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- PDB-2wwm: Crystal structure of the Titin M10-Obscurin like 1 Ig complex in ... -

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基本情報

登録情報
データベース: PDB / ID: 2wwm
タイトルCrystal structure of the Titin M10-Obscurin like 1 Ig complex in space group P1
要素
  • OBSCURIN-LIKE PROTEIN 1
  • TITIN
キーワードTRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE-STRUCTURAL PROTEIN COMPLEX / SARCOMERE / TPR REPEAT / IMMUNOGLOBULIN DOMAIN / LIMB-GIRDLE MUSCULAR DYSTROPHY / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE / CARDIOMYOPATHY / CALMODULIN-BINDING / NUCLEOTIDE-BINDING
機能・相同性
機能・相同性情報


3M complex / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / protein localization to Golgi apparatus / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cytoskeletal anchor activity ...3M complex / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / protein localization to Golgi apparatus / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cytoskeletal anchor activity / cardiac muscle tissue morphogenesis / protein kinase regulator activity / cardiac muscle hypertrophy / mitotic chromosome condensation / actinin binding / Striated Muscle Contraction / M band / I band / positive regulation of dendrite morphogenesis / cardiac muscle cell development / structural constituent of muscle / regulation of mitotic nuclear division / sarcomere organization / Golgi organization / skeletal muscle thin filament assembly / striated muscle thin filament / intercalated disc / cardiac muscle contraction / striated muscle contraction / cytoskeleton organization / muscle contraction / protein kinase A signaling / condensed nuclear chromosome / positive regulation of protein secretion / Z disc / microtubule cytoskeleton organization / response to calcium ion / actin filament binding / Platelet degranulation / Neddylation / protein tyrosine kinase activity / protease binding / non-specific serine/threonine protein kinase / calmodulin binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / calcium ion binding / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / protein homodimerization activity / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol / cytoplasm
類似検索 - 分子機能
: / PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain ...: / PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulins / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Obscurin-like protein 1 / Titin
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: 2.3 Å
データ登録者Pernigo, S. / Fukuzawa, A. / Gautel, M. / Steiner, R.A.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2010
タイトル: Structural Insight Into M-Band Assembly and Mechanics from the Titin-Obscurin-Like-1 Complex.
著者: Pernigo, S. / Fukuzawa, A. / Bertz, M. / Holt, M. / Rief, M. / Steiner, R.A. / Gautel, M.
履歴
登録2009年10月26日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02010年2月16日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Advisory / Version format compliance
改定 1.22011年8月24日Group: Derived calculations
改定 1.32023年12月20日Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
C: OBSCURIN-LIKE PROTEIN 1
D: TITIN
O: OBSCURIN-LIKE PROTEIN 1
T: TITIN


分子量 (理論値)分子数
合計 (水以外)44,2144
ポリマ－44,2144
非ポリマー00
水2,036113
1
O: OBSCURIN-LIKE PROTEIN 1
T: TITIN


分子量 (理論値)分子数
合計 (水以外)22,1072
ポリマ－22,1072
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-7.1 kcal/mol
Surface area10360 Å2
手法PISA
2
C: OBSCURIN-LIKE PROTEIN 1
D: TITIN


分子量 (理論値)分子数
合計 (水以外)22,1072
ポリマ－22,1072
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-7.53 kcal/mol
Surface area10810 Å2
手法PISA
単位格子
Length a, b, c (Å)37.650, 44.940, 68.010
Angle α, β, γ (deg.)87.29, 86.91, 68.79
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質 OBSCURIN-LIKE PROTEIN 1


分子量: 11125.619 Da / 分子数: 2 / 断片: RESIDUES 1-106 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): ROSETTA 2 / 参照: UniProt: O75147
#2: タンパク質 TITIN / CONNECTIN / RHABDOMYOSARCOMA ANTIGEN MU-RMS-40.14


