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- PDB-3kka: Co-crystal structure of the sam domains of EPHA1 AND EPHA2 -

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基本情報

登録情報
データベース: PDB / ID: 3kka
タイトルCo-crystal structure of the sam domains of EPHA1 AND EPHA2
要素
  • EPHRIN TYPE-A RECEPTOR 1
  • EPHRIN TYPE-A RECEPTOR 2
キーワードTRANSFERASE / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / RECEPTOR / TYROSINE-PROTEIN KINASE / STERILE ALPHA MOTIF / STRUCTURAL GENOMICS CONSORTIUM / SGC / GLYCOPROTEIN / MEMBRANE / PHOSPHOPROTEIN / POLYMORPHISM / TRANSMEMBRANE / Cataract
機能・相同性
機能・相同性情報


POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / regulation of blood vessel endothelial cell migration ...POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / response to growth factor / bone remodeling / positive regulation of bicellular tight junction assembly / activation of GTPase activity / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / tight junction / RND1 GTPase cycle / neural tube development / RND2 GTPase cycle / RND3 GTPase cycle / regulation of GTPase activity / mammary gland epithelial cell proliferation / positive regulation of cell-matrix adhesion / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / fibronectin binding / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / vasculogenesis / keratinocyte differentiation / positive regulation of stress fiber assembly / transmembrane receptor protein tyrosine kinase activity / RAC1 GTPase cycle / substrate adhesion-dependent cell spreading / osteoclast differentiation / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of angiogenesis / negative regulation of cell migration / molecular function activator activity / protein localization to plasma membrane / negative regulation of protein kinase activity / skeletal system development / cell chemotaxis / positive regulation of protein localization to plasma membrane / cell motility / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / neuron differentiation / positive regulation of angiogenesis / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / protein autophosphorylation / angiogenesis / receptor complex / cell surface receptor signaling pathway / protein kinase activity / defense response to Gram-positive bacterium / cell adhesion / positive regulation of cell migration / cadherin binding / inflammatory response / focal adhesion / positive regulation of cell population proliferation / protein kinase binding / cell surface / ATP binding
類似検索 - 分子機能
Ephrin type-A receptor 1, ligand binding domain / Ephrin type-A receptor 2, ligand binding domain / Transcription Factor, Ets-1 / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : ...Ephrin type-A receptor 1, ligand binding domain / Ephrin type-A receptor 2, ligand binding domain / Transcription Factor, Ets-1 / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / EGF-like domain signature 2. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / DNA polymerase; domain 1 / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Ephrin type-A receptor 1 / Ephrin type-A receptor 2
類似検索 - 構成要素
生物種HOMO SAPIENS (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å
データ登録者Walker, J.R. / Yermekbayeva, L. / Butler-Cole, C. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
引用ジャーナル: To be Published
タイトル: Co-Crystal Structure of the SAM Domains of Human Ephrin Type-A Receptor 1 and Human Ephrin Type-A Receptor 2
著者: Walker, J.R. / Yermekbayeva, L. / Butler-Cole, C. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
履歴
登録2009年11月5日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02009年11月24日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22023年9月6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 / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: EPHRIN TYPE-A RECEPTOR 1
B: EPHRIN TYPE-A RECEPTOR 1
C: EPHRIN TYPE-A RECEPTOR 2
D: EPHRIN TYPE-A RECEPTOR 2
E: EPHRIN TYPE-A RECEPTOR 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)49,3466
ポリマ－49,3105
非ポリマー351
水61334
1
A: EPHRIN TYPE-A RECEPTOR 1


分子量 (理論値)分子数
合計 (水以外)9,5601
ポリマ－9,5601
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
B: EPHRIN TYPE-A RECEPTOR 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)9,5952
ポリマ－9,5601
非ポリマー351
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
3
C: EPHRIN TYPE-A RECEPTOR 2


分子量 (理論値)分子数
合計 (水以外)10,0631
ポリマ－10,0631
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
4
D: EPHRIN TYPE-A RECEPTOR 2


分子量 (理論値)分子数
合計 (水以外)10,0631
ポリマ－10,0631
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
5
E: EPHRIN TYPE-A RECEPTOR 2


分子量 (理論値)分子数
合計 (水以外)10,0631
ポリマ－10,0631
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)57.554, 56.071, 107.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質 EPHRIN TYPE-A RECEPTOR 1 / TYROSINE-PROTEIN KINASE RECEPTOR EPH


