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- PDB-7kfw: Structural basis for a germline-biased antibody response to SARS-... -

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基本情報

登録情報
データベース: PDB / ID: 7kfw
タイトルStructural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B3 Fab)
要素
  • Spike glycoprotein
  • heavy chain of antibody C1A-B3 Fab
  • light chain of antibody C1A-B3 Fab
キーワードIMMUNE SYSTEM/Viral protein / COVID-19 / SARS-CoV-2 / neutralizing antibody / affinity maturation / IMMUNE SYSTEM / IMMUNE SYSTEM-Viral protein complex
機能・相同性
機能・相同性情報


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
類似検索 - ドメイン・相同性
Spike glycoprotein
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.792 Å
データ登録者Pan, J. / Abraham, J. / Clark, L. / Clark, S.
資金援助 米国, 1件
組織認可番号国
Other privateno grant number 米国
引用ジャーナル: Biorxiv / 年: 2020
タイトル: Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2.
著者: Clark, S.A. / Clark, L.E. / Pan, J. / Coscia, A. / McKay, L.G.A. / Shankar, S. / Johnson, R.I. / Griffiths, A. / Abraham, J.
履歴
登録2020年10月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年12月2日Provider: repository / タイプ: Initial release
改定 1.12021年1月20日Group: Database references / Source and taxonomy / Structure summary
カテゴリ: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct.pdbx_descriptor / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
改定 1.22023年10月18日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.32024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _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: Spike glycoprotein
B: Spike glycoprotein
C: heavy chain of antibody C1A-B3 Fab
D: light chain of antibody C1A-B3 Fab
E: Spike glycoprotein
F: heavy chain of antibody C1A-B3 Fab
G: light chain of antibody C1A-B3 Fab
H: heavy chain of antibody C1A-B3 Fab
L: light chain of antibody C1A-B3 Fab
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)218,20012
ポリマ－217,5369
非ポリマー6643
水7,206400
1
A: Spike glycoprotein
H: heavy chain of antibody C1A-B3 Fab
L: light chain of antibody C1A-B3 Fab
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,7334
ポリマ－72,5123
非ポリマー2211
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Spike glycoprotein
C: heavy chain of antibody C1A-B3 Fab
D: light chain of antibody C1A-B3 Fab
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,7334
ポリマ－72,5123
非ポリマー2211
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Spike glycoprotein
F: heavy chain of antibody C1A-B3 Fab
G: light chain of antibody C1A-B3 Fab
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,7334
ポリマ－72,5123
非ポリマー2211
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)84.174, 112.843, 267.846
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質 Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


分子量: 25467.650 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2 / プラスミド: pHLSec / 細胞株 (発現宿主): HEK-293T / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2
#2: 抗体 heavy chain of antibody C1A-B3 Fab


分子量: 23824.607 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pVRC-8400 / 細胞株 (発現宿主): HEK-293T / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 light chain of antibody C1A-B3 Fab


分子量: 23219.746 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pVRC-8400 / 細胞株 (発現宿主): HEK-293T / 発現宿主: Homo sapiens (ヒト)
#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: 3 / 由来タイプ: 合成 / 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
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 400 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN
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 / 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: 3.1 Å3/Da / 溶媒含有率: 60.27 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl, pH 7.5 mother liquor composition (equal volume): 0.2 M Ammonium phosphate dibasic, 20% w/v PEG 3350

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データ収集

回折平均測定温度: 80 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-E / 波長: 0.9792 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年7月25日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9792 Å / 相対比: 1
反射解像度: 2.77→200 Å / Num. obs: 63645 / % possible obs: 98.1 % / 冗長度: 6.94 % / CC1/2: 0.983 / Rrim(I) all: 0.382 / Χ2: 0.89 / Net I/σ(I): 5.41
反射 シェル解像度: 2.79→2.94 Å / 冗長度: 6.51 % / Mean I/σ(I) obs: 0.68 / Num. unique obs: 17922 / CC1/2: 0.233 / % possible all: 88.6

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解析

ソフトウェア
名称バージョン分類
BUSTER2.10.3精密化
PHENIX1.18.2-3874data processing
O15.1.0モデル構築
XDS20200131データ削減
XDS20200131データスケーリング
PHASER2.8.3位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7KFV