分子量: 10981.231 Da / 分子数: 2 / 断片: M10, RESIDUES 34252-34350 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): ROSETTA 2
参照: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 113 / 由来タイプ: 天然 / 式: H2O
配列の詳細INITIAL GSS ARE FROM THE EXPRESSION VECTOR

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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: 2.49 Å3/Da / 溶媒含有率: 50.27 % / 解説: NONE
結晶化pH: 5 / 詳細: 0.1 M MIB BUFFER PH 5.0, 25% PEG 1500

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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: Diamond / ビームライン: I03 / 波長: 0.9763
検出器タイプ: ADSC CCD / 検出器: CCD / 日付: 2009年8月12日 / 詳細: MIRRORS
放射モノクロメーター: SI (111) DOUBLE CRYSTAL / 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: 0.9763 Å / 相対比: 1
反射解像度: 2.3→36.13 Å / Num. obs: 17094 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / 冗長度: 3.8 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.2
反射 シェル解像度: 2.3→2.42 Å / 冗長度: 3.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.3 / % possible all: 93.1

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解析

ソフトウェア
名称バージョン分類
REFMAC5.5.0109精密化
MOSFLMデータ削減
SCALAデータスケーリング
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 2WP3

2wp3


解像度: 2.3→35.88 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.898 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.263 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
Rfactor反射数%反射Selection details
Rfree0.25219 879 5.1 %RANDOM
Rwork0.19718 ---
obs0.19997 16215 92.66 %-
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: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK
原子変位パラメータBiso mean: 17.149 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-1.11 Å20.03 Å2
2--3.93 Å2-1.46 Å2
3----1.83 Å2
精密化ステップサイクル: LAST / 解像度: 2.3→35.88 Å
タンパク質核酸リガンド溶媒全体
原子数2917 0 0 113 3030
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223025
X-RAY DIFFRACTIONr_bond_other_d0.0010.022039
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9774133
X-RAY DIFFRACTIONr_angle_other_deg0.78735005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8375402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.29423.917120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09615469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6451521
X-RAY DIFFRACTIONr_chiral_restr0.070.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213415
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02574
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3051.51981
X-RAY DIFFRACTIONr_mcbond_other0.0781.5799
X-RAY DIFFRACTIONr_mcangle_it0.56323198
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9631044
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4944.5930
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS精密化 シェル解像度: 2.3→2.36 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.36 67 -