分子量: 9559.910 Da / 分子数: 2 / 断片: SAM DOMAIN, UNP RESIDUES 911-974 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 遺伝子: EPH, EPHA1, EPHT, EPHT1, MGC163163 / プラスミド: PET28-MHL / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P21709, receptor protein-tyrosine kinase
#2: タンパク質 EPHRIN TYPE-A RECEPTOR 2 / TYROSINE-PROTEIN KINASE RECEPTOR ECK / EPITHELIAL CELL KINASE


分子量: 10063.460 Da / 分子数: 3 / 断片: SAM DOMAIN, UNP RESIDUES 903-971 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 遺伝子: EPHA2 / プラスミド: PET28-MHL / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P29317, receptor protein-tyrosine kinase
#3: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 34 / 由来タイプ: 天然 / 式: H2O

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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

結晶化温度: 293.1 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.2
詳細: 2.1 M AMMONIUM SULPHATE, 2% PEG 400, 0.1 M NA HEPES PH 7.2.PRIOR TO SETTING UP CRYSTALLIZATION PLATES, CHYMOTRYPSIN WAS ADDED TO THE PROTEIN SAMPLE TO A FINAL CONCENTRATION OF 0.57 MICROMOLAR. ...詳細: 2.1 M AMMONIUM SULPHATE, 2% PEG 400, 0.1 M NA HEPES PH 7.2.PRIOR TO SETTING UP CRYSTALLIZATION PLATES, CHYMOTRYPSIN WAS ADDED TO THE PROTEIN SAMPLE TO A FINAL CONCENTRATION OF 0.57 MICROMOLAR., VAPOR DIFFUSION, HANGING DROP, temperature 293.1K

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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: 19-ID / 波長: 0.97932 / 波長: 0.97932 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2009年10月14日
放射モノクロメーター: DOUBLE CRYSTAL MONOCHOMATOR / 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: 0.97932 Å / 相対比: 1
反射解像度: 2.4→33 Å / Num. all: 14362 / Num. obs: 14362 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 6.9 % / Rsym value: 0.106 / Net I/σ(I): 20.16304
反射 シェル解像度: 2.4→2.44 Å / 冗長度: 6.4 % / Mean I/σ(I) obs: 2.2083 / Num. unique all: 704 / Rsym value: 0.891 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
HKL-3000データ収集
PHASER位相決定
REFMAC5.5.0102精密化
HKL-3000データ削減
HKL-3000データスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 3HIL

