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- PDB-4xoi: Structure of hsAnillin bound with RhoA(Q63L) at 2.1 Angstroms res... -

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基本情報

登録情報
データベース: PDB / ID: 4xoi
タイトルStructure of hsAnillin bound with RhoA(Q63L) at 2.1 Angstroms resolution
要素
  • Actin-binding protein anillin
  • Transforming protein RhoA
キーワードCELL CYCLE / RhoA-anillin complex
機能・相同性
機能・相同性情報


septin ring organization / positive regulation of bleb assembly / actomyosin contractile ring assembly / podocyte cell migration / septin ring assembly / actomyosin contractile ring / alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity ...septin ring organization / positive regulation of bleb assembly / actomyosin contractile ring assembly / podocyte cell migration / septin ring assembly / actomyosin contractile ring / alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / bleb / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / regulation of neural precursor cell proliferation / regulation of exit from mitosis / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / apical junction assembly / cell junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / establishment of epithelial cell apical/basal polarity / beta selection / regulation of systemic arterial blood pressure by endothelin / negative regulation of cell size / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / positive regulation of podosome assembly / apolipoprotein A-I-mediated signaling pathway / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / positive regulation of leukocyte adhesion to vascular endothelial cell / wound healing, spreading of cells / motor neuron apoptotic process / PI3K/AKT activation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / apical junction complex / RHOB GTPase cycle / EPHA-mediated growth cone collapse / myosin binding / regulation of neuron projection development / stress fiber assembly / cellular response to cytokine stimulus / RHOC GTPase cycle / positive regulation of cytokinesis / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / mitotic cytokinesis / semaphorin-plexin signaling pathway / androgen receptor signaling pathway / ficolin-1-rich granule membrane / RHOA GTPase cycle / mitotic spindle assembly / negative regulation of cell-substrate adhesion / Rho protein signal transduction / positive regulation of protein serine/threonine kinase activity / endothelial cell migration / positive regulation of T cell migration / hematopoietic progenitor cell differentiation / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / skeletal muscle tissue development / RHO GTPases activate PKNs / GPVI-mediated activation cascade / negative regulation of reactive oxygen species biosynthetic process / positive regulation of stress fiber assembly / cytoplasmic microtubule organization / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / regulation of microtubule cytoskeleton organization / regulation of cell migration / secretory granule membrane / small monomeric GTPase / cell-matrix adhesion / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery
類似検索 - 分子機能
Anillin homology domain / Anillin, N-terminal domain / Anillin, PH domain / : / Cell division protein anillin / Anillin N-terminus / Small GTPase Rho / small GTPase Rho family profile. / PH domain / PH domain profile. ...Anillin homology domain / Anillin, N-terminal domain / Anillin, PH domain / : / Cell division protein anillin / Anillin N-terminus / Small GTPase Rho / small GTPase Rho family profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
GUANOSINE-5'-TRIPHOSPHATE / Transforming protein RhoA / Anillin
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 / 解像度: 2.092 Å
データ登録者Sun, L. / Guan, R. / Lee, I.-J. / Liu, Y. / Chen, M. / Wang, J. / Wu, J. / Chen, Z.
資金援助 中国, 米国, 2件
組織認可番号国
National Natural Science Foundation of China31270762 中国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM086546 米国
引用ジャーナル: Dev.Cell / 年: 2015
タイトル: Mechanistic insights into the anchorage of the contractile ring by anillin and mid1
著者: Sun, L. / Guan, R. / Lee, I.J. / Liu, Y. / Chen, M. / Wang, J. / Wu, J.Q. / Chen, Z.
