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- PDB-4bss: Structure of the ectodomain of LGR5 in complex with R-spondin-1 (... -

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基本情報

登録情報
データベース: PDB / ID: 4bss
タイトルStructure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P21 crystal form
要素
  • LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
  • R-SPONDIN-1
キーワードSIGNALING PROTEIN / ADULT STEM CELL / LEUCINE-RICH REPEAT G-PROTEIN COUPLED RECEPTOR / LEUCINE-RICH REPEAT / FURIN DOMAIN / WNT SIGNALING / CONGENITAL ANONYCHIA
機能・相同性
機能・相同性情報


oocyte differentiation / epithelial cell proliferation involved in renal tubule morphogenesis / protein-hormone receptor activity / regulation of receptor internalization / inner ear development / positive regulation of Wnt signaling pathway / hair follicle development / Regulation of FZD by ubiquitination / trans-Golgi network membrane / G protein-coupled receptor activity ...oocyte differentiation / epithelial cell proliferation involved in renal tubule morphogenesis / protein-hormone receptor activity / regulation of receptor internalization / inner ear development / positive regulation of Wnt signaling pathway / hair follicle development / Regulation of FZD by ubiquitination / trans-Golgi network membrane / G protein-coupled receptor activity / G protein-coupled receptor binding / Wnt signaling pathway / positive regulation of protein phosphorylation / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / heparin binding / regulation of cell population proliferation / G protein-coupled receptor signaling pathway / signaling receptor binding / extracellular space / extracellular region / nucleus / plasma membrane
類似検索 - 分子機能
R-spondin, Fu-CRD domain / : / Furin-like repeat, cysteine-rich / Glycoprotein hormone receptor family / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Thrombospondin type-1 (TSP1) repeat superfamily ...R-spondin, Fu-CRD domain / : / Furin-like repeat, cysteine-rich / Glycoprotein hormone receptor family / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeats, bacterial type / Alpha-Beta Horseshoe / Leucine-rich repeat, SDS22-like subfamily / Furin-like repeat / Furin-like repeats / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Growth factor receptor cysteine-rich domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Ribbon / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Leucine-rich repeat-containing G-protein coupled receptor 5 / R-spondin-1
類似検索 - 構成要素
生物種HOMO SAPIENS (ヒト)
手法X線回折 / シンクロトロン / OTHER / 解像度: 3.2 Å
データ登録者Peng, W.C. / de Lau, W. / Forneris, F. / Granneman, J.C.M. / Huch, M. / Clevers, H. / Gros, P.
引用ジャーナル: Cell Rep. / 年: 2013
タイトル: Structure of Stem Cell Growth Factor R-Spondin 1 in Complex with the Ectodomain of its Receptor Lgr5.
著者: Peng, W.C. / De Lau, W. / Forneris, F. / Granneman, J.C.M. / Huch, M. / Clevers, H. / Gros, P.
履歴
登録2013年6月11日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02013年6月19日Provider: repository / タイプ: Initial release
改定 1.12013年7月24日Group: Database references
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / struct_asym / struct_conn / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12024年11月6日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
B: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
C: R-SPONDIN-1
D: R-SPONDIN-1
E: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
F: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
G: R-SPONDIN-1
H: R-SPONDIN-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)298,87516
ポリマ－296,2938
非ポリマー2,5828
水00
1
A: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
B: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
C: R-SPONDIN-1
D: R-SPONDIN-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,8629
ポリマ－148,1464
非ポリマー1,7165
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-36.8 kcal/mol
Surface area62190 Å2
手法PISA
2
E: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
F: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
G: R-SPONDIN-1
H: R-SPONDIN-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,0137
ポリマ－148,1464
非ポリマー8673
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-52.5 kcal/mol
Surface area61460 Å2
手法PISA
単位格子
Length a, b, c (Å)120.362, 111.298, 130.611
Angle α, β, γ (deg.)90.00, 109.19, 90.00
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
22
/ NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5 / G-PROTEIN COUPLED RECEPTOR 49 / G-PROTEIN COUPLED RECEPTOR 67 / G-PROTEIN COUPLED RECEPTOR HG38