3hil


解像度: 2.4→30.44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU B: 19.095 / SU ML: 0.199 / 交差検証法: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.25 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
Rfactor反射数%反射Selection details
Rfree0.23463 705 5 %RANDOM
Rwork0.19961 ---
obs0.2015 13463 99.93 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 54.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--2.55 Å20 Å2
3----3.1 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→30.44 Å
タンパク質核酸リガンド溶媒全体
原子数2527 0 1 34 2562
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222577
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9553482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.75923.796108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.2515464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3981514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211895
X-RAY DIFFRACTIONr_mcbond_it0.5611.51589
X-RAY DIFFRACTIONr_mcangle_it1.03822562
X-RAY DIFFRACTIONr_scbond_it1.7563988
X-RAY DIFFRACTIONr_scangle_it2.8174.5920
LS精密化 シェル解像度: 2.4→2.462 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.322 58 -
Rwork0.247 948 -
obs--99.6 %
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)
116.4253-2.4869-5.78610.52410.00868.0853-0.0518-0.10891.21730.070.0843-0.2362-0.51920.3854-0.03250.3326-0.0606-0.01490.42630.03470.36495.80046.8826-25.1736
215.34328.28443.499322.356312.96457.6647-0.26050.02040.2535-0.1440.17820.1513-0.11230.06540.08240.42510.12240.00230.30830.04140.17510.07795.7011-19.0493
326.029-2.77318.12218.6929-6.102522.6285-0.2347-0.13081.08930.44740.3530.8999-0.5815-0.7965-0.11820.20350.00850.08190.23390.02710.1809-5.88382.3769-21.2212
48.2769-5.70824.46525.5636-6.816110.995-0.2448-0.4776-0.060.25980.46410.1328-0.3184-0.5816-0.21930.3078-0.01790.0810.31650.01760.2254-5.5468-0.1871-13.1725
518.263618.7938-10.025820.1994-6.305424.53630.9391-0.5982.10651.0149-0.75692.3332-0.8182-0.071-0.18230.72620.0053-0.18770.2453-0.02530.44421.94720.1047-8.7584
627.7124-9.64547.34767.4158-0.029112.41050.1014-0.3430.8040.36170.2353-0.3631-1.00110.8215-0.33670.3718-0.1084-0.05950.1072-0.0180.25057.84894.1986-14.9107
75.06738.2117-2.00629.8622-6.12594.9156-0.2618-0.0624-0.12190.19960.0429-0.80920.0430.52810.21890.1809-0.0072-0.07260.26240.02670.1568.5813-5.1926-17.2613
810.3594-5.7424.92987.4681-1.86452.56680.09010.0883-0.02270.3362-0.0957-0.07060.04410.17960.00560.3895-0.131-0.05260.55140.05360.17073.7047-9.4223-10.9978
94.4347-2.22722.40531.8375-0.89757.6956-0.1028-0.0164-0.25030.08830.08110.27610.3681-0.47390.02170.2075-0.04570.00970.22530.03430.1817-3.269-9.5692-17.9242
1010.25511.6152-2.66255.43740.84326.0660.08030.2782-0.3378-0.3971-0.034-0.50640.25030.0465-0.04620.17-0.0108-0.010.19420.030.18824.6168-4.111-25.9629
117.3466-6.05487.62337.1467-2.172415.7703-0.144-0.6679-0.25030.17220.18750.356-0.0592-1.3814-0.04340.1086-0.01880.06770.48060.12020.2252-12.3941-0.6498-30.3665
126.90783.38784.639312.0676-2.60945.45390.0702-0.72990.18940.7123-0.04280.2204-0.235-0.7176-0.02750.22580.07180.00110.3420.06460.2042-6.8663.192-31.6881
133.5885-1.6653-0.5096.09115.786816.7686-0.0925-0.28110.5250.16630.2606-0.2766-1.1731-0.1432-0.16810.27660.02750.02450.2197-0.00320.2609-2.40066.8667-36.3007
140.4521-0.3856-2.219910.244-1.312711.97050.13380.13360.0277-0.19480.08350.3504-0.6191-0.7956-0.21720.21510.0236-0.01330.31970.06430.2474-8.79073.8666-44.1759
157.44780.7752-7.27290.92962.997423.7294-0.569-0.01050.1264-0.2885-0.36830.2671-0.4382-1.70560.93730.2077-0.0049-0.0820.59610.13840.2708-13.2154-2.1245-40.8306