履歴
登録2015年1月16日登録サイト: RCSB / 処理サイト: PDBJ
改定 1.02015年7月15日Provider: repository / タイプ: Initial release
改定 1.12017年10月18日Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
カテゴリ: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
改定 1.22022年3月23日Group: Author supporting evidence / Database references / Derived calculations
カテゴリ: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
改定 1.32024年5月29日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

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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: Transforming protein RhoA
B: Actin-binding protein anillin
C: Transforming protein RhoA
D: Actin-binding protein anillin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,9758
ポリマ－99,8804
非ポリマー1,0954
水7,512417
1
A: Transforming protein RhoA
B: Actin-binding protein anillin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)50,4884
ポリマ－49,9402
非ポリマー5472
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-29 kcal/mol
Surface area19640 Å2
手法PISA
2
C: Transforming protein RhoA
D: Actin-binding protein anillin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)50,4884
ポリマ－49,9402
非ポリマー5472
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-29 kcal/mol
Surface area19290 Å2
手法PISA
単位格子
Length a, b, c (Å)54.311, 52.434, 103.101
Angle α, β, γ (deg.)77.87, 74.14, 85.73
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質 Transforming protein RhoA / Rho cDNA clone 12 / h12


分子量: 20348.336 Da / 分子数: 2 / 断片: UNP residues 1-180 / 変異: Q63L / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RHOA, ARH12, ARHA, RHO12 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61586
#2: タンパク質 Actin-binding protein anillin


分子量: 29591.893 Da / 分子数: 2 / 断片: RBD domain, UNP residues 712-981 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ANLN / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9NQW6
#3: 化合物 ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP


分子量: 523.180 Da / 分子数: 2 / 由来タイプ: 天然 / 式: C10H16N5O14P3 / コメント: GTP, エネルギー貯蔵分子*YM
#4: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 417 / 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

結晶マシュー密度: 2.76 Å3/Da / 溶媒含有率: 55.5 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 12% PEG 3,350, 3% PEG 10000, 0.2 M sodium malonate, 5 mM DTT

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データ収集

回折平均測定温度: 103 K
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL17U / 波長: 0.987 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2012年9月16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: 0.987 Å / 相対比: 1
反射解像度: 2.092→29.688 Å / Num. obs: 61564 / % possible obs: 98.1 % / 冗長度: 3.3 % / Net I/σ(I): 3

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解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: 1.7.1_743)精密化
HKL-2000データ削減
HKL-2000データスケーリング
SHARP位相決定