Rwork0.262 1254 -
obs--92.77 %
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6115-3.31310.690310.0151-7.94854.17660.06710.0371-0.4136-0.07310.32680.78690.1817-0.5054-0.39380.2612-0.0253-0.0020.436-0.0060.25057.650414.882-39.7016
28.2331-7.3232-1.3155-9.69612.33914.5697-0.3887-1.1573-1.92060.16280.25580.09081.0495-1.35340.13290.2884-0.08920.05610.33530.13170.460316.66028.8281-31.7085
370.1092-16.9708-8.367310.12828.40969.615-0.7736-1.78560.60021.23320.6837-0.33560.84760.4830.08990.4079-0.0395-0.04880.17080.0520.277931.94297.31-29.7992
428.0682-12.32448.60954.9689-1.21835.85240.36620.3031-2.52050.2669-0.01050.76850.7812-0.097-0.35570.3159-0.0123-0.05510.3971-0.07190.614827.54084.126-37.3196
57.0454-7.66028.84044.6362-7.630827.4471-0.48850.1114-0.0080.14570.17730.03430.45660.64970.31120.2571-0.09480.02140.4103-0.05240.29829.267410.3984-41.4142
618.1972-2.1824-0.03840.4421-2.37957.5276-1.07720.8149-0.4783-0.06530.3818-0.0271-0.5655-0.32890.69540.3121-0.2094-0.10670.33620.02470.17715.773314.6113-45.4018
7-0.4179-1.4564.73613.68624.259933.1555-0.19070.24430.11540.15910.6409-0.5438-1.33731.7956-0.45020.314-0.1152-0.03840.3251-0.00320.3228.206320.049-43.4127
844.85-30.97172.475131.7189-6.7047-1.39820.74690.0759-0.3415-0.9949-0.7133-0.85270.2630.3763-0.03360.2789-0.0174-0.09930.5152-0.3570.580432.55849.357-47.9823
927.5764-1.76433.08725.75321.44861.57710.36230.2682-1.09290.6965-0.12870.02460.2334-0.0321-0.23360.2429-0.01670.02920.2382-0.03980.208220.95755.9064-46.1685
1039.9936-3.35643.1356-0.2303-0.28460.36260.1388-0.0355-1.49060.1169-0.11380.14310.12580.1012-0.02490.2451-0.05970.07420.3056-0.05470.28319.67056.4672-42.1201
1117.013413.64558.293729.07322.611614.0552-0.37860.2331-1.3582-0.49671.0123-1.0321-0.14390.9122-0.63370.30830.00540.00580.44380.04130.23836.56338.8353-39.2714
126.1241-3.62163.7941.757-2.62010.53790.04650.05060.0980.0136-0.1688-0.1726-0.10840.0710.12230.1978-0.0642-0.05930.25360.05010.218729.307815.4653-36.5203
1370.47076.490227.03620.3002-4.883836.3428-0.89742.35031.6819-0.28750.3539-0.1308-0.88641.0150.54360.5301-0.1320.23840.1932-0.14390.246114.456219.4634-44.6076
1428.4876-4.122922.72871.0731-5.596825.3181-0.1962-0.18140.38350.0452-0.10030.0735-0.02450.11660.29650.24530.04510.01660.1878-0.1210.107413.013320.524-40.7531
1545.668-14.447511.61334.4256-2.29966.83210.16640.50330.377-0.1014-0.0751-0.2881-0.27180.3939-0.09130.2259-0.07330.01250.18460.05270.292838.48779.0768-29.8127
1611.04184.9458-0.30361.6046-8.681626.3771-0.5941-0.7118-0.6733-0.9926-0.9187-1.04732.30731.8961.51270.3020.1070.12110.34710.13910.328723.913514.6372-12.4955
175.93151.3925-0.22990.7501-2.28987.4102-0.0580.1999-0.1453-0.3309-0.2218-0.20980.62640.65940.27980.29670.0449-0.00480.2032-0.03980.24720.322823.2285-33.3193