1622.23655.1975-14.86085.7622-2.528610.1381-0.29050.9342-0.1334-0.06030.15010.33470.2766-0.67940.14040.5103-0.2093-0.24590.4770.11180.2659-9.9139-8.6264-38.1843
175.23327.4137-0.980313.5607-9.089919.74980.03030.124-0.1421-0.5431-0.0337-0.16511.43180.19850.00340.36560.1421-0.06180.4658-0.09280.2334-0.1017-6.9544-44.3482
184.1054-1.15572.4174.2899-1.56999.68650.0290.2036-0.1844-0.322-0.0889-0.234-0.03760.5290.060.18840.01730.02120.23130.03180.16292.6378-0.0196-43.1756
193.74692.4035-0.28679.38381.006115.16230.10970.2555-0.23460.0141-0.0489-0.19140.68750.2628-0.06090.15120.037-0.010.21240.03440.19372.1617-2.8047-35.3454
2010.10536.96020.655113.4016-9.328611.15420.55080.103-0.6568-0.08790.22650.1930.5697-0.176-0.77740.2946-0.0381-0.0160.2741-0.01540.283-3.7165-7.0821-30.2894
2161.249419.0652-14.688529.0613-4.30853.52570.05051.09390.30011.28160.0553-0.2328-0.0024-0.2585-0.10570.09510.11870.00950.68140.10390.2959-26.63473.8444-32.4002
223.7547-4.04221.967127.043115.18614.2439-0.21050.25070.4901-0.90240.1379-0.8451-1.00280.53350.07260.2166-0.1416-0.05940.56060.25190.3456-31.7439.4383-31.5527
232.61925.79480.663414.9642-0.10742.5036-0.1705-0.12380.4833-0.22860.03410.12760.305-0.02670.13640.28380.0652-0.26890.6821-0.11350.9379-30.62314.9509-24.2436
2414.4932-9.5469.275314.2753-1.469118.84250.37680.51990.8013-0.0431-0.5612-0.42130.25581.11260.18440.340.15270.00270.51760.08210.3622-27.9667-2.8743-24.4981
2521.3689-3.78674.701926.426520.223918.36260.1237-0.1821-2.013-1.03541.3686-1.0195-0.70191.4423-1.49230.38110.2590.09271.21540.26640.5663-24.5815-4.6186-32.8304
2638.2577-2.16-7.67611.08754.967422.8885-1.42332.9577-0.48010.15280.07780.28670.77740.38981.34550.59810.08750.05520.43850.07070.5703-33.0857-7.3672-34.3166
2717.084916.886313.521649.8507-2.389918.20270.85880.5999-0.8519-0.2342-0.383-1.23611.29110.988-0.47590.54160.22090.04440.39330.06870.3125-36.5533-6.2932-26.3446
289.6274.0399-6.40291.8486-3.54039.04070.1334-0.5357-0.273-0.0777-0.1621-0.09490.6504-0.1930.02870.22190.0138-0.05760.32320.08630.282-41.63342.0607-26.8834
2912.49098.12366.44216.71379.051619.8947-0.1507-0.92140.3084-0.0078-0.51210.35590.2666-0.00330.66270.20680.1276-0.01290.39480.05880.2639-39.75922.9693-35.2507
303.1898-1.4235-0.43430.6976-0.844419.83350.31190.3623-0.791-0.1205-0.10680.36710.03711.2396-0.20510.48640.21350.02420.8650.01730.6706-33.4098-1.1984-40.4952
313.95783.2779-2.00172.722-1.64921.0289-0.34790.3868-0.0401-0.34230.30860.0060.0887-0.22670.03930.52740.0842-0.12770.389-0.0470.3584-20.9399-13.8351-12.4298
329.82684.96-0.56310.2634-0.191322.8998-0.15560.46020.2638-0.2347-0.15411.0413-0.054-0.96060.30970.17680.025-0.0120.2344-0.00270.3106-24.1477-18.2357-5.699
336.06570.6610.825511.6032-0.38215.8659-0.08740.05570.16990.14650.00110.8063-0.3135-0.21450.08630.15150.01190.06090.1939-0.02250.2415-21.7541-12.98941.4693
343.5721.3836-0.375310.29553.25097.63950.12130.00810.3496-0.56470.0599-0.0652-0.37490.7024-0.18110.29480.00950.01250.24430.04020.2426-14.933-7.4572-2.4329
3532.9117-7.9337-5.67766.4522-5.71912.04810.01520.7032-0.63330.0433-0.30940.0373-0.10740.12640.29410.4906-0.13450.07930.2362-0.02530.1116-12.5733-11.3467-9.4797
369.9866-5.9242-8.47389.15057.885121.04610.0501-0.02190.11540.36040.0994-0.77870.24341.2323-0.14950.12560.0597-0.03050.4761-0.03170.4032-7.8894-17.3168-1.8824
376.52773.142-4.01799.69622.29914.6653-0.1488-0.864-0.22590.5397-0.0346-0.03980.38530.7450.18340.29680.0373-0.02820.42480.01750.2229-13.2071-16.78945.3836
384.38758.1957-3.853515.6099-5.579616.2218-0.0392-0.1673-0.38240.1466-0.1652-0.56010.50020.06870.20440.52190.22920.34370.31750.20960.3994-18.1114-24.80894.8144
