
#5: タンパク質 A6-TCR Vbeta


分子量: 16919.906 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: TRBV6-5 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A0K0K1A5

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タンパク質・ペプチド / 非ポリマー , 2種, 75分子 CH

#3: タンパク質・ペプチド Melanoma derived Mart-1 peptide


分子量: 985.176 Da / 分子数: 2 / Mutation: A2L / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: Q16655*PLUS
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 73 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 2.8 Å3/Da / 溶媒含有率: 56.01 %
結晶化温度: 300 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.6 / 詳細: PEG 4000, 0.002 M Zinc Acetate, 5% 2- propanol. / PH範囲: 5.4 - 5.8

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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: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2014年10月8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: 1 Å / 相対比: 1
反射解像度: 2.5→20.04 Å / Num. obs: 47876 / % possible obs: 92.4 % / 冗長度: 3.3 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 10.1
反射 シェル解像度: 2.5→2.59 Å / 冗長度: 2.7 % / Rmerge(I) obs: 0.548 / % possible all: 74.3

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位相決定

位相決定手法: 分子置換
Phasing MRR rigid body: 0.616
最高解像度最低解像度
Rotation20.04 Å2.81 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
HKL-2000データ収集
SCALEPACKデータスケーリング
MOLREP11.1.03位相決定
PDB_EXTRACT3.15データ抽出
PHENIXモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 4FTV