1812.4355-5.31287.49358.0231-7.726210.3012-0.21580.48890.455-0.21560.04540.0821-0.4394-0.26850.17040.27740.0305-0.05180.1838-0.04560.09069.763425.3296-39.6952
19-1.99323.25362.28469.131111.00821.47830.21950.1091-0.32940.9754-0.38830.08850.9606-0.25810.16880.3149-0.01440.05660.17050.07780.360518.247614.899-17.0904
203.39080.50230.910213.0688-7.93212.05950.0666-0.3107-0.13040.3357-0.0766-0.1463-0.537-0.31480.010.1228-0.022-0.01830.0738-0.00590.06413.502623.656-20.2564
219.23985.54154.344433.607214.04946.83920.20590.4490.5060.244-0.33760.77530.172-0.21790.13160.25540.0529-0.05980.12960.04590.18211.561834.9468-24.0203
2217.02354.7705-16.319311.1164-1.079522.7987-0.31090.75150.82910.12140.25021.5330.0863-0.9580.06070.2791-0.0104-0.06660.4869-0.01960.7826-0.25728.2436-26.0232
239.4353-1.7961-3.3591-3.29945.4873-0.72110.0961-0.67590.4421-0.19450.17280.1912-0.7129-0.3143-0.2690.42740.070.00490.3935-0.04460.18543.862128.0742-31.4084
2417.67571.2734-18.31910.9473-3.721621.5879-0.4354-0.1048-1.2558-0.33190.34050.831.2249-0.78790.09490.2563-0.2971-0.15380.27310.17160.689211.054415.8507-23.8602
2512.4023-12.32389.026421.6821-7.28923.7615-0.21420.4602-0.33510.05440.34460.7401-0.20070.1278-0.13040.24140.0623-0.00060.2528-0.0280.10246.53425.0937-34.183
2612.39786.3929-3.013125.5101-2.3748-0.8725-0.44710.74940.908-0.32590.52440.9364-0.0438-0.385-0.07730.4960.1258-0.09310.28610.07470.32648.526735.6569-38.7489
2710.2562-2.91195.07290.77281.75381.65790.28220.59880.7672-0.3898-0.6467-0.469-0.19690.08680.36460.26340.02570.06250.16270.00420.170817.282128.9646-26.6405
281.0903-1.40136.818611.1674-0.028214.8722-0.2326-0.12320.21280.9633-0.2453-0.3697-0.332-0.01140.47780.1222-0.0638-0.01990.27340.05160.115220.004620.9668-10.6594
294.88620.17025.94956.6423-2.4736.4578-0.29280.23250.16060.26630.0174-0.2236-0.56140.33910.27530.227-0.03470.0330.18510.0090.065720.639528-28.5947
3012.19531.5186-0.4626-4.0634-1.658525.2444-0.0260.69140.5916-0.3857-0.01880.1415-1.0602-0.82860.04480.93740.0419-0.18060.4526-0.06120.321114.917332.2779-45.2655
311.61482.26476.374613.6814-4.47664.56230.03370.21480.2257-0.02680.48921.34210.0518-0.173-0.52290.14090.01920.03030.22320.01090.2621-10.24183.01785.4069
3214.93384.2844-14.77986.27212.94496.22480.63922.63870.9129-1.1402-0.94881.7223-1.0422-2.09570.30960.32620.2409-0.18110.6653-0.05910.5144-1.27239.8092-1.4168
3317.34353.7044-5.73484.2226-0.56120.34760.12020.3510.1921-0.3947-0.01190.0537-0.0494-0.0854-0.10830.1998-0.0332-0.01410.23240.08850.181513.61413.5988-3.4177
343.86025.2881-4.91849.02780.39497.43770.3554-0.07491.29270.31620.0931.5717-0.46890.0553-0.44850.13690.01040.01450.14370.06240.37268.826415.1774.1993
3530.5818.3028-21.782911.0655-11.038929.29160.034-0.01750.30430.13060.08970.1346-0.82080.6755-0.12370.22310.0273-0.05840.07850.01360.1891-9.08447.47677.577
3620.771-2.7247-6.1566-0.66191.20521.2392-0.2458-1.1455-0.41070.05980.07230.01770.02870.26630.17350.1004-0.02620.0510.2203-0.0310.2054-6.49033.94713.4998
