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- PDB-3rjr: Crystal Structure of pro-TGF beta 1 -

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基本情報

登録情報
データベース: PDB / ID: 3rjr
タイトルCrystal Structure of pro-TGF beta 1
要素Transforming growth factor beta-1
キーワードCYTOKINE / TGF beta / activation / integrin
機能・相同性
機能・相同性情報


Platelet degranulation / Cell surface interactions at the vascular wall / Molecules associated with elastic fibres / TGF-beta receptor signaling activates SMADs / Syndecan interactions / RUNX3 regulates CDKN1A transcription / RUNX3 regulates p14-ARF / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of RUNX3 expression and activity ...Platelet degranulation / Cell surface interactions at the vascular wall / Molecules associated with elastic fibres / TGF-beta receptor signaling activates SMADs / Syndecan interactions / RUNX3 regulates CDKN1A transcription / RUNX3 regulates p14-ARF / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of RUNX3 expression and activity / regulation of binding / regulation of DNA binding / positive regulation of microglia differentiation / negative regulation of skeletal muscle tissue development / regulation of striated muscle tissue development / regulation of protein import into nucleus / type III transforming growth factor beta receptor binding / negative regulation of hyaluronan biosynthetic process / extracellular matrix assembly / negative regulation of macrophage cytokine production / odontoblast differentiation / positive regulation of isotype switching to IgA isotypes / membrane protein intracellular domain proteolysis / hyaluronan catabolic process / regulation of transforming growth factor beta receptor signaling pathway / ATP biosynthetic process / receptor catabolic process / type II transforming growth factor beta receptor binding / type I transforming growth factor beta receptor binding / positive regulation of chemotaxis / negative regulation of myoblast differentiation / cell-cell junction organization / response to cholesterol / positive regulation of fibroblast migration / phosphate-containing compound metabolic process / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of cell-cell adhesion / negative regulation of fat cell differentiation / positive regulation of interleukin-17 production / positive regulation of SMAD protein signal transduction / negative regulation of blood vessel endothelial cell migration / positive regulation of cell division / negative regulation of cell cycle / positive regulation of collagen biosynthetic process / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / lymph node development / chondrocyte differentiation / hematopoietic progenitor cell differentiation / positive regulation of epithelial to mesenchymal transition / salivary gland morphogenesis / extrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / cellular response to transforming growth factor beta stimulus / positive regulation of protein metabolic process / transforming growth factor beta receptor signaling pathway / extracellular matrix / positive regulation of superoxide anion generation / negative regulation of protein phosphorylation / cytokine activity / response to progesterone / positive regulation of protein secretion / antigen binding / growth factor activity / positive regulation of protein-containing complex assembly / negative regulation of cell growth / response to wounding / positive regulation of protein import into nucleus / negative regulation of epithelial cell proliferation / response to estradiol / regulation of cell population proliferation / positive regulation of ERK1 and ERK2 cascade / blood microparticle / positive regulation of cell migration / inflammatory response / negative regulation of cell population proliferation / protein phosphorylation / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / nucleus / cytoplasm
類似検索 - 分子機能
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2330 / Jelly Rolls - #970 / Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2330 / Jelly Rolls - #970 / Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Transforming growth factor beta-1 proprotein
類似検索 - 構成要素
生物種Sus scrofa (ブタ)
手法X線回折 / シンクロトロン / 多波長異常分散 / 解像度: 3.05 Å
データ登録者Zhu, J.H. / Shi, M.L. / Springer, T.A.
引用ジャーナル: Nature / 年: 2011
タイトル: Latent TGF-Beta structure and activation
著者: Shi, M. / Zhu, J. / Wang, R. / Chen, X. / Mi, L. / Walz, T. / Springer, T.A.
履歴
登録2011年4月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02011年6月15日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22013年2月13日Group: Database references
改定 1.32017年11月8日Group: Refinement description / カテゴリ: software
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation

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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 growth factor beta-1
B: Transforming growth factor beta-1
C: Transforming growth factor beta-1
D: Transforming growth factor beta-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)167,46310
ポリマ－165,7304
非ポリマー1,7346
水00
1
A: Transforming growth factor beta-1
B: Transforming growth factor beta-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)83,5104
ポリマ－82,8652
非ポリマー6462
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-55 kcal/mol
Surface area34660 Å2
手法PISA
2
C: Transforming growth factor beta-1
D: Transforming growth factor beta-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)83,9536
ポリマ－82,8652
非ポリマー1,0884
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-51 kcal/mol
Surface area35870 Å2
手法PISA
単位格子
Length a, b, c (Å)54.690, 126.940, 137.930
Angle α, β, γ (deg.)90.000, 96.720, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
31C
41D
12A
22B
32C
42D