精密化解像度: 2.092→29.688 Å / SU ML: 0.5 / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 20.81 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2061 2017 3.28 %
Rwork0.1726 --
obs0.1737 61564 97.58 %
溶媒の処理減衰半径: 0.83 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 44.837 Å2 / ksol: 0.357 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1-2.1418 Å20.7282 Å20.0782 Å2
2--1.0376 Å2-3.2 Å2
3----3.1794 Å2
精密化ステップサイクル: LAST / 解像度: 2.092→29.688 Å
タンパク質核酸リガンド溶媒全体
原子数6039 0 66 417 6522
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0076208
X-RAY DIFFRACTIONf_angle_d1.0488406
X-RAY DIFFRACTIONf_dihedral_angle_d17.0652351
X-RAY DIFFRACTIONf_chiral_restr0.072978
X-RAY DIFFRACTIONf_plane_restr0.0041069
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0919-2.14420.24471260.20413887X-RAY DIFFRACTION90
2.1442-2.20220.21711460.19734273X-RAY DIFFRACTION97
2.2022-2.2670.26361510.19414269X-RAY DIFFRACTION97
2.267-2.34010.27641350.18964255X-RAY DIFFRACTION98
2.3401-2.42370.24741470.194231X-RAY DIFFRACTION98
2.4237-2.52070.27261510.19294275X-RAY DIFFRACTION98
2.5207-2.63540.20911380.18754304X-RAY DIFFRACTION98
2.6354-2.77420.22991440.18734288X-RAY DIFFRACTION98
2.7742-2.94790.25221460.18584266X-RAY DIFFRACTION98
2.9479-3.17520.19871490.18374305X-RAY DIFFRACTION98
3.1752-3.49430.21971420.16654319X-RAY DIFFRACTION99
3.4943-3.99890.16651450.15744287X-RAY DIFFRACTION99
3.9989-5.03420.16951430.14324302X-RAY DIFFRACTION99
5.0342-29.69070.17981540.17034286X-RAY DIFFRACTION98
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)
14.27551.85631.79514.85944.76128.9148-0.0006-0.1357-0.0321-0.20870.0102-0.06350.5110.18120.01460.510.0915-0.05150.30930.03470.1632-51.25518.233931.4028
22.0074-0.2234-1.07452.01742.73772.0176-0.20020.18970.3196-0.4765-0.12191.2139-0.2145-1.33830.21560.44950.0149-0.02880.5612-0.02130.4515-63.94829.586428.891
32.00299.30391.27249.53611.39264.7319-0.10160.07780.3793-0.30710.11960.49140.1095-0.6425-0.00280.32030.0321-0.02290.40540.01480.2045-56.26118.471719.5384
42.82540.0901-1.23853.856-1.29822.00660.0996-0.35020.60640.7447-0.26910.2061-1.2614-0.74920.15390.62770.11240.01380.4479-0.12990.3608-55.853217.398840.3981
53.70311.2885-0.3933.6767-1.11233.052-0.08590.1421-0.2855-0.12270.0768-0.431.30760.51360.02210.59630.1406-0.02250.3308-0.01450.2106-48.0846.563926.6104
62.00157.07572.76385.75510.95053.37920.13570.5935-0.9203-0.62860.0267-0.30070.78930.198-0.1571.78690.3533-0.11730.1851-0.02210.4486-50.7633-9.11128.335
72.0026-0.51842.67167.5197-1.50773.3591-0.0279-0.0977-0.3650.27480.0936-0.42480.34620.4057-0.09330.86160.4756-0.00850.7537-0.01260.4139-41.2099-0.251929.6215
80.1479-0.2186-0.62361.3875-0.48974.2899-0.065-0.147-0.19670.3247-0.0261-0.19420.81290.26910.09080.84470.1705-0.08340.45950.02490.1892-48.83891.919235.3034
93.9771-0.55545.00160.90291.03659.94910.1209-0.5143-0.6729-0.05790.13770.55311.0102-1.2773-0.32081.3651-0.5438-0.18910.91910.30610.4562-67.1372-8.642731.909