3733.0286-6.51273.64298.016.59448.51660.13090.56020.10110.6869-0.4307-0.27011.9740.34330.29980.64070.22520.28380.15920.18040.18897.86321.67087.3249
383.485210.709-1.447928.01533.562517.22540.12150.2-0.62181.010.1374-1.43971.0814-0.656-0.25890.1918-0.0091-0.04360.15540.02050.268310.51351.568313.0164
397.6730.0148-3.82396.50435.73676.48110.6872-0.61950.31280.4567-0.1833-0.39880.11330.1834-0.50390.12690.0079-0.00630.16820.04380.135810.793611.466213.2154
4037.17573.1164-4.40462.51630.01020.458-0.11660.42921.65260.18680.22730.4155-0.0242-0.027-0.11070.17960.02380.00860.10770.01960.12911.656712.60449.5648
4110.7677-2.44795.29878.6157-0.24540.76150.13290.5071-0.0646-0.1442-0.0988-0.5834-0.06770.1728-0.0340.1275-0.022-0.01470.14470.09410.160918.802210.4645.3891
4226.73758.8958-3.24973.2369-0.20894.43230.21860.0996-0.1286-0.1362-0.1150.0613-0.0822-0.0763-0.10360.18690.0872-0.06040.1355-0.01740.1588.97343.35112.8776
4360.173218.5105-18.9516.722-2.800310.14320.2061-2.6344-2.48810.2502-0.7576-0.904-0.0020.97180.55150.151-0.0480.02370.1780.03160.1928-4.0482-1.536611.7629
4413.211-3.64413.99371.573.48958.5294-1.0387-0.1911-0.34421.4350.95430.10661.69611.08270.08440.6180.27810.10170.2758-0.02180.0232-4.636-2.58136.5163
4542.85599.924-9.76412.9251-1.02128.7741-0.4231.7027-1.1353-0.1810.3131-0.5530.3760.52570.10990.11850.03650.04920.27910.05790.220118.043110.7936-3.0862
466.55442.7645-3.78159.5889-4.2487.7002-0.3349-0.00540.22430.1134-0.0219-0.8054-0.66590.47290.35680.2763-0.0769-0.0570.21960.01440.13265.59326.051-21.5324
475.67995.4456-5.545.906-10.888424.29290.5252-0.0825-0.03081.1392-0.5424-0.1271-1.49291.05740.01720.3888-0.0877-0.0330.20310.01610.19434.4162-2.9435-2.3927
483.10311.75024.66236.4028-2.20619.590.5267-0.3457-0.28630.7454-0.15180.46050.45570.0346-0.3750.31660.01960.0920.14730.10160.2554-7.9798-10.2789.0956
493.03233.5928-6.42710.37-13.221617.4168-0.18130.20920.028-0.25230.0464-0.0940.3882-0.26420.13480.0851-0.0129-0.02560.1299-0.08630.1221-3.063-0.6025-4.1092
50-0.98363.0694-2.5908-2.18061.7997-5.1283-0.3601-1.241.4371-0.92-0.37820.9868-0.9281-0.67570.73830.63930.1732-0.24550.3291-0.2110.5425-0.66464.7739-19.0837
516.70615.2054-5.85768.1623-0.30775.9854-0.29160.1885-0.1093-0.05750.07820.22020.4337-0.38250.21340.18050.0016-0.03580.1014-0.03610.0952-4.0654-7.7469-11.7128
527.3232-0.3195-3.458510.76687.5152.8543-0.0007-0.1049-0.2182-0.5037-0.21910.7637-0.202-0.16340.21980.3571-0.010.02710.21340.00670.2475-6.7635-14.639-10.7731
5314.769412.133527.992732.754628.31918.35693.27570.3645-0.3762-0.8908-2.90222.30022.5102-1.8336-0.37350.59420.117-0.09510.81750.1890.9864-17.8857-10.7985-4.9516
5414.123513.814-12.115231.8187-24.467118.3819-0.40310.60180.64690.26171.30771.2540.0473-1.2-0.90460.2239-0.0561-0.04020.2867-0.09240.1559-11.388-5.006-6.4748