4ftv


解像度: 2.51→20.04 Å / SU ML: 0.31 / 交差検証法: FREE R-VALUE / σ(F): 0 / 位相誤差: 28.78 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.232 1847 4.17 %Random Selection
Rwork0.18 ---
obs0.183 44297 84.9 %-
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
精密化ステップサイクル: LAST / 解像度: 2.51→20.04 Å
タンパク質核酸リガンド溶媒全体
原子数9610 0 0 73 9683
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00310008
X-RAY DIFFRACTIONf_angle_d0.72413565
X-RAY DIFFRACTIONf_dihedral_angle_d13.2483629
X-RAY DIFFRACTIONf_chiral_restr0.0281416
X-RAY DIFFRACTIONf_plane_restr0.0031766
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5054-2.5730.3843900.31512119X-RAY DIFFRACTION55
2.573-2.64850.3432850.29562397X-RAY DIFFRACTION62
2.6485-2.73380.31131290.2852447X-RAY DIFFRACTION65
2.7338-2.83130.31861190.26592844X-RAY DIFFRACTION73
2.8313-2.94430.29671430.24743151X-RAY DIFFRACTION83
2.9443-3.07780.27371500.2383471X-RAY DIFFRACTION90
3.0778-3.23950.28931640.20873570X-RAY DIFFRACTION93
3.2395-3.44150.23771570.19783721X-RAY DIFFRACTION96
3.4415-3.70560.23571570.17723683X-RAY DIFFRACTION96
3.7056-4.07570.22281620.16293704X-RAY DIFFRACTION96
4.0757-4.6590.20861630.13863765X-RAY DIFFRACTION97
4.659-5.84560.17211630.14043701X-RAY DIFFRACTION96
5.8456-20.03870.19631650.15193877X-RAY DIFFRACTION99
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)
13.7340.0737-0.19482.0371-0.10884.2085-0.14840.3256-0.5439-0.06130.0437-0.26420.16770.02360.0790.3464-0.03680.04480.4064-0.0650.46845.5057-4.24248.1546
20.80380.1116-0.57051.70680.24494.49350.11690.05510.2211-0.2395-0.0080.0341-0.84130.0507-0.04760.44010.0061-0.01140.34970.02680.42244.52326.99490.658
31.70090.81721.00891.1854-0.01283.0049-0.12480.26030.8379-0.57820.01610.2482-0.7242-0.0839-0.16891.119-0.00410.04850.5010.12850.71118.012812.4862-23.1397
40.98720.16861.13372.86550.12711.2049-0.2769-0.17850.4413-0.20310.23930.14050.477-0.15590.05040.6804-0.0488-0.11780.48550.02430.36595.1236-5.5034-17.0801
52.9792-0.4532-1.94081.56391.03152.5525-0.46220.142-0.11940.50010.01750.20120.9321-0.52430.38220.7585-0.13460.00490.46750.01840.3663.9211-10.758-13.1399
61.4726-0.0928-0.09062.7425-0.06364.6612-0.49450.6584-0.84750.44790.3697-0.63782.05750.10910.12510.8528-0.10840.1580.584-0.04590.6518.8471-19.4473-16.181
73.7122-1.0749-3.67732.61321.97085.9567-0.16170.29860.1477-0.1367-0.0139-0.12510.6925-0.40620.34770.6372-0.1284-0.05310.36990.04020.32487.1405-8.5068-12.9999
82.14411.4716-1.1210.9363-0.50471.4487-0.56240.1829-0.20780.37650.13960.57940.4272-0.68630.06660.8026-0.3820.07780.8269-0.11710.443-4.3221-13.9019-16.1665
94.83770.3924-1.84852.3243-0.21742.85250.69160.61880.8057-0.4788-0.0088-0.1084-0.0388-0.1173-0.23650.8598-0.03060.0410.65390.12820.41564.2242-6.9557-25.5057
100.38880.1595-0.43481.4597-0.42670.53140.5038-0.3058-0.1071-0.06010.1805-0.95210.0107-0.15130.2885-0.0804-0.0734-0.02010.47990.00470.63943.8148-0.513717.3122
113.1237-3.9653-4.07564.98035.1055.23550.2421-0.36880.39280.44770.2328-0.4091-0.34940.9699-0.44940.568-0.11790.03410.4183-0.03290.493218.66789.156142.3313
120.80490.8773-0.05973.67381.44653.1711-0.0090.025-0.25860.3787-0.1135-0.0655-0.33170.1336-0.07870.2004-0.0704-0.03740.3702-0.04580.657213.831514.829237.1568