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)A26 - 60
121chain A and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)A75 - 190
131chain A and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)A216 - 239
141chain A and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)A264 - 295
151chain A and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)A328 - 360
211chain B and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)B26 - 60
221chain B and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)B75 - 190
231chain B and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)B216 - 239
241chain B and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)B264 - 295
251chain B and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)B328 - 360
311chain C and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)C26 - 60
321chain C and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)C75 - 190
331chain C and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)C216 - 239
341chain C and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)C264 - 295
351chain C and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)C328 - 360
411chain D and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)D26 - 60
421chain D and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)D75 - 190
431chain D and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)D216 - 239
441chain D and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)D264 - 295
451chain D and (resid 26:60 or resid 75:190 or resid 216:239 or resid 264:295 or resid 328:360)D328 - 360
112chain A and resid 193:208A193 - 208
212chain B and resid 193:208B193 - 208
312chain C and resid 193:208C193 - 208
412chain D and resid 193:208D193 - 208

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Transforming growth factor beta-1 / TGF-beta-1 / Latency-associated peptide / LAP


分子量: 41432.410 Da / 分子数: 4 / 変異: C4S, N147Q / 由来タイプ: 組換発現 / 由来: (組換発現) Sus scrofa (ブタ) / 遺伝子: TGFB1 / プラスミド: pcDNA3.1
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
株 (発現宿主): Lec 3.2.8.1 / 参照: UniProt: P07200
#2: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 4 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
配列の詳細THE AUTHORS SEQUENCE CORRESPONDS TO REFERENCE SEQUENCE NP_999180.1

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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: 2.87 Å3/Da / 溶媒含有率: 57.13 %
結晶化温度: 293 K / 手法: 蒸気拡散法 / pH: 5.6
詳細: 7% PEG 3350, 17% isopropanol, 0.1m Na citrate pH 5.6, vapor diffusion, temperature 293K, VAPOR DIFFUSION

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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: 23-ID-B / 波長: 0.97934, 0.97932, 0.97956, 0.95667
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2009年11月12日
放射プロトコル: MAD / 散乱光タイプ: x-ray
放射波長
ID波長 (Å)相対比
10.979341
20.979321
30.979561
40.956671
反射解像度: 3.05→50 Å / Num. obs: 35401 / % possible obs: 97.9 % / 冗長度: 5.6 % / Rmerge(I) obs: 0.047