分子量: 60366.457 Da / 分子数: 4 / 断片: EXTRACELLULAR LRR DOMAIN, RESIDUES 22-543 / 由来タイプ: 組換発現 / 詳細: N-LINKED GLYCOSYLATIONS AT ASN 63,77,208,500 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 細胞株 (発現宿主): HEK293 / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: O75473
#2: タンパク質
R-SPONDIN-1 / ROOF PLATE-SPECIFIC SPONDIN-1 / HRSPO1


分子量: 13706.780 Da / 分子数: 4 / 断片: FU1FU2, RESIDUES 31-146 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 細胞株 (発現宿主): HEK293 / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: Q2MKA7
#3: 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: 4 / 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
#4: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / 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
Has protein modificationY
配列の詳細N-TERMINAL 6XHISTAG, PLUS ENLYFQGS AND C-TERMINAL AAA INTRODUCED BY CLONING N-TERMINAL GS AND C- ...N-TERMINAL 6XHISTAG, PLUS ENLYFQGS AND C-TERMINAL AAA INTRODUCED BY CLONING N-TERMINAL GS AND C-TERMINAL AAA ADDED BY CLONING PLASMID, PLUS C-TERMINAL 6XHIS TAG

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶マシュー密度: 2.79 Å3/Da / 溶媒含有率: 55.89 % / 解説: NONE

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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: ESRF / ビームライン: ID23-1 / 波長: 1
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 3.2→28.9 Å / Num. obs: 52333 / % possible obs: 97.4 % / Observed criterion σ(I): 1.21 / 冗長度: 2.6 % / Biso Wilson estimate: 96.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.39

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解析

ソフトウェア名称: PHENIX / バージョン: (PHENIX.REFINE) / 分類: 精密化
精密化構造決定の手法: OTHER
開始モデル: NONE