7kfv


解像度: 2.792→133.92 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 1.156 / 交差検証法: THROUGHOUT / SU R Blow DPI: 1.319 / SU Rfree Blow DPI: 0.309 / SU Rfree Cruickshank DPI: 0.312
Rfactor反射数%反射Selection details
Rfree0.2293 3092 -RANDOM
Rwork0.1893 ---
obs0.1913 63645 99 %-
原子変位パラメータBiso mean: 86.67 Å2
Baniso -1Baniso -2Baniso -3
1--11.333 Å20 Å20 Å2
2--11.0801 Å20 Å2
3---0.2529 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
精密化ステップサイクル: LAST / 解像度: 2.792→133.92 Å
タンパク質核酸リガンド溶媒全体
原子数14459 0 42 400 14901
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00815131HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9820650HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5032SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2587HARMONIC5
X-RAY DIFFRACTIONt_it15126HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1979SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies36HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact11024SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion18.18
LS精密化 シェル解像度: 2.8→2.82 Å
Rfactor反射数%反射
Rfree0.31 61 -
Rwork0.2521 --
obs--67.86 %
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)
10.22511.9928-1.78490.194-1.631200.04110.08220.06950.0822-0.1978-0.1390.0695-0.1390.15670.05320.14850.1520.04060.139-0.0111-25.2246-1.500225.9361
20-1.01752.91040.67050.04445.86980.04-0.34740.0159-0.34740.0212-0.250.0159-0.25-0.06130.304-0.01110.1156-0.1612-0.0025-0.0839-32.51733.189226.7566
30-0.1016-0.18032.57662.910400.1547-0.54420.5442-0.5442-0.3896-0.15420.5442-0.15420.23490.28550.12970.152-0.1533-0.081-0.0511-34.1946-12.522323.8222
40.64762.91042.910402.91042.73780.0675-0.06560.0919-0.0656-0.1096-0.36590.0919-0.36590.04210.304-0.07410.01860.07980.152-0.304-41.7694-5.95416.5579
50-2.41071.023602.45510-0.25720.4772-0.10810.47720.0035-0.0125-0.1081-0.01250.25370.01640.03860.0349-0.0160.11470.0683-34.7861-5.158635.7845
60.2569-0.26751.636400.08970.7281-0.0709-0.3058-0.0234-0.3058-0.071-0.044-0.0234-0.0440.14190.10310.04010.0514-0.01180.0743-0.0125-37.2474-6.011336.6618
70-0.6189-0.8361.12752.910400.1244-0.09030.2303-0.0903-0.1953-0.07740.2303-0.07740.07080.08310.09240.05970.01280.11890.033-28.1168-1.82247.9568
800.5871-0.621800.47871.20390.32690.0528-0.05750.0528-0.2173-0.1408-0.0575-0.1408-0.10950.0352-0.1198-0.04630.04150.08650.029-35.45726.903553.1642
90.5007-0.3591-0.57940-0.48480.00360.0043-0.2953-0.0671-0.2953-0.0662-0.2051-0.0671-0.20510.06190.17160.1520.0419-0.0435-0.0152-0.0249-33.1403-5.139130.566
100-1.25451.94430-2.91040.3969-0.08050.18-0.20980.180.46370.0026-0.20980.0026-0.38320.20780.00430.152-0.11210.1520.1025-108.02833.3736100.602
1100.4495-0.31630-2.910400.0560.54420.17140.54420.43230.4230.17140.423-0.48830.10550.1520.0285-0.10540.0881-0.0188-102.24124.1112111.391
