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- PDB-5cmn: FLRT3 LRR domain in complex with LPHN3 Olfactomedin domain -

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基本情報

登録情報
データベース: PDB / ID: 5cmn
タイトルFLRT3 LRR domain in complex with LPHN3 Olfactomedin domain
要素
  • Latrophilin-3
  • Leucine-rich repeat transmembrane protein FLRT3
キーワードCell Adhesion/Carbohydrate Binding / LRR repeats / Cell Adhesion-Carbohydrate Binding complex / ADGRL3
機能・相同性
機能・相同性情報


proepicardium cell migration involved in pericardium morphogenesis / Rho-activating G protein-coupled receptor signaling pathway / cell adhesion mediator activity / excitatory synapse assembly / head development / growth cone membrane / synaptic membrane adhesion / cell-cell adhesion via plasma-membrane adhesion molecules / fibroblast growth factor receptor binding / embryonic morphogenesis ...proepicardium cell migration involved in pericardium morphogenesis / Rho-activating G protein-coupled receptor signaling pathway / cell adhesion mediator activity / excitatory synapse assembly / head development / growth cone membrane / synaptic membrane adhesion / cell-cell adhesion via plasma-membrane adhesion molecules / fibroblast growth factor receptor binding / embryonic morphogenesis / Signaling by ROBO receptors / Downstream signaling of activated FGFR1 / chemorepellent activity / positive regulation of synapse assembly / neuron projection extension / fibroblast growth factor receptor signaling pathway / response to axon injury / axonal growth cone / synapse assembly / axon terminus / extracellular matrix / axon guidance / synaptic membrane / molecular condensate scaffold activity / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / neuron migration / neuron projection development / cell-cell junction / cell junction / heart development / carbohydrate binding / protein-macromolecule adaptor activity / postsynaptic membrane / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / axon / focal adhesion / calcium ion binding / endoplasmic reticulum membrane / glutamatergic synapse / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytosol
類似検索 - 分子機能
: / GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / D-galactoside/L-rhamnose binding SUEL lectin domain / D-galactoside/L-rhamnose binding SUEL lectin domain / SUEL-type lectin domain profile. / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain ...: / GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / D-galactoside/L-rhamnose binding SUEL lectin domain / D-galactoside/L-rhamnose binding SUEL lectin domain / SUEL-type lectin domain profile. / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / : / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / Alpha-Beta Horseshoe / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Leucine-rich repeat domain superfamily / Immunoglobulin-like fold / Alpha Beta
類似検索 - ドメイン・相同性
Adhesion G protein-coupled receptor L3 / Leucine-rich repeat transmembrane protein FLRT3
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: 3.605 Å
データ登録者Lu, Y. / Salzman, G. / Arac, D.
引用ジャーナル: Structure / 年: 2015
タイトル: Structural Basis of Latrophilin-FLRT-UNC5 Interaction in Cell Adhesion.
著者: Lu, Y.C. / Nazarko, O.V. / Sando, R. / Salzman, G.S. / Sudhof, T.C. / Arac, D.
履歴
登録2015年7月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年8月12日Provider: repository / タイプ: Initial release
改定 1.12015年9月16日Group: Database references
改定 1.22020年7月29日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.32023年9月27日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.42024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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 transmembrane protein FLRT3
B: Leucine-rich repeat transmembrane protein FLRT3
C: Leucine-rich repeat transmembrane protein FLRT3
D: Leucine-rich repeat transmembrane protein FLRT3
E: Latrophilin-3
F: Latrophilin-3
G: Latrophilin-3
H: Latrophilin-3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)272,93116
ポリマ－271,8868
非ポリマー1,0458
水00
1
A: Leucine-rich repeat transmembrane protein FLRT3
E: Latrophilin-3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,2334
ポリマ－67,9722
非ポリマー2612
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Leucine-rich repeat transmembrane protein FLRT3
F: Latrophilin-3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,2334
ポリマ－67,9722
非ポリマー2612
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Leucine-rich repeat transmembrane protein FLRT3
G: Latrophilin-3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,2334
ポリマ－67,9722
非ポリマー2612
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Leucine-rich repeat transmembrane protein FLRT3
H: Latrophilin-3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,2334
ポリマ－67,9722
非ポリマー2612
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)102.268, 102.268, 419.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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要素