解像度: 3.2→28.902 Å / SU ML: 0.58 / σ(F): 1.34 / 位相誤差: 34.31 / 立体化学のターゲット値: ML
詳細: EXTENDED C-TERMINAL REGION MODELLED WITH ZERO OCCUPANCY
Rfactor反射数%反射
Rfree0.2901 2663 5.1 %
Rwork0.2465 --
obs0.2487 52277 97.06 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 126.6 Å2
精密化ステップサイクル: LAST / 解像度: 3.2→28.902 Å
タンパク質核酸リガンド溶媒全体
原子数17757 0 168 0 17925
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00518360
X-RAY DIFFRACTIONf_angle_d1.16624885
X-RAY DIFFRACTIONf_dihedral_angle_d17.9566757
X-RAY DIFFRACTIONf_chiral_restr0.0442903
X-RAY DIFFRACTIONf_plane_restr0.0063198
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.25810.40651530.35682605X-RAY DIFFRACTION98
3.2581-3.32070.43621140.35732640X-RAY DIFFRACTION98
3.3207-3.38840.45921270.36522645X-RAY DIFFRACTION98
3.3884-3.46190.38851520.33852482X-RAY DIFFRACTION93
3.4619-3.54230.31561280.30782640X-RAY DIFFRACTION98
3.5423-3.63080.30271210.27912642X-RAY DIFFRACTION98
3.6308-3.72870.36221120.29592490X-RAY DIFFRACTION92
3.7287-3.83820.31321360.25972630X-RAY DIFFRACTION98
3.8382-3.96180.29851640.26052453X-RAY DIFFRACTION93
3.9618-4.1030.30231490.22292609X-RAY DIFFRACTION98
4.103-4.26680.27611700.22092612X-RAY DIFFRACTION98
4.2668-4.46030.25441270.21022676X-RAY DIFFRACTION98
4.4603-4.69460.2451320.20562642X-RAY DIFFRACTION98
4.6946-4.98730.23691490.20112641X-RAY DIFFRACTION98
4.9873-5.37010.25581480.21462636X-RAY DIFFRACTION98
5.3701-5.90630.29921300.23522645X-RAY DIFFRACTION98
5.9063-6.75150.31961810.25272581X-RAY DIFFRACTION98
6.7515-8.47050.29611320.26892676X-RAY DIFFRACTION98
8.4705-28.9030.24661380.22842669X-RAY DIFFRACTION96
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)
10.2148-0.28890.14891.445-1.21372.0230.1803-0.08110.11630.01380.08920.1399-0.0858-0.37430.9330.5125-0.00470.23020.852-0.37510.533477.264224.2076108.1894
21.11770.17830.270.15920.17190.27740.108-0.8859-0.14160.054-0.0301-0.19750.0018-0.076-0.02020.3733-0.0681-0.0083-0.2930.20020.3197101.15420.573883.3555
30.15790.05930.00630.0975-0.10760.16930.1760.0267-0.07610.0010.07980.05130.0064-0.19220.44750.23670.10120.03940.01180.48720.327793.18922.28842.3817
40.0148-0.00060.01560.0062-0.00770.01620.25240.0377-0.0522-0.1130.1466-0.07720.11740.06270.00040.77280.0658-0.11290.97380.040.5762100.55982.4287-2.8945
50.5965-0.05230.36810.10320.10250.4830.25010.56660.13650.0513-0.0369-0.2804-0.16070.4722-0.11190.24830.05080.06130.125-0.21970.2127119.25949.162833.5108
60.00470.012-0.01620.0239-0.01820.02610.0378-0.00710.03270.0113-0.00240.03690.0074-0.06020.09160.081-0.37740.0005-0.2017-0.08040.20893.158821.11765.3076
7-0.00010.00110.00280.00040.0020.0015-0.1983-0.04210.1284-0.03270.04740.11140.0406-0.0471-0.00010.5177-0.1565-0.03890.5099-0.04140.517487.013628.939882.4375
80.0028-0.00060.00270.003-0.00190.0045-0.007-0.0004-0.0037-0.0011-0.008-0.0181-0.00180.0019-0.00011.5566-0.2537-0.06431.7857-0.01541.74477.180520.780573.0403
90.00540.00240.00040.0091-0.00320.00130.064-0.0067-0.07780.0285-0.0195-0.00480.0591-0.03330.00020.5345-0.0836-0.02240.6933-0.33150.687282.25321.870987.8816
100.0125-0.01690.0020.0179-0.00020.00520.18330.0179-0.0654-0.06510.12320.010.0725-0.00290.00010.6159-0.090.14080.5214-0.08460.650986.21312.212987.5681