108.7019-4.18283.69422.00341.29832.55340.1034-0.2943-0.1890.4355-0.12480.14810.3454-0.2820.07451.647-0.1475-0.23780.7037-0.04190.4918-65.9932-15.42623.9953
114.6054-0.75984.7912.64133.77852.00010.72151.26040.3689-2.0214-0.6884-0.5013-3.3036-0.80530.03932.0705-0.2052-0.04070.81440.04310.357-58.5131-17.958626.9698
124.79832.45784.0191.64512.3483.5830.22310.292-1.02030.0417-0.1040.1282.3098-0.5334-0.12371.791-0.1218-0.12590.6554-0.0650.3852-57.4831-12.59638.1435
131.3517-0.3806-0.42530.66481.15622.0621-0.0665-0.0268-0.40070.0414-0.0487-0.12180.70680.10760.03891.87510.6357-0.30810.07370.7109-0.3804-48.7127-5.847140.7101
149.2681-7.09746.95757.7027-7.31092.0087-0.5004-0.6329-0.11550.40480.47870.2872-0.0043-0.7504-0.01010.9501-0.33880.06390.76520.00270.3248-64.69681.120635.6586
156.74274.61772.88137.09192.80632.0230.0768-0.866-0.08090.6726-0.15140.02420.4334-0.21080.04840.8304-0.0151-0.02130.4956-0.00930.1509-55.11858.145942.9106
162.00335.51183.61227.53472.79292.00430.28210.0679-0.4886-0.0817-0.28680.01370.1029-0.19070.02590.2274-0.0175-0.08070.28020.05450.4013-72.06914.66670.4915
178.22.74116.18372.60652.01997.86830.2436-0.65840.07870.181-0.15560.23370.2869-0.404-0.10280.1430.02460.02410.20020.03880.2349-56.880313.302411.9835
184.1709-4.19195.21612.0027-1.9878.0726-0.1449-0.66870.53350.7492-0.1059-1.0619-0.56861.05860.2220.3449-0.1253-0.10790.8803-0.12720.4905-35.918119.659123.9558
196.956-0.87423.372.6326-0.67455.9402-0.0273-0.2982-0.10060.00620.0473-0.15370.10930.2269-0.08520.09510.02760.03210.16380.02470.2141-47.545713.01278.4265
202.0125-1.01514.32422.0129-1.97392.015-0.01261.47030.3808-1.4870.3561.15020.0504-0.1984-0.10780.4024-0.0301-0.07210.51010.09710.5254-66.712413.2614-5.3725
214.23251.63823.234.91280.46214.06280.15270.4935-0.9762-0.37690.10790.18230.9773-0.6027-0.41280.4182-0.15850.02760.3949-0.13920.4883-43.0957-2.0735-8.7654
222.01710.02136.7862.66840.232.0133-0.3759-0.32570.73640.24480.003-0.2508-0.63610.08810.28310.1663-0.027-0.01080.3882-0.05390.3839-21.668414.78431.8542
239.47833.11483.97836.3452.4737.7323-0.0075-0.54-0.10880.07040.3054-0.5223-0.1480.4373-0.19670.09990.0220.03710.2868-0.06210.3198-34.235412.5115.3742
241.9998-2.493-1.22465.15821.42199.4086-0.0219-0.4332-0.72180.2083-0.03111.60170.8229-1.77120.04130.4054-0.15930.0790.762-0.07850.776-54.28914.7092-3.1306
259.74992.2659-2.17893.0259-0.00854.0896-0.2075-0.0624-0.51910.1155-0.0536-0.39240.23150.44250.25260.22440.04060.01360.21290.07480.3534-34.00785.88353.7079
266.77881.89132.79744.73010.85265.29570.1186-0.3528-0.8597-0.26340.00760.46851.0307-1.1319-0.13740.352-0.18440.05880.42480.00170.5653-46.5089-0.1967-7.0462
278.75570.92337.79526.84115.48422.0807-0.3708-0.22190.65810.04880.02690.1952-0.4552-0.32160.58160.213-0.15720.10020.3740.00460.2616-39.071714.65941.8138