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位相決定

位相決定手法: 多波長異常分散

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解析

ソフトウェア
名称バージョン分類NB
DENZOデータ削減
SCALEPACKデータスケーリング
SOLVE位相決定
PHENIXdev_276精密化
PDB_EXTRACT3.1データ抽出
HKL-2000データ収集
HKL-2000データ削減
HKL-2000データスケーリング
精密化解像度: 3.05→46.554 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.51 / σ(F): 1.44 / 立体化学のターゲット値: MLHL
Rfactor反射数%反射
Rfree0.3106 1040 2.95 %
Rwork0.2737 --
obs0.2748 35267 98.8 %
溶媒の処理減衰半径: 1.2 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 242.989 Å2 / ksol: 0.297 e/Å3
原子変位パラメータBiso max: 561.41 Å2 / Biso mean: 214.8624 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--11.6111 Å2-0 Å2-4.7692 Å2
2---17.9314 Å2-0 Å2
3----22.1104 Å2
精密化ステップサイクル: LAST / 解像度: 3.05→46.554 Å
タンパク質核酸リガンド溶媒全体
原子数10843 0 112 0 10955
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00211236
X-RAY DIFFRACTIONf_angle_d0.48815215
X-RAY DIFFRACTIONf_chiral_restr0.0321690
X-RAY DIFFRACTIONf_plane_restr0.0021939
X-RAY DIFFRACTIONf_dihedral_angle_d12.4614211
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A1945X-RAY DIFFRACTIONPOSITIONAL0.002
12B1945X-RAY DIFFRACTIONPOSITIONAL0.002
13C1945X-RAY DIFFRACTIONPOSITIONAL0.004
14D1945X-RAY DIFFRACTIONPOSITIONAL0.004
21A124X-RAY DIFFRACTIONPOSITIONAL0.009
22B124X-RAY DIFFRACTIONPOSITIONAL0.009
23C124X-RAY DIFFRACTIONPOSITIONAL0.004
24D124X-RAY DIFFRACTIONPOSITIONAL0.004
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.05-3.21080.41881500.36684857500798
3.2108-3.41190.39011240.33664853497798
3.4119-3.67530.35121450.32074859500499
3.6753-4.04490.32941440.29124873501799
4.0449-4.62980.29771390.25654907504699
4.6298-5.83120.31861590.254907506699
5.8312-46.55950.26811790.24594971515099
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)
10.20170.21360.19290.39060.2850.1301-0.2655-0.7811-0.03490.5686-0.1133-0.4492-1.0960.0066-0.00021.94450.4269-0.69680.784-0.38381.6305-84.699655.2195-39.7024
20.0790.34790.26020.2226-0.03230.02370.4059-1.2910.13290.19880.22710.5414-1.9573-0.2670.00033.32880.4194-0.07951.71240.230.9648-87.804162.7726-16.2105
3-0.01220.28690.60860.8710.2027-0.14370.4943-0.37240.2889-0.2277-0.02880.7157-0.0351-0.2523-0.00011.31450.3273-0.28891.7773-0.3081.8771-85.760350.29191.162
40.1077-0.3149-0.0361.55210.60510.0606-0.744-0.23091.2277-0.63450.1635-0.24930.50870.2131-0.00011.9685-0.02880.02051.7428-0.01650.8955-76.385143.88731.3589
50.08350.0751-0.01380.2811-0.11270.2881-1.22050.03060.08-0.7787-0.13890.3328-0.23781.5903-0.01112.5101-0.38710.04111.765-0.48311.2361-70.138752.19296.9298
60.0442-0.3586-0.09230.3989-0.195-0.05260.3612-0.33411.08170.6895-0.42850.4315-0.06230.8831-02.7190.1987-0.43211.13090.1231.5895-80.279549.4094-24.5551
70.28030.22450.30480.5407-0.64170.6123-0.1371-1.3340.0784-0.65640.1235-0.7324-0.93020.02540.00022.80560.4189-0.26111.5360.16781.1763-80.938357.0859-33.3787
80.0037-0.0015-0.00490.0016-0.00230.0031-0.2822-0.1285-0.1447-0.021-0.1336-0.0203-0.05320.0109-0.00013.98691.2569-0.27831.80390.33691.9711-62.19532.7115-44.6607
9-0.0070.0127-0.0136-0.00140.0243-0.0149-0.3458-0.04-0.006-0.2327-0.5981-0.7786-0.37381.2158-0.00042.1059-0.13380.59930.92430.41073.9801-70.018333.625-39.9448
101.7831.3041-0.76241.3698-0.96531.4357-2.34570.32760.1892-0.0793-0.8912-0.7051-2.36610.7507-0.67052.52780.3234-0.96860.7765-0.29050.5442-83.888451.501-25.1319
110.3836-0.69590.55161.8099-0.9292-0.52471.23240.40922.23880.1263-0.0049-0.0282-0.6485-0.44960.0541.42350.37490.10151.35230.14480.5432-76.544122.4656-43.3148