1202.9104-1.86320-1.04532.6341-0.148-0.02650.0328-0.02650.39620.12680.03280.1268-0.24810.10450.1138-0.1227-0.1157-0.05060.0555-99.525826.185895.2318
1300.06850.26690.3711-0.229700.02870.18640.10270.18640.19080.02180.10270.0218-0.21960.06120.0353-0.0681-0.0332-0.01340.0785-99.283227.526190.34
140-1.755-0.321601.1981.14260.33770.1146-0.03580.1146-0.13120.0624-0.03580.0624-0.20650.10250.0227-0.0807-0.0221-0.06180.0343-92.368539.264583.0867
150.1754-0.3144-0.36360.0310.1100.25440.1977-0.14370.19770.0354-0.0167-0.1437-0.0167-0.28980.10680.0439-0.01860.00810.0056-0.0132-101.67128.514484.4682
165.6328-2.2094-2.910402.91042.3285-0.18930.19450.1820.19450.3029-0.51730.182-0.5173-0.11360.3040.02480.04670.1130.152-0.2705-98.42236.7732118.212
170.4359-0.22390.552100.06980-0.30210.20810.04550.20810.24210.1860.04550.1860.06-0.00420.055-0.03560.0537-0.06050.0465-78.787121.09873.7059
180-0.7349-0.78930.7885-0.06430.4302-0.1283-0.06680.0204-0.06680.1130.12010.02040.12010.0153-0.0441-0.0199-0.04820.0913-0.08120.0429-77.539114.510660.1035
190-0.17930.59040.3892-0.26660.1492-0.1434-0.114-0.0492-0.1140.1665-0.0729-0.0492-0.0729-0.02310.06560.02240.0689-0.0241-0.03090.0648-70.453712.457544.0011
2001.5794-0.09270.16870.05040-0.19280.174-0.34840.174-0.1487-0.0897-0.3484-0.08970.3414-0.16910.043-0.05520.0703-0.1520.2122-101.9678.449561.4078
2101.7463-1.26960.25820.65921.406-0.14360.06330.00880.0633-0.04480.08490.00880.08490.1884-0.05710.10820.04920.0528-0.12650.1206-95.673517.343565.1797
220-0.1272-2.91042.6818-0.16950.7527-0.0131-0.5442-0.2552-0.5442-0.5181-0.0272-0.2552-0.02720.5312-0.08910.0916-0.07550.1159-0.13660.0643-102.46322.588861.9597
230-1.569-0.39870-2.02275.1510.2193-0.28560.2437-0.28560.10570.23440.24370.2344-0.325-0.0377-0.0861-0.08910.0767-0.1520.0329-101.3515.190254.5951
241.03910.81740.087302.91043.0993-0.18160.1177-0.45420.1177-0.02480.1819-0.45420.18190.2063-0.06370.07030.07390.0064-0.08970.1535-94.33113.598669.7245
2502.9104-2.91041.63061.9184.0538-0.22840.3673-0.04520.3673-0.08740.0819-0.04520.08190.3158-0.15790.1135-0.03340.1795-0.06140.051-95.11226.084544.5139
260-0.0369-0.400600.26320-0.0203-0.4047-0.1354-0.40470.1391-0.231-0.1354-0.231-0.11880.04140.0360.0717-0.058-0.10860.1191-65.77232.71236.8328
270-1.07730.12920.85190.06040-0.0206-0.1538-0.0176-0.1538-0.1537-0.1671-0.0176-0.16710.17430.07860.0795-0.0026-0.0341-0.00880.0524-80.037-1.767539.5123
280.9702-1.55750.495202.06771.9772-0.0394-0.5356-0.082-0.53560.0643-0.0493-0.082-0.0493-0.02490.2016-0.09520.0925-0.05660.0431-0.0404-74.6289-8.264541.9797
290.3474-2.7344-2.91040.0849-2.764800.1076-0.5442-0.3702-0.54420.2952-0.0833-0.3702-0.0833-0.40290.07530.0321-0.03770.0082-0.03430.0192-88.778310.004644.0038
300-0.1522-0.52420.0229-1.40800.02080.00280.35430.0028-0.4075-0.42780.3543-0.42780.3867-0.02920.04220.1270.0685-0.04690.0717-65.3968-5.739340.0409