282.3389-0.6224-0.7982.34550.27753.2283-0.11510.2689-0.0256-0.24150.00380.14150.0566-0.40210.10020.1176-0.074-0.01580.2020.02860.2572-43.227311.1559-5.0648
291.34472.43030.59247.42122.87283.6502-0.27230.2951-0.17-0.15630.2484-0.24080.13050.07030.06190.1938-0.06030.0090.22560.03950.3104-34.141812.8347-9.4786
301.99749.52784.78898.79144.42892.22480.6437-0.5169-0.80570.497-0.3377-1.13410.4047-0.0235-0.29280.5851-0.09430.03010.3634-0.03140.6301-44.3598-7.364-12.0813
316.38252.48652.41192.00255.87916.72120.17380.2926-0.7048-0.0966-0.2640.15260.7959-0.08180.07120.5339-0.04550.06990.4112-0.05330.28-24.2732-23.6664-35.4056
323.5434-1.0273-0.22532.97070.6863.6957-0.23780.052-0.03520.27780.35530.353-0.3184-0.0041-0.12750.3996-0.01190.06250.24630.02360.2496-32.3504-11.4748-26.9731
332.0031-3.64622.49332.002222.0027-0.43770.4194-0.59480.0858-0.8992.22880.4736-1.77541.31550.5882-0.1437-0.06030.6509-0.13410.8197-43.2504-14.8594-26.7714
348.8045-5.0992-2.68053.82210.11173.24580.16880.2592-0.1733-0.21590.11620.492-0.2826-0.263-0.28580.53080.01610.05530.30410.04450.2326-32.7201-14.5331-17.8726
352.71490.62560.33033.5219-4.38492.0042-0.07210.4765-0.4051-0.6880.03650.290.7879-0.86890.0090.6383-0.0555-0.0150.4896-0.15820.3516-32.2265-22.2107-36.5898
362.1010.31163.07772.75253.39522.00910.1590.1863-0.5257-0.5763-0.21250.50590.5214-0.3861-0.00280.5577-0.0596-0.030.3031-0.06850.2944-28.6228-22.5547-35.2132
378.2009-1.6048-0.30052.0065-4.44392.002-0.2148-0.8660.88951.4569-0.0526-0.2369-0.89630.18760.27010.6596-0.0086-0.04080.3278-0.07790.3625-23.5055-10.698-15.6234
380.93350.53550.49730.8398-0.671.9036-0.13920.12490.025-0.23130.195-0.0465-0.3480.2197-0.0670.441-0.06240.040.316-0.01190.2086-24.0448-10.0724-28.6298
392.0036-9.0346-2.07716.7947-1.71759.8770.0123-0.63911.68890.1635-0.009-0.9527-1.29310.5138-0.0530.6696-0.15460.02430.3849-0.04410.4304-22.33792.4111-26.3515
404.6859-1.515-0.86663.07840.75132.94670.09810.36250.4761-0.3027-0.0828-0.3742-0.55930.2801-0.02160.4601-0.11720.00850.35640.04810.2391-24.4706-5.5431-30.6131
412.00777.77746.67646.06725.17662.00430.00090.1921.1071-0.2503-0.31780.8668-0.9089-0.65030.29560.75410.11350.02760.38150.05030.4839-40.265610.4948-23.5277
425.69570.5642-0.43289.02199.33139.82810.03980.05330.5606-0.49230.18070.1346-0.84370.0124-0.15470.89620.00010.05270.35510.04260.3942-32.297211.4452-26.3756
432.004-6.12720.26576.2599-2.62365.82270.34340.48440.7962-0.4949-0.2632-0.3913-0.60140.0639-0.09971.0412-0.1990.09470.54020.10340.3081-26.03884.0691-38.0667
445.08310.8491-2.26964.1946-0.42022.7154-0.09260.82490.187-0.7811-0.02420.3144-0.7612-0.09230.09740.6214-0.0609-0.05650.41770.04110.1781-32.4592-6.8866-36.862
454.3433-0.88462.78958.27081.62032.00780.14690.6098-0.0479-0.640.0876-0.20790.13510.435-0.20140.786-0.07920.04860.4835-0.06630.1758-25.7955-15.6817-42.7094
462.0037-0.7099-1.42478.34436.06822.00870.35910.25221.0271-0.157-0.26760.8995-0.7836-0.8602-0.05010.26480.01270.09930.33690.08550.5635-48.2434-11.79270.4546