120.73780.71460.09210.2152-0.07290.21450.7355-0.23021.23861.0330.7795-1.42931.80870.68540.00061.6999-0.47450.07111.5372-0.29960.8526-61.2312.9337-26.4307
130.04610.7583-0.19960.5656-0.37740.1512-0.03190.35290.0329-0.82610.0339-1.0775-1.30361.0347-0.00271.1049-0.1420.09531.6017-0.43120.8237-53.386423.5162-9.73
140.6198-0.86160.67670.410.87330.4917-1.4615-0.49170.45260.62350.6340.87020.2669-0.3103-0.00331.3227-0.1977-0.3221.4963-0.27730.9061-61.064529.1959-4.2023
151.193-0.83830.24530.06791.48390.77120.13170.02590.15660.29070.38240.818-0.1862-0.3311-0.00110.8955-0.5087-0.0051.01720.13631.2443-68.401725.2558-14.7882
16-0.1119-0.0801-0.0040.05450.1826-0.2030.34160.4873-0.92371.04350.2437-0.11560.3934-0.55040.00031.6558-0.2251-0.18551.1146-0.17320.9573-79.091419.0512-35.9327
170.24360.56820.25910.4280.09670.11960.52920.41650.0382-1.11170.2298-0.36430.43670.255601.6443-0.044-0.30221.0635-0.55691.0219-72.604117.1603-36.3774
18-0.03080.0947-0.0263-0.0035-0.06270.0238-0.0323-0.267-1.2834-0.214-0.72720.48040.1794-0.5089-0.00041.8264-0.2497-0.19992.5049-0.09022.1282-95.662239.969-31.9919
19-0.01270.0471-0.0693-0.01280.04530.0358-0.0806-0.7964-0.66420.0979-0.25190.33970.7071-0.501-02.1362-0.6798-0.12741.31750.28791.6361-85.442342.9772-32.7974
200.04820.61530.47630.84980.20410.69670.599-0.50860.7163-0.3895-0.1331-0.45850.8253-0.307101.0504-0.04020.00581.2699-0.02990.6984-69.21724.8029-30.5868
210.40140.2768-0.03831.2791.65270.4588-0.26330.07350.6191.3079-0.0266-0.4164-2.09510.22790.00131.24410.1487-0.32830.3947-0.04831.3973-40.150955.667471.9351
220.1381-0.0684-0.06870.4173-0.22580.49570.4155-0.18690.5966-0.59560.052-1.37421.0482-0.43980.00031.03510.0528-0.010.80680.1851.3587-44.200749.903141.3836
230.20150.28760.01281.6659-0.2463-0.0059-0.37320.9671-0.2128-0.34260.0907-0.6504-0.52380.32740.00011.14490.0312-0.06470.98290.01171.0975-46.13647.40938.4754
240.48350.470.53351.25750.94082.3138-0.29631.11140.4617-0.7254-0.4956-0.13610.5839-0.226-0.35631.54270.19530.350.88050.33410.7728-49.176241.222534.5191
252.30270.790.88550.233-1.21622.3945-1.8827-1.39341.54170.36210.1302-1.3543-0.9201-1.3335-0.09031.04530.32290.42560.59240.03941.3315-48.063448.220537.7475
260.00450.0174-0.0134-0.0526-0.0801-0.0064-0.2461-0.5337-0.395-0.0421-0.91460.1873-0.7988-0.4384-00.79050.5222-0.11052.00890.10912.7489-61.874545.249674.1571
270.0922-0.02780.1290.03440.08510.2170.0593-0.23980.03870.39590.05360.4015-0.77510.34970.00021.55760.4538-0.82510.7447-0.58982.1068-49.686653.869972.5897
280.8847-0.7108-0.18310.84990.45872.0665-2.0485-1.6562.8682.25380.2404-1.0347-1.7441.7293-1.69380.84840.1882-0.1423-0.6881-1.50980.0687-44.846754.432770.4582
29-0.0205-0.10720.13710.02620.03020.03071.77630.50781.53710.6173-0.4929-0.7664-0.6081-0.93180.00031.41460.59170.61591.18650.11671.3869-62.463327.469985.446
302.74381.3742-0.56415.0819-4.4885.512-6.33180.61542.4809-0.1435-1.45020.1731-4.58270.3692-7.1854-4.89233.55321.7252-1.8958-0.9553-0.4432-45.972844.780365.5754
310.53380.22250.08871.46560.34840.76111.0397-1.8659-0.1641.3201-1.4039-0.67410.49630.5556-0.22060.5056-0.02530.12151.03250.4750.5721-53.616117.871978.3028
320.0026-0.02270.07420.0573-0.23150.13890.4651.0687-0.2223-0.7993-0.80651.56291.4696-0.3748-0.00421.67740.045-0.33050.96490.18850.6371-65.679.178258.4109
330.07610.0413-0.00250.0060.028-0.0231-0.29430.3625-0.23171.29960.3642-0.3131-0.67250.19990.00032.34811.08220.08382.0234-0.65930.6937-61.087831.389559