#1: タンパク質
Leucine-rich repeat transmembrane protein FLRT3 / Fibronectin-like domain-containing leucine-rich transmembrane protein 3


分子量: 37962.219 Da / 分子数: 4 / 断片: UNP residues 29-357 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FLRT3, KIAA1469, UNQ856/PRO1865 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9NZU0
#2: タンパク質
Latrophilin-3 / Calcium-independent alpha-latrotoxin receptor 3 / CIRL-3 / Lectomedin-3


分子量: 30009.295 Da / 分子数: 4 / 断片: UNP residues 132-392 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LPHN3, KIAA0768, LEC3 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9HAR2
#3: 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
#4: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Ca
Has protein modificationY

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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: 4.03 Å3/Da / 溶媒含有率: 69.49 %
結晶化温度: 295 K / 手法: 蒸発脱水法 / pH: 6
詳細: 10% (w/v) PEG 3000, 100mM MES pH6.0, 200mM Lithium sulfate

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データ収集

回折平均測定温度: 295 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 19-BM / 波長: 1.00883 Å
検出器タイプ: ADSC QUANTUM 210r / 検出器: CCD / 日付: 2014年12月12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: 1.00883 Å / 相対比: 1
反射解像度: 3.6→75 Å / Num. obs: 45263 / % possible obs: 92 % / 冗長度: 3.6 % / Rmerge(I) obs: 0.229 / Net I/σ(I): 6.031
反射 シェル解像度: 3.6→3.66 Å / 冗長度: 1.7 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 1.347 / % possible all: 60.6

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
Cootモデル構築
HKL-2000データスケーリング
HKL-2000データ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4WXQ