478.653-3.6798-8.16243.30082.45188.3510.2620.3587-0.0613-0.2953-0.09320.3117-0.3047-0.3307-0.180.1477-0.0345-0.00890.17090.01210.1956-33.3907-19.9132-10.0322
482.00182.8304-0.66149.89920.37947.7320.2440.4532-0.2588-0.4239-0.0435-0.89140.4691.1675-0.27820.37290.09760.0350.4913-0.05760.3417-15.2642-26.9069-20.4163
494.02890.3447-1.5631.5527-0.16594.37660.0975-0.0265-0.017-0.1172-0.0057-0.10460.01040.4508-0.12640.1213-0.0050.00060.2298-0.01460.2329-21.8848-20.1084-8.4666
502.0121-1.2027-4.43167.3906-0.5862.01120.0874-0.8563-0.08750.61320.2320.4803-0.0492-0.0434-0.33760.1560.0309-0.02360.39410.08160.3603-42.1291-19.57295.7479
511.98651.5939-0.74921.2551-0.58760.27130.1384-0.71261.07450.8471-0.28770.89550.154-0.4820.04650.77860.24590.22251.039-0.09721.0044-37.3529-4.012217.5207
526.4267-4.1172-1.70319.79951.62475.15370.0552-0.27150.85230.06090.1835-0.3926-0.57680.0467-0.23310.18710.004-0.01560.13410.00860.3267-15.6625-5.91068.2594
539.935-1.1917-3.92284.14111.60562.012-0.23430.3707-0.7999-0.20960.2623-0.3540.41740.4909-0.02110.1470.01610.01730.3282-0.04730.42931.4192-21.06570.1645
540.8971-0.7233-2.32724.50812.35736.34890.0470.60620.1297-0.1880.08580.0975-0.083-0.283-0.17970.13170.0113-0.07450.2893-0.01290.3952-17.293-16.5822-0.4223
552.0051-2.23113.20293.16630.56234.7031-0.23770.09340.2173-0.1537-0.0494-0.9309-0.32750.82730.29360.1862-0.0281-0.02440.32140.08860.5253-11.0409-12.0422-1.5947
563.9791-1.0245-0.45044.93010.60334.49070.00380.04420.24140.275-0.01420.3923-0.3085-0.3931-0.01860.13930.0259-0.01050.20960.04180.3274-21.4927-10.74676.8477
570.41640.7077-0.35921.2115-0.59210.31290.02130.1816-0.9777-0.33310.0036-0.13460.37070.0099-0.00720.22970.0445-0.01510.2739-0.12060.3706-19.9511-28.4035-9.4788
581.7762-0.1932-0.40685.40573.11425.5316-0.038-0.22910.02080.5663-0.18280.1690.0273-0.15290.11560.1530.02680.00440.18980.00150.29-17.3458-13.601213.7166
594.2188-5.6801-1.7928.1733.62533.4815-0.1637-0.2772-0.03170.25770.1694-0.18420.14480.1035-0.03210.17660.03410.00990.21750.02970.2876-10.3591-22.432410.4379
609.3032-6.6701-8.74182.02387.81698.4629-0.0924-0.34371.54290.17040.0357-0.4364-0.9039-0.3555-0.00930.29820.1135-0.03730.2691-0.03860.6155-17.3672-2.337512.7407
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:18)A4 - 18
2X-RAY DIFFRACTION2(CHAIN A AND RESID 19:32)A19 - 32
3X-RAY DIFFRACTION3(CHAIN A AND RESID 33:40)A33 - 40
4X-RAY DIFFRACTION4(CHAIN A AND RESID 41:54)A41 - 54
5X-RAY DIFFRACTION5(CHAIN A AND RESID 55:86)A55 - 86
6X-RAY DIFFRACTION6(CHAIN A AND RESID 87:97)A87 - 97
7X-RAY DIFFRACTION7(CHAIN A AND RESID 98:105)A98 - 105
8X-RAY DIFFRACTION8(CHAIN A AND RESID 106:119)A106 - 119
9X-RAY DIFFRACTION9(CHAIN A AND RESID 120:124)A120 - 124
10X-RAY DIFFRACTION10(CHAIN A AND RESID 125:133)A125 - 133
11X-RAY DIFFRACTION11(CHAIN A AND RESID 134:138)A134 - 138