110.0283-0.00120.04590.0017-00.07110.04070.0173-0.0210.01330.0117-0.0553-0.01140.03880.00880.6907-0.30640.0130.63210.16750.963581.21090.236694.1262
120.0973-0.05670.06980.0408-0.03690.05360.00170.00690.01180.01470.0330.00840.02130.0102-01.645-0.2568-0.0761.73510.09211.720679.7496-10.798397.3524
130.0022-0.0004-0.00130-0.00010.0006-0.03570.00070.0168-0.0429-0.0274-0.01920.0178-0.00630.00011.09270.0621-0.04261.21130.10540.979879.1382-5.2501104.0817
140.00210.00070.00010.0002-0.00060.00180.02210.0121-0.0133-0.02290.0078-0.0565-0.00180.00901.00770.0597-0.00211.36320.01891.281388.4186-3.871922.1612
150.0039-0.0005-0.0041-0.00060.00050.00070.0556-0.0168-0.0692-0.05260.0402-0.1075-0.0438-0.01280.00010.83850.06560.06920.55330.02830.686395.18510.617723.3653
160.00320.0033-0.00140.0036-0.00130.00070.00320.01850.0150.0260.01770.01950.02610.0034-0.00031.01420.12370.14751.07860.09171.0588.162812.424527.7296
170.00310.00020.00170.00230.00070.0024-0.05730.05160.0379-0.0445-0.05850.01370.02010.03740.00030.9009-0.0891-0.10940.938-0.06830.567397.53756.036317.6325
180.00710.004-0.0030.0022-0.00040.00480.11540.03460.1121-0.01980.0643-0.0164-0.0216-0.003900.73590.2068-0.2160.81350.03360.5931104.99442.749623.9497
190.00210.0067-0.00130.0132-0.00420.00080.10250.00180.0697-0.00580.0773-0.0332-0.01980.0111-0.00020.6603-0.08770.16760.6909-0.05840.3502104.707116.089922.8463
200.00280.0005-0.00240.0006-0.0020.00490.03390.00880.0057-0.04180.0369-0.0168-0.0016-0.00150.00010.60320.07530.0960.71830.2570.5401110.804914.828719.2577
210.0013-0.00080.00180.0013-0.00120.0045-0.0650.0152-0.0208-0.0027-0.03860.0047-0.0207-0.0038-0.00040.8748-0.0765-0.02570.71350.14970.8483112.506723.184712.3792
220.0033-0.00250.00080.0038-0.00150.0003-0.00630.01520.0224-0.02560.00930.0137-0.00050.005801.059-0.0488-0.07831.17090.19111.3678117.280622.165718.6527
230.0066-0.00240.00090.0007-0.0002-00.00460.01560.0086-0.01860.00010.0139-0.00770.0302-01.60470.04110.11731.58940.04451.7493123.463127.171512.5822
240.01850.00440.0030.00220.00080.00070.0048-0.0134-0.00590.01110.00410.02410.00310.0028-01.60930.13450.19291.5709-0.06721.4746117.398723.17176.0808
250.01340.010.01630.01030.01240.0120.0252-0.0027-0.11830.0060.0961-0.0091-0.0026-0.04910.00030.9239-0.0085-0.11691.7237-0.00810.7656138.56390.5586167.6132
260.280.22930.03140.22260.08670.0672-0.2421-0.2892-0.2154-0.143-0.2460.10430.0015-0.1379-0.39930.4470.1956-0.10991.4951-0.06270.3345119.83396.2833131.1367
270.0105-0.0133-0.00470.01350.0050.00040.0936-0.04640.02610.0634-0.02170.0415-0.01370.045200.70780.1663-0.22441.1325-0.01260.7852138.117121.344898.0045
280.10160.00520.10860.0571-0.04590.1629-0.05040.0290.02130.0068-0.0408-0.0119-0.03640.0154-0.14270.03770.0204-0.04590.15710.01670.0147150.994920.009299.0299
290.00710.0069-0.00880.01540.00620.0176-0.024-0.13620.0335-0.1527-0.0174-0.24090.18240.2342-00.66960.0580.01381.1024-0.03110.6905158.094720.26755.6731
300.05610.03210.02430.0618-0.00060.04370.4191-0.0824-0.15590.1386-0.02710.30230.2712-0.12270.00330.8346-0.1999-0.00991.1705-0.1550.5026137.81532.728167.1435