5515.9923.3115-4.063333.1787-43.333148.38140.28230.90073.3857-1.41021.01441.3971.3996-0.8162-1.29670.42340.1553-0.16010.14380.06020.7297-5.52824.0281-9.7032
5614.448712.3499-8.710214.4456-14.780124.21960.06530.44830.77060.10460.71771.3430.5123-1.2889-0.7830.1899-0.0590.08750.1227-0.03370.4015-11.161-7.75910.4136
5733.12713.2544-8.162431.40326.9805-0.2505-0.32940.8647-1.64590.6559-0.23220.78210.2451-0.29260.56160.34140.0310.04140.098-0.01660.2734-7.6814-17.35323.8582
585.34411.7747-4.71331.17060.92281.8309-0.1791-0.1946-0.31320.1334-0.1136-0.12650.34430.1580.29270.17480.029-0.00040.0605-0.01440.11740.4031-8.0598-9.9935
590.77211.3781-1.78642.8185-8.124729.4458-0.23430.1256-0.1289-0.1153-0.0666-0.2057-0.18310.57110.3010.16170.03450.04540.1350.0250.16184.0257-3.4636-16.5243
6013.972212.5409-3.503611.9673-2.4715-7.44250.5479-1.2643-0.49621.2342-0.7408-0.0747-0.12270.6090.19290.5120.20920.15040.33990.12820.2964-0.4494-12.41746.2179
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C9 - 15
2X-RAY DIFFRACTION2C16 - 19
3X-RAY DIFFRACTION3C20 - 25
4X-RAY DIFFRACTION4C26 - 32
5X-RAY DIFFRACTION5C33 - 38
6X-RAY DIFFRACTION6C39 - 46
7X-RAY DIFFRACTION7C47 - 52
8X-RAY DIFFRACTION8C53 - 58
9X-RAY DIFFRACTION9C59 - 64
10X-RAY DIFFRACTION10C65 - 70
11X-RAY DIFFRACTION11C71 - 77
12X-RAY DIFFRACTION12C78 - 83
13X-RAY DIFFRACTION13C84 - 88
14X-RAY DIFFRACTION14C89 - 96
15X-RAY DIFFRACTION15C97 - 106
16X-RAY DIFFRACTION16D0 - 6
17X-RAY DIFFRACTION17D7 - 16
18X-RAY DIFFRACTION18D17 - 26
19X-RAY DIFFRACTION19D27 - 32
20X-RAY DIFFRACTION20D33 - 39
21X-RAY DIFFRACTION21D40 - 45
22X-RAY DIFFRACTION22D46 - 50
23X-RAY DIFFRACTION23D51 - 55
24X-RAY DIFFRACTION24D56 - 62
25X-RAY DIFFRACTION25D63 - 68
26X-RAY DIFFRACTION26D69 - 74
27X-RAY DIFFRACTION27D75 - 81
28X-RAY DIFFRACTION28D82 - 87
29X-RAY DIFFRACTION29D88 - 94
30X-RAY DIFFRACTION30D95 - 99
31X-RAY DIFFRACTION31O9 - 15
32X-RAY DIFFRACTION32O16 - 19
33X-RAY DIFFRACTION33O20 - 25
34X-RAY DIFFRACTION34O26 - 32
35X-RAY DIFFRACTION35O33 - 38
36X-RAY DIFFRACTION36O39 - 44
37X-RAY DIFFRACTION37O45 - 48
38X-RAY DIFFRACTION38O49 - 55
39X-RAY DIFFRACTION39O56 - 62
40X-RAY DIFFRACTION40O63 - 71
41X-RAY DIFFRACTION41O72 - 78
42X-RAY DIFFRACTION42O79 - 84
43X-RAY DIFFRACTION43O85 - 89
44X-RAY DIFFRACTION44O90 - 95
45X-RAY DIFFRACTION45O96 - 105
46X-RAY DIFFRACTION46T0 - 6
47X-RAY DIFFRACTION47T7 - 14
48X-RAY DIFFRACTION48T15 - 21
49X-RAY DIFFRACTION49T22 - 28
50X-RAY DIFFRACTION50T29 - 34
51X-RAY DIFFRACTION51T35 - 40
52X-RAY DIFFRACTION52T41 - 47
53X-RAY DIFFRACTION53T48 - 52
54X-RAY DIFFRACTION54T53 - 57
55X-RAY DIFFRACTION55T58 - 63
56X-RAY DIFFRACTION56T64 - 68
57X-RAY DIFFRACTION57T69 - 74
58X-RAY DIFFRACTION58T75 - 83
59X-RAY DIFFRACTION59T84 - 92
60X-RAY DIFFRACTION60T93 - 97

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る