318.3155-1.1745-2.91040.77730.614200.0337-0.25620.3385-0.25620.0825-0.33580.3385-0.3358-0.11620.12840.07260.047-0.07050.01270.0335-74.9868-7.336533.4427
320.0146-2.9104-1.08981.5494-1.21210-0.1836-0.49930.017-0.4993-0.1770.03830.0170.03830.36060.1092-0.0730.06920.0075-0.0337-0.0186-76.625-4.119529.5525
330-2.91042.91041.38992.91044.74050.00630.17910.54420.17910.5316-0.54420.5442-0.5442-0.5379-0.14360.0067-0.01130.3040.1520.2773-62.632-5.1759-18.8338
344.3164-0.09672.063802.15622.30420.1998-0.21420.2178-0.21420.1446-0.54420.2178-0.5442-0.3444-0.22490.152-0.00950.304-0.0425-0.0155-70.13991.4765-25.517
350-2.91042.91040-0.48850-0.21-0.1494-0.5442-0.14940.33430.4056-0.54420.4056-0.12430.03870.152-0.04370.2394-0.0936-0.1746-64.394110.8396-20.0599
360-0.7507-2.910401.18283.1647-0.10750.5442-0.19150.5442-0.1909-0.4118-0.1915-0.41180.2984-0.0176-0.08290.1520.3040.152-0.304-66.2269-0.7773-1.48
370.0849-0.6737-0.4950.13050.98360.9548-0.23720.009-0.23650.0090.3071-0.3522-0.2365-0.3522-0.0699-0.00370.1520.02550.304-0.0501-0.2018-56.50288.753-12.9806
381.8797-0.51610.427901.09590.50420.1828-0.2363-0.5442-0.2363-0.19740.5442-0.54420.54420.01460.23770.06230.11750.16350.152-0.304-54.803537.6618-4.4308
390-2.76971.27140-0.0461.57010.14280.2947-0.2250.2947-0.40150.456-0.2250.4560.25870.13990.152-0.01210.134-0.0353-0.1678-63.320430.568-3.7865
401.7890.1908-2.009900.73230.5274-0.1163-0.5442-0.5442-0.5442-0.2287-0.0704-0.5442-0.07040.3450.24960.1520.06110.1110.0147-0.2449-59.446635.0627-10.5268
410-1.2617-0.54760.16030.61580.89970.07650.0236-0.26190.0236-0.11510.5442-0.26190.54420.03860.21170.11010.00920.06230.0066-0.1667-62.613737.04950.2368
420-0.20842.91040-1.53250-0.19180.2182-0.43350.21820.3524-0.3754-0.4335-0.3754-0.16060.3036-0.0123-0.002-0.3040.07070.0973-72.93962.476228.5484
4302.6683-2.910402.140.1548-0.0321-0.054-0.5442-0.054-0.03450.1535-0.54420.15350.06660.182-0.12240.0354-0.23640.00970.1644-70.575458.867221.3832
443.52492.91041.927402.91042.86950.2626-0.386-0.5126-0.386-0.0512-0.07-0.5126-0.07-0.21150.08960.0608-0.0466-0.175-0.06550.1318-61.925257.550916.4998
4500.42540.11430.2672-0.901600.217-0.2720.2184-0.272-0.0447-0.04550.2184-0.0455-0.17220.10360.022-0.0469-0.0796-0.11510.0909-65.793957.720322.4542
460-1.05010.695401.51270-0.1604-0.204-0.0361-0.2040.3838-0.1962-0.0361-0.1962-0.22340.2576-0.1058-0.0683-0.29130.06770.1565-66.379867.62322.6809
472.18770.62461.079602.38472.0060.2010.2189-0.18930.2189-0.04270.2773-0.18930.2773-0.15830.09480.0279-0.0077-0.0309-0.05840.0218-69.575924.007618.6162
4800.7832-0.1650-0.00070.41450.0294-0.00360.2278-0.0036-0.19390.27230.22780.27230.16460.16180.1454-0.02160.0546-0.0812-0.1142-61.071521.770212.0497