131.80090.1522-1.30032.3388-0.48133.76450.0639-0.1562-0.15410.451-0.00550.2095-0.0341-0.29060.05490.258-0.05460.01770.3724-0.03760.39255.25727.184941.6548
141.57110.6728-2.15032.862-1.98627.36490.21390.21460.2332-0.2152-0.17410.2757-0.8175-0.8516-0.17270.28-0.0542-0.0380.34970.03120.39274.935610.527731.2937
153.5856-4.1169-4.17364.6794.784.84590.28440.08170.6017-0.474-0.29070.568-0.527-0.3981-0.15590.4954-0.01910.08290.4908-0.07330.67622.849419.070832.0222
162.7647-1.7038-1.88361.58031.74044.22110.11470.0080.6671-0.4950.1581-0.3405-0.2340.6637-0.30.2596-0.07660.00790.4241-0.05760.483912.711515.674631.593
173.79831.8298-3.04113.7892-2.21982.6510.46060.41910.7661-0.08620.45211.2726-0.6305-0.915-0.41160.5758-0.03570.12350.5501-0.04620.52112.29521.206445.6805
181.78540.60780.764.09763.22676.0817-0.135-0.0394-0.0550.76440.09670.41550.57330.1631-0.34750.2355-0.0462-0.03840.3052-0.01350.364410.09997.358539.0963
192.22231.57040.30322.22231.32834.8912-0.1077-0.38290.08510.79640.15070.4212-0.0321-0.6689-0.04640.59060.02080.04270.4156-0.03880.52350.6011-8.364754.1177
205.1892-1.31144.27253.28-0.67576.1210.0883-0.7572-0.68320.22970.41690.63170.6489-1.277-0.23140.3192-0.09350.03420.4790.07650.4216-1.1188-12.096745.5487
211.151-0.4314-0.26243.59180.04074.183-0.1497-0.1009-0.18130.10880.0203-0.37410.3220.51130.11880.3491-0.0085-0.02910.3333-0.00710.35896.6686-11.324140.6243
220.51910.90470.59941.30660.36012.2222-0.03550.0328-0.11590.2211-0.1210.0187-0.10390.25870.11440.2207-0.00330.05290.34280.01660.39924.4432-7.041742.1607
235.0463-5.19934.88838.9155-4.89894.81960.2889-1.29010.12631.7121-0.1291-0.41310.1732-0.316-0.08240.9719-0.0831-0.02970.6323-0.00070.443110.3806-9.15658.9108
245.9203-1.06910.65341.8031-0.61964.1892-0.4676-0.56120.56170.49330.2923-0.0975-0.3204-0.15810.17930.47460.06430.00730.4011-0.07760.3868-3.9881-37.012367.1683
252.9757-0.18850.29732.336-0.82494.1774-0.2015-0.58640.77340.20510.028-0.3017-0.2390.16540.21460.4983-0.0209-0.00070.5911-0.17360.57897.0277-32.828969.414
268.3594-0.68952.07591.2466-0.53524.5469-0.31090.41840.80890.08220.1004-0.0885-0.10070.07770.23960.4741-0.0713-0.00470.2355-0.04550.3802-3.1762-34.508456.2466
275.2089-1.53570.73952.97780.28813.5290.0257-0.4489-0.3252-0.06880.18980.21010.3519-0.36480.04940.4848-0.06680.13120.3494-0.03110.3474-7.6543-45.834862.2333
282.8343-1.15320.03532.3593-0.19853.8782-0.34430.2257-0.5276-0.11530.10210.30690.7248-0.10380.07190.4083-0.08970.09380.294-0.04520.3672-4.5912-49.656156.1302
291.75450.2426-0.10312.00170.31442.32270.2342-0.7520.240.1468-0.0580.2720.6270.2438-0.02421.0106-0.04480.00040.59050.04610.4624-5.353-49.715993.8799
302.0230.92530.4523.6032-0.04472.92680.2322-0.2333-0.45630.2777-0.23810.52050.8468-0.30440.06561.1815-0.03390.16180.55930.0640.6627-11.5522-54.930393.7685
311.91540.0511-0.07792.66740.51521.7958-0.01010.0592-0.5925-0.05140.36210.1085-0.5226-0.15010.04160.84090.08690.210.50430.05640.4839-12.8487-37.577786.4335
320.90630.16081.07950.66060.6143.6373-0.1047-0.1238-0.0067-0.39370.0745-0.1422-0.9361-0.46270.00040.80470.11770.15140.52850.05540.4264-10.8839-32.317381.3408
333.1210.00442.86191.2874-0.05264.5552-0.0071-0.6741-0.32260.0089-0.18770.06040.0946-1.59620.2190.93670.25560.20040.84740.02250.483-18.4183-31.867390.4136