4wxq


解像度: 3.605→73.196 Å / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 42.79 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射
Rfree0.2618 1979 4.37 %
Rwork0.195 --
obs0.1987 45263 91.74 %
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
精密化ステップサイクル: LAST / 解像度: 3.605→73.196 Å
タンパク質核酸リガンド溶媒全体
原子数18360 0 60 0 18420
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00518888
X-RAY DIFFRACTIONf_angle_d0.93825664
X-RAY DIFFRACTIONf_dihedral_angle_d12.8126960
X-RAY DIFFRACTIONf_chiral_restr0.0372852
X-RAY DIFFRACTIONf_plane_restr0.0043316
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6087-3.70630.34381050.24892303X-RAY DIFFRACTION61
3.7063-3.81530.28181250.23292915X-RAY DIFFRACTION77
3.8153-3.93840.30051390.23243246X-RAY DIFFRACTION86
3.9384-4.07920.27641420.21873367X-RAY DIFFRACTION89
4.0792-4.24250.28141400.21283426X-RAY DIFFRACTION91
4.2425-4.43550.25451500.1953461X-RAY DIFFRACTION92
4.4355-4.66920.26041530.18873482X-RAY DIFFRACTION92
4.6692-4.96160.26191410.17733482X-RAY DIFFRACTION93
4.9616-5.34450.24321500.18093528X-RAY DIFFRACTION94
5.3445-5.88190.26861510.19913531X-RAY DIFFRACTION94
5.8819-6.7320.29221490.18993569X-RAY DIFFRACTION94
6.732-8.47780.24581520.19043529X-RAY DIFFRACTION93
8.4778-59.52930.23351520.17473549X-RAY DIFFRACTION94
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)
11.1365-1.42641.80351.8025-2.25332.8522-0.0071-0.19530.07470.33830.03410.2549-0.3081-0.6282-0.07891.2432-0.1937-0.14470.8461-0.13220.795842.21654.625642.5498
20.63070.14520.43031.28590.09540.2968-0.2603-0.17780.03110.5792-0.13040.3212-0.1079-0.17930.04771.41290.00950.06930.1866-0.05860.645949.974865.171643.9592
30.5543-0.0776-0.24781.50530.5191.14-0.0338-0.13-0.15510.5906-0.065-0.558-0.14050.0855-0.13721.29280.0198-0.17620.0299-0.14740.692764.18871.535143.9799
40.2592-0.22260.70510.1976-0.61271.92740.1251-0.7230.11770.3825-0.0301-0.2081-0.54480.2628-0.05430.8898-0.0775-0.24140.6815-0.10550.746877.187374.296739.6693
50.11870.09070.08510.495-0.3580.8835-0.2451-0.2479-0.24340.3447-0.149-0.6027-0.27710.38020.22490.5377-0.3031-0.18311.49410.09651.21986.428868.858932.6224
61.89090.0295-0.95390.5858-0.43821.3737-0.01390.1432-0.1329-0.022-0.2306-0.5252-0.04410.50660.17490.6848-0.015-0.06321.7199-0.36381.3895.287462.604522.7313
70.0345-0.0130.0090.0148-0.01760.0155-0.17430.07510.43180.13590.12990.4702-0.593-0.47610.04551.52210.26950.04132.16780.10471.80698.77564.891910.4554
80.4562-0.37210.16091.3251-0.25610.4357-0.0769-0.02320.2475-0.0915-0.13590.4007-0.2631-0.3888-0.01751.34880.3536-0.1818-0.0385-0.19590.851139.47488.673531.61
90.6023-0.1544-0.35421.2370.51780.5354-0.09050.255-0.2741-0.3479-0.31940.2957-0.288-0.2327-0.00851.4404-0.1018-0.17480.0481-0.05030.774652.346580.319315.2321
100.60490.1517-0.05091.2803-0.64892.35680.00080.3646-0.0592-0.1132-0.3511-0.0844-0.46110.40440.30771.2698-0.2948-0.06520.63460.02750.656672.298683.00457.0306
110.8564-0.5260.43510.538-0.3440.2458-0.09450.4170.35-0.264-0.0865-0.4765-0.13870.4382-0.01331.6701-0.88310.00071.5678-0.22151.011389.132587.9169.041
120.09940.28250.37811.15120.19314.10060.11550.38220.3035-0.2980.0244-0.3874-0.31050.1888-0.10321.0764-0.0332-0.0220.90670.16860.821563.377477.1691-33.8245
131.0294-0.07051.82432.1676-0.35263.24940.22160.97780.0887-0.0699-0.0603-0.23480.1182-0.193-0.07780.54510.2631-0.02640.8660.01790.609151.981865.7043-35.6704