4900.3661-0.16870-0.07570.5470.31730.04140.13730.0414-0.2270.12670.13730.1267-0.09030.14190.1042-0.02930.0471-0.0429-0.0911-64.202722.641513.5757
5001.6929-2.83741.8149-0.11550-0.30060.1629-0.41830.16290.2436-0.0822-0.4183-0.08220.0570.2150.1431-0.0212-0.0012-0.0839-0.138-68.569935.430631.183
511.693-0.52721.07882.6276-2.167100.14330.13990.36970.13990.2577-0.35060.3697-0.3506-0.4010.13820.0870.038-0.1741-0.01660.1227-78.189463.05623.8923
520.0888-0.38151.28210.8724-0.484900.1939-0.30040.3123-0.3004-0.33440.23180.31230.23180.14050.1104-0.0096-0.023-0.0539-0.02030.0691-78.76448.66926.1667
531.4617-0.34820.158401.84900.1723-0.54420.1237-0.54420.01130.40860.12370.4086-0.18370.1473-0.0151-0.0940.0179-0.0586-0.0666-85.04550.122820.9459
540-2.91042.85995.0822-2.91043.04260.14260.54420.32380.54420.2591-0.18990.3238-0.1899-0.40170.02270.0111-0.032-0.1171-0.01680.1588-64.654841.906628.3967
5500.98082.361800.55610-0.1062-0.29220.1014-0.2922-0.06880.2790.10140.2790.17490.0440.0377-0.068-0.0407-0.05690.1005-85.790856.791923.4601
561.41760.17592.91041.0886-0.79650-0.2720.32290.10410.3229-0.00030.06780.10410.06780.27230.07010.11770.1001-0.0606-0.09620.0947-84.437153.965433.6013
570-0.0662-0.55960.45050.02650-0.0649-0.1275-0.0437-0.12750.0733-0.0134-0.0437-0.0134-0.00830.0062-0.0233-0.04460.03620.03810.0574-49.165-9.891362.4241
580.10540.03580.24210-0.38910.1885-0.03670.03790.00470.03790.0738-0.0090.0047-0.009-0.0370.0234-0.0248-0.02010.06690.03540.0126-47.165-15.927369.6782
593.67612.00952.91041.08892.13123.1515-0.084-0.18330.2637-0.18330.0737-0.37010.2637-0.37010.01040.01040.0932-0.0636-0.0408-0.06140.0907-44.4771-23.8322103.819
600.79940.33140.75730-0.06360-0.33930.04480.03210.04480.2049-0.22890.0321-0.22890.13440.04070.0603-0.0851-0.0042-0.00460.0629-49.8403-18.803493.2285
6101.76440.47250.3201-0.70911.3807-0.2486-0.06580.4287-0.0658-0.047-0.07420.4287-0.07420.2956-0.09030.06780.00260.12410.10990.0839-23.9527-23.419367.735
620-1.93960.62480-0.30850.5619-0.0142-0.20420.0443-0.2042-0.21620.28540.04430.28540.2304-0.03040.01810.08570.0620.1520.0638-30.4855-14.297365.4827
630-0.5136-0.68181.45040.47960.30920.12950.33720.08790.3372-0.3785-0.43660.0879-0.43660.249-0.1902-0.025-0.11550.18430.1520.1006-23.1321-9.388566.7723
640-1.192-0.91950-2.15472.413-0.13720.3220.10470.3220.0438-0.29290.1047-0.29290.0934-0.0103-0.0021-0.14750.06050.14710.0431-22.3793-16.587274.3253
650.2495-2.4311-0.68880-0.70.40310.2143-0.08860.2497-0.08860.11560.19680.24970.1968-0.32990.0130.0519-0.02160.06970.11160.0295-33.4524-18.141561.9533
661.4045-2.9104-0.69480-1.30200.2649-0.41170.5441-0.4117-0.27940.11860.54410.11860.01450.0819-0.1239-0.09080.04320.0791-0.0274-25.8695-25.607385.8026
671.739-0.12811.12390.0149-2.91040-0.05380.2773-0.0920.27730.1971-0.1816-0.092-0.1816-0.1433-0.01990.0951-0.02830.1558-0.032-0.0278-52.3086-29.416101.145