340.72890.3774-1.13232.4749-1.16683.79530.06670.38670.0490.41140.3268-0.135-0.74740.1528-0.18260.4023-0.046-0.0860.3249-0.01910.4097-0.8037-41.844354.3287
350.9195-1.3085-1.26492.85834.17057.1379-0.6010.6009-0.3655-0.8512-0.3086-1.33380.60310.76570.26990.64550.04270.30110.6405-0.05650.68623.3567-48.503237.1681
363.9063-1.1261-0.894.802-3.09443.38790.10840.6957-0.5296-0.94130.30680.05220.8050.18990.26911.47330.19980.44260.5403-0.06480.911419.088-64.994429.6207
372.9097-0.8186-0.71533.2006-0.96553.1646-0.4995-0.19940.1961-0.39410.1208-1.02730.20580.29360.36520.29060.01450.05650.29250.04720.626117.5051-49.566446.2897
381.48730.711-0.82955.7106-1.06332.6721-0.22180.45690.1532-1.26650.0977-0.31160.10690.3150.19140.42-0.03180.00960.4029-0.04820.272710.3917-48.885832.4064
393.9808-1.3638-0.83022.9482-2.16057.7629-0.48760.1962-0.6552-0.51290.01160.25260.8932-0.75790.0770.4205-0.1013-0.05910.2416-0.04630.416.828-52.549442.0088
400.253-0.9669-1.55494.36266.47379.72910.040.1945-0.3509-0.37020.04410.46510.81610.31690.11511.10090.02870.01060.3870.02980.60896.5652-61.544640.663
412.31151.3364-0.68014.7475-1.86497.6254-0.53930.0261-0.5146-1.38220.128-0.10551.4496-0.2261-0.16090.4720.1758-0.06910.3683-0.02780.373613.8786-58.646139.412
421.34190.77821.75732.25293.74886.55520.24560.4468-0.00120.1360.1874-0.4419-0.42460.5516-0.21040.6581-0.00250.06570.22640.07280.31514.0095-48.673636.2423
432.422-2.0948-2.78432.47722.61053.63630.1938-0.02270.6514-0.72030.1157-0.6348-0.38410.508-0.25790.413-0.05420.08580.38010.00560.513111.1226-40.209344.0574
443.5102-0.8249-0.42060.5499-0.57754.214-1.14080.024-0.937-0.5517-0.9239-0.1240.09950.23321.0271.06250.11330.23310.4961-0.00360.661819.6391-57.900527.0275
452.9008-1.247-0.82491.09080.45764.05250.27020.16470.0312-0.7666-0.30440.24770.3009-0.0711-0.07750.8096-0.10930.02750.45150.03060.53588.3393-33.813518.5642
469.26533.9799-4.42325.3639-0.38733.65610.16890.631.0498-1.30260.36890.3348-0.2197-0.37930.05570.4985-0.0128-0.18990.48940.10080.34258.5266-27.276621.5808
472.54090.86843.22872.19121.95484.5171-0.21230.8431-0.1323-0.7710.4280.6150.4194-0.72080.0760.5129-0.08650.05390.70680.08290.7444-5.6235-35.993433.2712
481.08391.8681-1.70925.2273-0.75664.797-0.3346-0.51920.1687-0.15220.0563-1.06250.17090.83140.2690.3435-0.0375-0.06190.43450.06470.423612.7813-35.032332.6431
490.05990.0879-0.18412.01180.13260.2858-0.5839-0.29580.3324-0.32180.5047-0.6076-0.19881.00080.02790.4309-0.0436-0.01680.6828-0.06320.50759.5771-26.501337.2829
503.22730.1718-3.04763.65310.56373.0534-0.2612-0.00010.724-1.37760.26090.0043-0.724-0.17030.13080.3853-0.0097-0.12940.4159-0.00710.30252.4828-26.362330.2542
511.54371.26460.90362.8438-0.89162.14070.5667-0.58221.0028-0.2422-0.4991-0.2185-0.52750.3109-0.23220.8466-0.17640.34470.5703-0.06240.618517.0828-25.783824.0368
523.1838-0.4816-2.19411.6277-0.65113.21880.64010.0520.2732-0.2532-0.3264-0.17940.05740.2636-0.29470.4098-0.0082-0.01980.38560.03670.30428.7171-36.777929.2286
533.09591.28553.30380.93561.80174.0015-0.1125-0.6242-0.03010.37930.29830.0576-0.1969-0.4235-0.15470.4809-0.10450.06230.2853-0.00060.3787-2.698-37.311844.8949
542.42351.0356-1.32933.0684-1.22663.351-0.21950.3857-0.1343-0.47630.0484-0.15290.0975-0.08510.03240.6742-0.04320.10640.3486-0.03670.37198.9009-38.57127.0368