310.0030.0003-0.00120.0023-0.00590.0069-0.1747-0.0057-0.04560.0985-0.08920.0873-0.1284-0.0297-0.00020.9494-0.31450.19661.1287-0.00250.9407136.4953-9.66293.9789
320.00260.0032-0.00360.00170.00620.0085-0.08420.0506-0.1152-0.049-0.1204-0.09690.16090.0935-0.00021.40550.00880.12111.2082-0.10081.188141.7756-9.7541114.3333
330.1042-0.2143-0.03670.46630.06810.24010.0334-0.01230.0026-0.127-0.0599-0.1252-0.10870.1447-0.07890.4942-0.0170.09390.75950.06940.4146148.49455.0798124.6653
340.0013-0.0014-0.00120.00160.00090.00210.0065-0.0185-0.00910.0048-0.02560.024-0.0024-0.015-01.622-0.13260.13411.7489-0.03071.7487151.7017-5.163143.2262
350.0051-0.0030.00440.002-0.0030.00350.02590.01530.0087-0.00360.01470.0228-0.02640.0142-01.05890.09720.11271.13550.0961.4088144.5737-0.9931141.9156
360.0079-0.0006-0.0020.00050.00130.00360.01540.00080.0027-0.0203-0.0006-0.02390.0205-0.0022-01.67020.10140.22851.5679-0.05381.6888151.171111.5428137.7913
370.0005-0.0043-0.00110.0070.00660.00240.208-0.09170.09690.0585-0.02260.0770.03050.01810.00011.03460.19160.02271.15120.04060.7929135.75166.8516144.074
380.0029-0.002-0.00240.00130.00270.00270.02850.01160.03050.03070.0110.0095-0.0118-0.02210.00010.93140.1574-0.07871.1376-0.13580.8715127.848915.0649147.6842
39-0.0006-0-0.00150.00040.00280.00510.0299-0.01640.0394-0.0011-0.00290.0394-0.00250.0079-01.027-0.1353-0.04521.146-0.27180.7996119.257221.6971152.1386
400.0031-0.00160.0010.0007-0.00040.0003-0.02810.01080.00660.01190.0064-0.04960.01740.000701.64030.1534-0.08121.7922-0.10991.7647151.609632.295981.2821
410.00530.00120.00350.00190.00410.00880.024-0.01570.02030.0484-0.0252-0.0543-0.01850.0189-0.00011.3327-0.096-0.25461.3985-0.08711.4762148.912326.561681.1536
420.00350.00020.00450.0022-0.00010.0082-0.0061-0.0049-0.0204-0.0331-0.01530.0427-0.01410.00170.00011.026-0.1488-0.07781.1590.03370.8908153.369820.351979.05
430.00080.00030.00080.0010.00020.0004-0.02070.00010.00540.0108-0.00910.0085-0.00670.0071-0.00012.13280.0997-0.25612.22610.01242.4077161.785520.089489.6456
440.0005-0.00030.00060.00210.00310.00270.03-0.00750.0085-0.0172-0.0007-0.00350.01620.0129-0.00011.2097-0.08190.00531.48320.08951.3432156.025619.903875.4468
450.0024-0.00160.00230.00260.00110.00380.0144-0.00240.0264-0.0060.00190.04930.00350.0127-01.03340.14630.19111.3174-0.06931.2331148.60521577.7934
460.0001-0.0007-0.00090.00070.00160.00090.00370.0017-0.0065-0.0424-0.00290.03420.0182-0.0137-0.00011.28920.23740.05281.1454-0.02631.1474158.42953.925675.4112
470.00480.00280.00280.0075-0.00250.00470.0265-0.00680.01260.0169-0.0127-0.04350.0005-0.00701.03850.04630.16961.2703-0.02241.234158.9068-0.035870.4984
480.01630.00390.0030.0019-0.00030.00170.0028-0.00410.0040.0189-0.0092-0.0027-0.00120.003-01.6018-0.01330.0931.5961-0.06131.5132156.5263-5.876771.9894
490.14030.10360.0950.09780.06930.064-0.0082-0.00520.01030.00810.0041-0.0101-0-0.00250.00022.96930.09540.04752.79820.06682.9093160.4574-12.813568.1318
500.41160.1929-0.03190.0921-0.01450.0026-0.0093-0.00380.0010.01430.00580.0027-0.00140.0020.00071.74110.0909-0.02921.7911-0.05961.6921157.6762-11.975561.6857
510.00640.0060.00030.00670.00110.00020.0057-0.00590.01580.00310.01270.01970.0058-0.0068-01.5470.0372-0.29121.7607-0.1741.3725162.8079-4.559360.8089