12X-RAY DIFFRACTION12(CHAIN A AND RESID 139:143)A139 - 143
13X-RAY DIFFRACTION13(CHAIN A AND RESID 144:156)A144 - 156
14X-RAY DIFFRACTION14(CHAIN A AND RESID 157:165)A157 - 165
15X-RAY DIFFRACTION15(CHAIN A AND RESID 166:180)A166 - 180
16X-RAY DIFFRACTION16(CHAIN B AND RESID 4:8)B4 - 8
17X-RAY DIFFRACTION17(CHAIN B AND RESID 9:33)B9 - 33
18X-RAY DIFFRACTION18(CHAIN B AND RESID 34:40)B34 - 40
19X-RAY DIFFRACTION19(CHAIN B AND RESID 41:63)B41 - 63
20X-RAY DIFFRACTION20(CHAIN B AND RESID 64:72)B64 - 72
21X-RAY DIFFRACTION21(CHAIN B AND RESID 88:101)B88 - 101
22X-RAY DIFFRACTION22(CHAIN B AND RESID 102:114)B102 - 114
23X-RAY DIFFRACTION23(CHAIN B AND RESID 115:125)B115 - 125
24X-RAY DIFFRACTION24(CHAIN B AND RESID 126:131)B126 - 131
25X-RAY DIFFRACTION25(CHAIN B AND RESID 132:147)B132 - 147
26X-RAY DIFFRACTION26(CHAIN B AND RESID 148:166)B148 - 166
27X-RAY DIFFRACTION27(CHAIN B AND RESID 167:176)B167 - 176
28X-RAY DIFFRACTION28(CHAIN B AND RESID 222:244)B222 - 244
29X-RAY DIFFRACTION29(CHAIN B AND RESID 245:263)B245 - 263
30X-RAY DIFFRACTION30(CHAIN B AND RESID 264:269)B264 - 269
31X-RAY DIFFRACTION31(CHAIN C AND RESID 4:8)C4 - 8
32X-RAY DIFFRACTION32(CHAIN C AND RESID 9:26)C9 - 26
33X-RAY DIFFRACTION33(CHAIN C AND RESID 27:32)C27 - 32
34X-RAY DIFFRACTION34(CHAIN C AND RESID 33:40)C33 - 40
35X-RAY DIFFRACTION35(CHAIN C AND RESID 41:49)C41 - 49
36X-RAY DIFFRACTION36(CHAIN C AND RESID 50:59)C50 - 59
37X-RAY DIFFRACTION37(CHAIN C AND RESID 60:70)C60 - 70
38X-RAY DIFFRACTION38(CHAIN C AND RESID 71:89)C71 - 89
39X-RAY DIFFRACTION39(CHAIN C AND RESID 90:97)C90 - 97
40X-RAY DIFFRACTION40(CHAIN C AND RESID 98:124)C98 - 124
41X-RAY DIFFRACTION41(CHAIN C AND RESID 125:133)C125 - 133
42X-RAY DIFFRACTION42(CHAIN C AND RESID 134:139)C134 - 139
43X-RAY DIFFRACTION43(CHAIN C AND RESID 140:149)C140 - 149
44X-RAY DIFFRACTION44(CHAIN C AND RESID 150:171)C150 - 171
45X-RAY DIFFRACTION45(CHAIN C AND RESID 172:180)C172 - 180
46X-RAY DIFFRACTION46(CHAIN D AND RESID 4:11)D4 - 11
47X-RAY DIFFRACTION47(CHAIN D AND RESID 12:30)D12 - 30
48X-RAY DIFFRACTION48(CHAIN D AND RESID 31:37)D31 - 37
49X-RAY DIFFRACTION49(CHAIN D AND RESID 38:61)D38 - 61
50X-RAY DIFFRACTION50(CHAIN D AND RESID 62:71)D62 - 71
51X-RAY DIFFRACTION51(CHAIN D AND RESID 72:91)D72 - 91
52X-RAY DIFFRACTION52(CHAIN D AND RESID 92:101)D92 - 101
53X-RAY DIFFRACTION53(CHAIN D AND RESID 102:114)D102 - 114
54X-RAY DIFFRACTION54(CHAIN D AND RESID 115:131)D115 - 131
55X-RAY DIFFRACTION55(CHAIN D AND RESID 132:147)D132 - 147
56X-RAY DIFFRACTION56(CHAIN D AND RESID 148:175)D148 - 175
57X-RAY DIFFRACTION57(CHAIN D AND RESID 176:227)D176 - 227
58X-RAY DIFFRACTION58(CHAIN D AND RESID 228:248)D228 - 248
59X-RAY DIFFRACTION59(CHAIN D AND RESID 249:261)D249 - 261
60X-RAY DIFFRACTION60(CHAIN D AND RESID 262:268)D262 - 268

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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