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:118 )A1 - 118
2X-RAY DIFFRACTION2( CHAIN A AND RESID 119:206 )A119 - 206
3X-RAY DIFFRACTION3( CHAIN A AND RESID 207:275 )A207 - 275
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2:19 )B2 - 19
5X-RAY DIFFRACTION5( CHAIN B AND RESID 20:41 )B20 - 41
6X-RAY DIFFRACTION6( CHAIN B AND RESID 42:51 )B42 - 51
7X-RAY DIFFRACTION7( CHAIN B AND RESID 52:77 )B52 - 77
8X-RAY DIFFRACTION8( CHAIN B AND RESID 78:90 )B78 - 90
9X-RAY DIFFRACTION9( CHAIN B AND RESID 91:99 )B91 - 99
10X-RAY DIFFRACTION10( CHAIN C AND RESID 1:10 )C1 - 10
11X-RAY DIFFRACTION11( CHAIN D AND RESID 2:9 )D2 - 9
12X-RAY DIFFRACTION12( CHAIN D AND RESID 10:30 )D10 - 30
13X-RAY DIFFRACTION13( CHAIN D AND RESID 31:43 )D31 - 43
14X-RAY DIFFRACTION14( CHAIN D AND RESID 44:52 )D44 - 52
15X-RAY DIFFRACTION15( CHAIN D AND RESID 53:59 )D53 - 59
16X-RAY DIFFRACTION16( CHAIN D AND RESID 60:75 )D60 - 75
17X-RAY DIFFRACTION17( CHAIN D AND RESID 76:83 )D76 - 83
18X-RAY DIFFRACTION18( CHAIN D AND RESID 84:111 )D84 - 111
19X-RAY DIFFRACTION19( CHAIN E AND RESID 2:14 )E2 - 14
20X-RAY DIFFRACTION20( CHAIN E AND RESID 15:30 )E15 - 30
21X-RAY DIFFRACTION21( CHAIN E AND RESID 31:75 )E31 - 75
22X-RAY DIFFRACTION22( CHAIN E AND RESID 76:109 )E76 - 109
23X-RAY DIFFRACTION23( CHAIN E AND RESID 110:116 )E110 - 116
24X-RAY DIFFRACTION24( CHAIN F AND RESID 1:37 )F1 - 37
25X-RAY DIFFRACTION25( CHAIN F AND RESID 38:56 )F38 - 56
26X-RAY DIFFRACTION26( CHAIN F AND RESID 57:85 )F57 - 85
27X-RAY DIFFRACTION27( CHAIN F AND RESID 86:118 )F86 - 118
28X-RAY DIFFRACTION28( CHAIN F AND RESID 119:174 )F119 - 174
29X-RAY DIFFRACTION29( CHAIN F AND RESID 175:195 )F175 - 195
30X-RAY DIFFRACTION30( CHAIN F AND RESID 198:274 )F198 - 274
31X-RAY DIFFRACTION31( CHAIN G AND RESID 2:19 )G2 - 19
32X-RAY DIFFRACTION32( CHAIN G AND RESID 20:71 )G20 - 71
33X-RAY DIFFRACTION33( CHAIN G AND RESID 72:99 )G72 - 99
34X-RAY DIFFRACTION34( CHAIN H AND RESID 1:10 )H1 - 10
35X-RAY DIFFRACTION35( CHAIN I AND RESID 2:9 )I2 - 9
36X-RAY DIFFRACTION36( CHAIN I AND RESID 10:17 )I10 - 17
37X-RAY DIFFRACTION37( CHAIN I AND RESID 18:30 )I18 - 30
38X-RAY DIFFRACTION38( CHAIN I AND RESID 31:43 )I31 - 43
39X-RAY DIFFRACTION39( CHAIN I AND RESID 44:52 )I44 - 52
40X-RAY DIFFRACTION40( CHAIN I AND RESID 53:59 )I53 - 59
41X-RAY DIFFRACTION41( CHAIN I AND RESID 60:83 )I60 - 83
42X-RAY DIFFRACTION42( CHAIN I AND RESID 84:91 )I84 - 91
43X-RAY DIFFRACTION43( CHAIN I AND RESID 92:103 )I92 - 103
44X-RAY DIFFRACTION44( CHAIN I AND RESID 104:109 )I104 - 109
45X-RAY DIFFRACTION45( CHAIN J AND RESID 2:14 )J2 - 14
46X-RAY DIFFRACTION46( CHAIN J AND RESID 15:25 )J15 - 25
47X-RAY DIFFRACTION47( CHAIN J AND RESID 26:30 )J26 - 30
48X-RAY DIFFRACTION48( CHAIN J AND RESID 31:49 )J31 - 49
49X-RAY DIFFRACTION49( CHAIN J AND RESID 50:63 )J50 - 63
50X-RAY DIFFRACTION50( CHAIN J AND RESID 64:75 )J64 - 75
51X-RAY DIFFRACTION51( CHAIN J AND RESID 76:86 )J76 - 86
52X-RAY DIFFRACTION52( CHAIN J AND RESID 87:94 )J87 - 94
53X-RAY DIFFRACTION53( CHAIN J AND RESID 95:99 )J95 - 99
54X-RAY DIFFRACTION54( CHAIN J AND RESID 100:115 )J100 - 115

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万見について

-
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