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESID 28 THROUGH 111 )
2X-RAY DIFFRACTION2CHAIN B AND (RESID 112 THROUGH 419 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 420 THROUGH 543 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 33 THROUGH 92 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 93 THROUGH 419 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 420 THROUGH 543 )
7X-RAY DIFFRACTION7CHAIN D AND (RESID 40 THROUGH 65 )
8X-RAY DIFFRACTION8CHAIN D AND (RESID 66 THROUGH 71 )
9X-RAY DIFFRACTION9CHAIN D AND (RESID 72 THROUGH 82 )
10X-RAY DIFFRACTION10CHAIN D AND (RESID 83 THROUGH 106 )
11X-RAY DIFFRACTION11CHAIN D AND (RESID 107 THROUGH 126 )
12X-RAY DIFFRACTION12CHAIN D AND (RESID 127 THROUGH 131 )
13X-RAY DIFFRACTION13CHAIN D AND (RESID 132 THROUGH 143 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 40 THROUGH 49 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 50 THROUGH 65 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 66 THROUGH 71 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 72 THROUGH 82 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 83 THROUGH 92 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 93 THROUGH 101 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 102 THROUGH 111 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 112 THROUGH 121 )
22X-RAY DIFFRACTION22CHAIN C AND (RESID 122 THROUGH 126 )
23X-RAY DIFFRACTION23CHAIN C AND (RESID 127 THROUGH 136 )
24X-RAY DIFFRACTION24CHAIN C AND (RESID 137 THROUGH 142 )
25X-RAY DIFFRACTION25CHAIN F AND (RESID 33 THROUGH 92 )
26X-RAY DIFFRACTION26CHAIN F AND (RESID 93 THROUGH 419 )
27X-RAY DIFFRACTION27CHAIN F AND (RESID 420 THROUGH 459 )
28X-RAY DIFFRACTION28CHAIN F AND (RESID 460 THROUGH 543 )
29X-RAY DIFFRACTION29CHAIN E AND (RESID 33 THROUGH 125 )
30X-RAY DIFFRACTION30CHAIN E AND (RESID 126 THROUGH 278 )
31X-RAY DIFFRACTION31CHAIN E AND (RESID 279 THROUGH 363 )
32X-RAY DIFFRACTION32CHAIN E AND (RESID 364 THROUGH 443 )
33X-RAY DIFFRACTION33CHAIN E AND (RESID 444 THROUGH 543 )
34X-RAY DIFFRACTION34CHAIN H AND (RESID 40 THROUGH 49 )
35X-RAY DIFFRACTION35CHAIN H AND (RESID 50 THROUGH 65 )
36X-RAY DIFFRACTION36CHAIN H AND (RESID 66 THROUGH 71 )
37X-RAY DIFFRACTION37CHAIN H AND (RESID 72 THROUGH 106 )
38X-RAY DIFFRACTION38CHAIN H AND (RESID 107 THROUGH 116 )
39X-RAY DIFFRACTION39CHAIN H AND (RESID 117 THROUGH 143 )
40X-RAY DIFFRACTION40CHAIN G AND (RESID 40 THROUGH 49 )
41X-RAY DIFFRACTION41CHAIN G AND (RESID 50 THROUGH 59 )
42X-RAY DIFFRACTION42CHAIN G AND (RESID 60 THROUGH 65 )
43X-RAY DIFFRACTION43CHAIN G AND (RESID 66 THROUGH 71 )
44X-RAY DIFFRACTION44CHAIN G AND (RESID 72 THROUGH 82 )
45X-RAY DIFFRACTION45CHAIN G AND (RESID 83 THROUGH 96 )
46X-RAY DIFFRACTION46CHAIN G AND (RESID 97 THROUGH 106 )
47X-RAY DIFFRACTION47CHAIN G AND (RESID 107 THROUGH 121 )
48X-RAY DIFFRACTION48CHAIN G AND (RESID 122 THROUGH 126 )
49X-RAY DIFFRACTION49CHAIN G AND (RESID 127 THROUGH 131 )
50X-RAY DIFFRACTION50CHAIN G AND (RESID 132 THROUGH 136 )
51X-RAY DIFFRACTION51CHAIN G AND (RESID 137 THROUGH 142 )

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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