341.07750.581-1.1931.62880.07890.4089-0.04260.0089-0.5402-0.39240.15950.84780.2265-0.236300.8030.1661-0.18810.909-0.14550.7312-70.812721.276743.7745
350.5485-0.3684-0.34770.5212-1.2151-0.182-0.60080.47740.2981-0.52340.153-0.3306-0.14650.0956-0.00021.21790.0744-0.41620.8063-0.08680.9426-66.646729.593438.5411
360.3264-0.47580.31050.18320.0261.1398-0.42732.6128-0.3880.07741.1162-0.1447-0.60791.90090.00270.95450.5192-0.18990.7752-0.50951.3495-60.947225.128426.2959
371.0551-0.74350.62871.1777-0.51321.16170.2392-2.57460.2169-0.2190.2935-0.45330.5230.14640.06950.36080.3009-0.11620.52440.16310.3042-64.529322.130858.7252
38-0.0204-0.03850.23980.26940.02190.2931-0.2439-0.8349-2.69190.165-0.1681-2.4304-1.09492.02520.04120.20960.47740.10580.29970.23031.0551-43.426217.630670.6728
391.1854-0.96630.22431.54310.60031.2295-0.6094-0.1770.1667-0.16460.5301-0.78090.2850.4977-0.38590.2920.3727-0.12580.63060.13380.9859-44.136427.360670.1682
400.9412-1.3594-0.73811.3020.92841.1865-0.5377-0.1991-0.07180.0027-0.0078-0.30490.3959-0.3684-1.12690.30350.02890.04580.4543-0.07580.5608-57.914921.659766.2035
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1:30A1 - 30
2X-RAY DIFFRACTION2chain A and resid 31:61A31 - 61
3X-RAY DIFFRACTION3chain A and resid 62:116A62 - 116
4X-RAY DIFFRACTION4chain A and resid 117:202A117 - 202
5X-RAY DIFFRACTION5chain A and resid 203:227A203 - 227
6X-RAY DIFFRACTION6chain A and resid 228:263A228 - 263
7X-RAY DIFFRACTION7chain A and resid 264:299A264 - 299
8X-RAY DIFFRACTION8chain A and resid 300:313A300 - 313
9X-RAY DIFFRACTION9chain A and resid 314:324A314 - 324
10X-RAY DIFFRACTION10chain A and resid 325:361A325 - 361
11X-RAY DIFFRACTION11chain B and resid 1:30B1 - 30
12X-RAY DIFFRACTION12chain B and resid 31:61B31 - 61
13X-RAY DIFFRACTION13chain B and resid 62:116B62 - 116
14X-RAY DIFFRACTION14chain B and resid 117:200B117 - 200
15X-RAY DIFFRACTION15chain B and resid 201:263B201 - 263
16X-RAY DIFFRACTION16chain B and resid 264:274B264 - 274
17X-RAY DIFFRACTION17chain B and resid 275:296B275 - 296
18X-RAY DIFFRACTION18chain B and resid 297:311B297 - 311
19X-RAY DIFFRACTION19chain B and resid 312:324B312 - 324
20X-RAY DIFFRACTION20chain B and resid 325:361B325 - 361
21X-RAY DIFFRACTION21chain C and resid -1:49C-1 - 49
22X-RAY DIFFRACTION22chain C and resid 50:100C50 - 100
23X-RAY DIFFRACTION23chain C and resid 101:142C101 - 142
24X-RAY DIFFRACTION24chain C and resid 143:200C143 - 200
25X-RAY DIFFRACTION25chain C and resid 201:240C201 - 240
26X-RAY DIFFRACTION26chain C and resid 251:263C251 - 263
27X-RAY DIFFRACTION27chain C and resid 264:274C264 - 274
28X-RAY DIFFRACTION28chain C and resid 275:298C275 - 298
29X-RAY DIFFRACTION29chain C and resid 299:314C299 - 314
30X-RAY DIFFRACTION30chain C and resid 315:361C315 - 361
31X-RAY DIFFRACTION31chain D and resid 1:36D1 - 36
32X-RAY DIFFRACTION32chain D and resid 37:59D37 - 59
33X-RAY DIFFRACTION33chain D and resid 60:73D60 - 73
34X-RAY DIFFRACTION34chain D and resid 74:137D74 - 137
35X-RAY DIFFRACTION35chain D and resid 138:200D138 - 200
36X-RAY DIFFRACTION36chain D and resid 201:223D201 - 223
37X-RAY DIFFRACTION37chain D and resid 224:255D224 - 255
38X-RAY DIFFRACTION38chain D and resid 256:275D256 - 275
39X-RAY DIFFRACTION39chain D and resid 276:324D276 - 324
40X-RAY DIFFRACTION40chain D and resid 325:361D325 - 361

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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://pdbjlvh1.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