141.4047-0.6261-1.92060.78780.44523.25820.12620.6702-0.185-0.13320.12760.03520.1438-0.1934-0.16820.79310.1993-0.25230.6248-0.20480.873150.072254.3954-32.7968
150.3470.6306-0.17572.39161.60163.26-0.04940.318-0.291-0.3959-0.01460.21570.4318-0.33590.18491.32190.0233-0.46730.3305-0.21810.98847.421444.6842-29.8695
160.1122-0.0239-0.15270.07150.16881.143-0.06930.6006-0.4972-0.4866-0.0632-0.00430.1198-0.29570.08391.39410.0393-0.29430.4908-0.4360.777551.066841.178-26.4526
171.29960.85991.46513.87441.73261.846-0.20590.5061-0.67710.072-0.183-0.01380.386-0.21460.23351.374-0.12380.01450.9464-0.29151.144453.114534.3056-24.456
180.7554-0.6305-0.46521.2841.27931.4548-0.3570.2431-0.3433-0.3482-0.0174-0.23120.1746-0.14380.18451.98750.2826-0.30810.635-0.44911.389355.898330.7865-15.6277
190.03650.02140.08090.0180.0630.1827-0.1347-0.02120.0743-0.0505-0.2815-0.123-0.06320.08740.12722.27330.0035-0.55970.412-0.05641.852959.192623.6014-8.1138
204.10220.9092-1.65490.4868-0.74651.18210.2288-0.03040.6529-0.05490.0910.1891-0.4996-0.2476-0.23740.93950.3932-0.07631.6057-0.09250.910227.275684.8767-27.0886
210.6464-0.4645-0.11330.47530.30050.36270.1365-0.26370.36820.09220.05440.1544-0.5261-0.3991-0.24651.33260.2339-0.14870.4810.02750.858634.177382.8115-21.3742
220.47020.23710.12910.38020.68471.6401-0.2526-0.19170.41020.08950.0091-0.2355-0.4387-0.49840.08040.85090.0923-0.03970.1435-0.24260.906539.564177.0356-11.0857
232.5564-2.5323-0.69783.8156-0.66981.6427-0.031-0.20080.03940.19730.2104-0.3129-0.0140.1625-0.13460.48860.0033-0.09190.286-0.19110.69243.109965.9983-4.3889
240.3117-0.3894-0.12381.4236-0.34771.2452-0.0714-0.72230.03770.3721-0.1487-0.04130.2149-0.35010.20370.962-0.1472-0.12890.5473-0.16320.700240.049754.71591.9791
251.16010.61540.19570.5509-0.34720.9699-0.0417-0.5394-0.63920.25210.15590.26420.2028-0.381-0.00422.1395-0.48270.01550.76480.20310.897134.827834.88450.8345
260.81070.48270.17690.32810.15890.1130.0279-0.1759-0.13340.3239-0.1081-0.25070.1101-0.00280.04681.6590.2805-0.18810.48380.08930.983564.077327.027822.2912
270.2085-0.04680.96040.2948-0.19314.35070.26650.1821-0.1799-0.10850.1578-0.43260.41240.5064-0.36381.59570.269-0.34210.4022-0.25230.679773.028941.700923.0029
280.14260.19030.03870.365-0.28450.9790.01020.0644-0.3137-0.163-0.0667-0.28450.26360.3652-0.1561.57610.1016-0.23590.4047-0.21231.166275.794448.477823.9125
291.55160.0959-0.85072.99560.19831.08670.0842-0.03440.05720.0616-0.0973-0.00420.10180.105-0.02491.0886-0.1168-0.2443-0.08090.09920.971863.632953.806719.8195
300.14830.1336-0.08150.3167-0.12790.04660.1122-0.0624-0.10360.1832-0.0918-0.13620.1983-0.1894-0.03221.4386-0.40620.0062-0.420.11850.583152.48246.708424.1416
310.39190.3140.40950.320.43510.59850.08180.0589-0.11030.1401-0.00420.09070.0651-0.04130.05931.6427-0.4159-0.2771-0.2970.04111.226251.628632.325625.4648
321.57760.51180.15612.20290.58510.15660.196-0.3929-0.12840.2519-0.1226-0.11370.2484-0.12090.00681.5359-0.2038-0.35020.54630.13160.714964.975134.069127.648
331.28810.64240.48942.31970.44410.46860.04580.0518-0.1151-0.0626-0.06120.24750.1319-0.03660.0331.96090.0848-0.34470.3189-0.01610.804968.888833.97627.6474
340.53350.63410.15750.84720.25030.07440.09910.08790.0108-0.1716-0.0579-0.1437-0.1170.1633-0.08861.7873-0.1165-0.4806-0.04440.00091.163369.6375108.456130.4996