397.4286-0.9578-5.96894.3797-1.069630.9709-0.03510.197-0.491-0.07-0.15550.23190.64520.20890.19070.19490.01370.03660.1599-0.01280.2311-15.8068-23.6161-6.0872
408.9379-11.9667-1.048317.5678-3.011920.54660.5980.35350.6957-1.007-0.5096-1.0762-0.22010.262-0.08840.2543-0.0928-0.01230.32240.02260.2522-10.1713-20.3657-14.728
412.9005-3.5743-1.07924.85790.277316.66320.6110.5005-0.2218-0.7931-0.15580.47250.7225-0.2301-0.45520.3186-0.00440.0190.67840.01480.3151-25.937-1.783-15.837
4210.7875-3.5295-0.43342.2089-4.106417.19250.46070.1591-0.5509-0.16430.06760.29470.0118-0.4604-0.52830.24720.0512-0.00770.2336-0.0120.1938-24.5052-1.9989-7.8664
435.04071.83411.360511.4874-4.77555.49410.44210.4101-0.04-0.125-0.04170.6223-0.2994-0.6552-0.40040.32320.13110.11580.3952-0.02960.2401-28.05533.7534-2.9534
4413.79933.305-7.21187.9784-0.12054.12830.18540.19311.1233-0.63560.21541.1656-0.2526-0.0595-0.40080.6130.2180.09850.32220.11220.4118-27.864711.061-7.6236
4523.540710.89714.415125.67210.926916.5742-0.31251.44210.6408-1.76950.57940.3537-2.365-0.0866-0.26690.47120.01280.16790.34220.03220.1602-22.95658.7792-15.2272
465.9909-6.43-3.39215.01260.928413.216-0.05480.3890.1840.0856-0.4338-0.1755-0.060.61770.48860.408-0.15160.18410.21650.12110.4949-16.060812.1138-7.363
4718.2983-8.67914.091916.243-16.960519.54010.4774-0.14740.09351.5047-0.14680.2565-2.14290.2084-0.33060.89620.05780.1510.114-0.09670.3667-21.390112.637-0.4761
481.27953.274-3.55829.1329-6.50420.71310.0261-0.15470.02380.109-0.0322-0.1074-0.31931.34070.00620.2872-0.05720.03010.4527-0.19590.414-17.11134.78242.5351
490.5709-0.4246-1.608810.6793-7.764112.32790.062-0.29280.270.49180.2044-0.8032-0.48260.8542-0.26650.3081-0.028-0.02380.3697-0.06960.3061-15.30081.2524-4.597
507.9132-6.45870.30766.182-4.658621.3691-0.33710.33720.62820.1694-0.2487-0.63190.4143-0.27440.58580.2685-0.00820.11240.43270.0160.2281-14.04591.6658-14.9247
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A911 - 916
2X-RAY DIFFRACTION2A917 - 921
3X-RAY DIFFRACTION3A922 - 926
4X-RAY DIFFRACTION4A927 - 932
5X-RAY DIFFRACTION5A933 - 938
6X-RAY DIFFRACTION6A939 - 943
7X-RAY DIFFRACTION7A944 - 951
8X-RAY DIFFRACTION8A952 - 956
9X-RAY DIFFRACTION9A957 - 967
10X-RAY DIFFRACTION10A968 - 974
11X-RAY DIFFRACTION11B912 - 919
12X-RAY DIFFRACTION12B920 - 925
13X-RAY DIFFRACTION13B926 - 930
14X-RAY DIFFRACTION14B931 - 936
15X-RAY DIFFRACTION15B937 - 942
16X-RAY DIFFRACTION16B943 - 948
17X-RAY DIFFRACTION17B949 - 954
18X-RAY DIFFRACTION18B955 - 963
19X-RAY DIFFRACTION19B964 - 968
20X-RAY DIFFRACTION20B969 - 974
21X-RAY DIFFRACTION21C907 - 912
22X-RAY DIFFRACTION22C913 - 917
23X-RAY DIFFRACTION23C918 - 922
24X-RAY DIFFRACTION24C923 - 928
25X-RAY DIFFRACTION25C929 - 933
26X-RAY DIFFRACTION26C934 - 941
27X-RAY DIFFRACTION27C942 - 947
28X-RAY DIFFRACTION28C948 - 954
29X-RAY DIFFRACTION29C955 - 959
30X-RAY DIFFRACTION30C960 - 965
31X-RAY DIFFRACTION31D903 - 910
32X-RAY DIFFRACTION32D911 - 918
33X-RAY DIFFRACTION33D919 - 925
34X-RAY DIFFRACTION34D926 - 932
35X-RAY DIFFRACTION35D933 - 937
36X-RAY DIFFRACTION36D938 - 942
37X-RAY DIFFRACTION37D943 - 950
38X-RAY DIFFRACTION38D951 - 956
39X-RAY DIFFRACTION39D957 - 965
40X-RAY DIFFRACTION40D966 - 970
41X-RAY DIFFRACTION41E903 - 910
42X-RAY DIFFRACTION42E911 - 917
43X-RAY DIFFRACTION43E918 - 923
44X-RAY DIFFRACTION44E924 - 929
45X-RAY DIFFRACTION45E930 - 937
46X-RAY DIFFRACTION46E938 - 945
47X-RAY DIFFRACTION47E946 - 950
48X-RAY DIFFRACTION48E951 - 956
49X-RAY DIFFRACTION49E957 - 961
50X-RAY DIFFRACTION50E962 - 968

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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