350.4720.6103-0.1741.2994-0.54920.57970.05930.05680.1299-0.13880.0619-0.3354-0.24070.10690.03751.7012-0.1191-0.26740.17530.05920.918972.8522100.507730.4086
360.5351-0.4276-0.20180.77140.16590.2631-0.06790.0694-0.10040.092-0.1938-0.0261-0.201-0.1151-0.12991.6481-0.00180.0013-0.0109-0.20490.709563.640392.47137.9828
370.1680.0237-0.05670.38640.31060.30050.0973-0.0872-0.0367-0.07740.04070.2323-0.06730.04130.10082.10440.063-0.30350.0244-0.29861.100757.8004102.859143.9058
380.27340.2365-0.17390.2854-0.18170.128-0.0508-0.1659-0.01730.18370.0337-0.03570.12730.0623-0.00952.39530.256-0.34710.554-0.19350.999856.8728114.289745.0776
390.6358-0.2273-0.66691.68870.61541.01910.23990.29060.2985-0.7996-0.215-0.0319-0.4525-0.2814-0.00441.8050.3064-0.07110.3068-0.09030.920662.2019116.347835.0794
401.52070.61920.02671.5410.06670.23690.1509-0.0240.216-0.15590.1612-0.0148-0.15920.2363-0.16031.9724-0.3434-0.49080.6079-0.07270.939866.2375116.009430.9329
410.99240.7960.55330.71330.7161.3315-0.1560.4708-0.65860.1686-0.0135-0.29490.6637-0.21630.09790.5581-0.0521-0.19731.5864-0.28551.170894.71157.6799-12.8102
420.04020.03560.08350.1642-0.10870.45880.0389-0.0699-0.33820.08020.09290.02590.3270.2137-0.16110.50770.5373-0.26371.6115-0.16420.697176.564747.9219-14.649
432.7914-1.2363-0.35051.18170.29290.274-0.00650.12610.1003-0.3513-0.1735-0.4110.10220.18480.06940.80520.43120.0920.7527-0.3750.818469.111449.6402-13.6614
440.4038-0.0366-0.26060.23090.06980.27820.13630.13930.06460.10610.32060.07080.05890.585-0.16130.199-0.16070.03691.1622-0.05560.623471.248163.1423-12.7333
451.125-0.4696-0.84520.61480.41371.89770.3281-0.29660.36670.17270.076-0.3007-0.20630.4923-0.23890.316-0.22220.14221.95320.10910.885182.34771.6935-14.8303
460.1172-0.11810.15830.1904-0.09710.2834-0.08140.05320.1417-0.02510.1554-0.2479-0.08010.3672-0.09010.59930.10240.18072.2552-0.08750.684988.257556.0733-18.5612
470.79340.091-0.41180.79510.10670.80060.27580.1381-0.3898-0.12920.11720.412-0.0031-0.1351-0.05570.25710.0814-0.0432.0902-0.14071.14228.524251.3478-23.9361
480.98611.2981-0.13782.371-0.54990.27210.00150.0365-0.3856-0.16950.19680.11430.1913-0.2193-0.07810.2083-0.42750.04961.4265-0.29341.147121.342450.4867-17.2982
491.0411-0.8099-0.66723.1335-0.00630.85210.10020.2280.1229-0.0608-0.09570.0130.1675-0.0743-0.02340.11110.0280.03541.4735-0.08690.736727.832356.9759-28.7666
505.35230.99551.06731.215-0.50510.8179-0.03530.0256-0.1047-0.00850.0531-0-0.0153-0.35260.05310.0701-0.0403-0.09181.4577-0.25290.718217.398962.458-30.2012
512.0889-0.9197-1.16330.97950.38150.6954-0.01840.3566-0.0163-0.1537-0.0727-0.28110.0087-0.17070.00350.15840.1213-0.03961.8655-0.15070.794716.640465.2806-35.9723
524.38350.1369-1.64990.9576-0.3080.69370.09890.16140.2146-0.0932-0.0253-0.0222-0.06650.1141-0.07080.26420.1056-0.02841.9361-0.25570.78346.512667.4603-38.008
530.24460.0759-0.48090.0167-0.13620.94620.2056-0.16850.0320.02850.32360.0748-0.2367-0.2614-0.34890.40390.02070.13332.1449-0.05031.10645.661759.7014-25.7604
540.58170.4101-0.52463.54492.88363.9815-0.0950.05580.11550.00560.20630.114-0.1245-0.31720.00370.6706-0.15290.25552.2861-0.0290.73995.997455.3578-21.6285
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 30:64 )A30 - 64
2X-RAY DIFFRACTION2( CHAIN A AND RESID 65:120 )A65 - 120
3X-RAY DIFFRACTION3( CHAIN A AND RESID 121:191 )A121 - 191
4X-RAY DIFFRACTION4( CHAIN A AND RESID 192:220 )A192 - 220
5X-RAY DIFFRACTION5( CHAIN A AND RESID 221:292 )A221 - 292
6X-RAY DIFFRACTION6( CHAIN A AND RESID 293:335 )A293 - 335
7X-RAY DIFFRACTION7( CHAIN A AND RESID 336:350 )A336 - 350
8X-RAY DIFFRACTION8( CHAIN B AND RESID 30:120 )B30 - 120
9X-RAY DIFFRACTION9( CHAIN B AND RESID 121:215 )B121 - 215
10X-RAY DIFFRACTION10( CHAIN B AND RESID 216:292 )B216 - 292
11X-RAY DIFFRACTION11( CHAIN B AND RESID 293:350 )B293 - 350
12X-RAY DIFFRACTION12( CHAIN C AND RESID 30:94 )C30 - 94
13X-RAY DIFFRACTION13( CHAIN C AND RESID 95:148 )C95 - 148
14X-RAY DIFFRACTION14( CHAIN C AND RESID 149:191 )C149 - 191
15X-RAY DIFFRACTION15( CHAIN C AND RESID 192:220 )C192 - 220
16X-RAY DIFFRACTION16( CHAIN C AND RESID 221:241 )C221 - 241
17X-RAY DIFFRACTION17( CHAIN C AND RESID 242:273 )C242 - 273
18X-RAY DIFFRACTION18( CHAIN C AND RESID 274:310 )C274 - 310
19X-RAY DIFFRACTION19( CHAIN C AND RESID 311:350 )C311 - 350
20X-RAY DIFFRACTION20( CHAIN D AND RESID 30:64 )D30 - 64
21X-RAY DIFFRACTION21( CHAIN D AND RESID 65:94 )D65 - 94
22X-RAY DIFFRACTION22( CHAIN D AND RESID 95:165 )D95 - 165
23X-RAY DIFFRACTION23( CHAIN D AND RESID 166:191 )D166 - 191
24X-RAY DIFFRACTION24( CHAIN D AND RESID 192:273 )D192 - 273
25X-RAY DIFFRACTION25( CHAIN D AND RESID 274:350 )D274 - 350
26X-RAY DIFFRACTION26( CHAIN E AND RESID 134:147 )E134 - 147
27X-RAY DIFFRACTION27( CHAIN E AND RESID 148:168 )E148 - 168
28X-RAY DIFFRACTION28( CHAIN E AND RESID 169:201 )E169 - 201
29X-RAY DIFFRACTION29( CHAIN E AND RESID 202:236 )E202 - 236
30X-RAY DIFFRACTION30( CHAIN E AND RESID 237:311 )E237 - 311
31X-RAY DIFFRACTION31( CHAIN E AND RESID 312:354 )E312 - 354
32X-RAY DIFFRACTION32( CHAIN E AND RESID 355:374 )E355 - 374
33X-RAY DIFFRACTION33( CHAIN E AND RESID 375:391 )E375 - 391
34X-RAY DIFFRACTION34( CHAIN F AND RESID 134:185 )F134 - 185
35X-RAY DIFFRACTION35( CHAIN F AND RESID 186:221 )F186 - 221
36X-RAY DIFFRACTION36( CHAIN F AND RESID 222:253 )F222 - 253
37X-RAY DIFFRACTION37( CHAIN F AND RESID 254:309 )F254 - 309
38X-RAY DIFFRACTION38( CHAIN F AND RESID 310:351 )F310 - 351
39X-RAY DIFFRACTION39( CHAIN F AND RESID 352:374 )F352 - 374
40X-RAY DIFFRACTION40( CHAIN F AND RESID 375:391 )F375 - 391
41X-RAY DIFFRACTION41( CHAIN G AND RESID 134:147 )G134 - 147
42X-RAY DIFFRACTION42( CHAIN G AND RESID 148:192 )G148 - 192
43X-RAY DIFFRACTION43( CHAIN G AND RESID 193:211 )G193 - 211
44X-RAY DIFFRACTION44( CHAIN G AND RESID 212:277 )G212 - 277
45X-RAY DIFFRACTION45( CHAIN G AND RESID 278:351 )G278 - 351
46X-RAY DIFFRACTION46( CHAIN G AND RESID 352:391 )G352 - 391
47X-RAY DIFFRACTION47( CHAIN H AND RESID 134:168 )H134 - 168
48X-RAY DIFFRACTION48( CHAIN H AND RESID 169:211 )H169 - 211
49X-RAY DIFFRACTION49( CHAIN H AND RESID 212:253 )H212 - 253
50X-RAY DIFFRACTION50( CHAIN H AND RESID 254:277 )H254 - 277
51X-RAY DIFFRACTION51( CHAIN H AND RESID 278:324 )H278 - 324
52X-RAY DIFFRACTION52( CHAIN H AND RESID 325:351 )H325 - 351
53X-RAY DIFFRACTION53( CHAIN H AND RESID 352:374 )H352 - 374
54X-RAY DIFFRACTION54( CHAIN H AND RESID 375:391 )H375 - 391

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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