681.05310.6853-1.55141.23060.21450-0.05310.25030.03510.25030.0389-0.07860.0351-0.07860.01410.0834-0.0654-0.06180.0509-0.0059-0.0341-39.2378-33.465294.527
692.6913-1.9129-1.01260-2.100500.13760.1060.12880.106-0.3499-0.18960.1288-0.18960.21220.183-0.11720.02840.059-0.0833-0.1736-44.9527-39.944193.5205
7002.91042.91040-2.91040-0.0787-0.3385-0.5244-0.33850.1515-0.5442-0.5244-0.5442-0.07280.1133-0.0831-0.06920.0440.0104-0.0338-31.9771-21.376588.0971
710.0351-0.3528-0.9820.6923-0.10240-0.0477-0.54420.1942-0.5442-0.28590.23280.19420.23280.33360.0281-0.09590.010.21620.0201-0.1431-53.3514-37.747697.9029
725.52832.9104-2.910400.06821.66570.2398-0.02090.029-0.0209-0.11650.13280.0290.1328-0.12340.16540.07680.0474-0.0427-0.0434-0.0207-42.3603-39.272101.564
731.90750.5048-0.87510.41621.78920-0.08130.07510.14740.0751-0.06980.01330.14740.01330.15110.24380.07780.01350.0140.0546-0.1483-39.7927-36.1565104.92
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|334 - A|349 }A334 - 349
2X-RAY DIFFRACTION2{ A|350 - A|364 }A350 - 364
3X-RAY DIFFRACTION3{ A|365 - A|380 }A365 - 380
4X-RAY DIFFRACTION4{ A|381 - A|393 }A381 - 393
5X-RAY DIFFRACTION5{ A|394 - A|409 }A394 - 409
6X-RAY DIFFRACTION6{ A|410 - A|442 }A410 - 442
7X-RAY DIFFRACTION7{ A|443 - A|459 }A443 - 459
8X-RAY DIFFRACTION8{ A|460 - A|494 }A460 - 494
9X-RAY DIFFRACTION9{ A|495 - A|528 }A495 - 528
10X-RAY DIFFRACTION10{ B|334 - B|358 }B334 - 358
11X-RAY DIFFRACTION11{ B|359 - B|393 }B359 - 393
12X-RAY DIFFRACTION12{ B|394 - B|409 }B394 - 409
13X-RAY DIFFRACTION13{ B|410 - B|459 }B410 - 459
14X-RAY DIFFRACTION14{ B|460 - B|479 }B460 - 479
15X-RAY DIFFRACTION15{ B|480 - B|516 }B480 - 516
16X-RAY DIFFRACTION16{ B|517 - B|528 }B517 - 528
17X-RAY DIFFRACTION17{ C|1 - C|82 }C1 - 82
18X-RAY DIFFRACTION19{ C|135 - C|215 }C135 - 215
19X-RAY DIFFRACTION20{ D|1 - D|25 }D1 - 25
20X-RAY DIFFRACTION21{ D|26 - D|48 }D26 - 48
21X-RAY DIFFRACTION22{ D|49 - D|69 }D49 - 69
22X-RAY DIFFRACTION23{ D|70 - D|83 }D70 - 83
23X-RAY DIFFRACTION24{ D|84 - D|101 }D84 - 101
24X-RAY DIFFRACTION25{ D|102 - D|113 }D102 - 113
25X-RAY DIFFRACTION26{ D|114 - D|128 }D114 - 128
26X-RAY DIFFRACTION27{ D|129 - D|150 }D129 - 150
27X-RAY DIFFRACTION28{ D|151 - D|163 }D151 - 163
28X-RAY DIFFRACTION29{ D|164 - D|174 }D164 - 174
29X-RAY DIFFRACTION30{ D|175 - D|188 }D175 - 188
30X-RAY DIFFRACTION31{ D|189 - D|198 }D189 - 198
31X-RAY DIFFRACTION32{ D|199 - D|214 }D199 - 214
32X-RAY DIFFRACTION33{ E|334 - E|358 }E334 - 358
33X-RAY DIFFRACTION34{ E|359 - E|409 }E359 - 409
34X-RAY DIFFRACTION35{ E|410 - E|437 }E410 - 437
35X-RAY DIFFRACTION36{ E|438 - E|451 }E438 - 451
36X-RAY DIFFRACTION37{ E|452 - E|528 }E452 - 528
37X-RAY DIFFRACTION38{ F|1 - F|33 }F1 - 33
38X-RAY DIFFRACTION39{ F|34 - F|59 }F34 - 59
39X-RAY DIFFRACTION40{ F|60 - F|82 }F60 - 82
40X-RAY DIFFRACTION42{ F|120 - F|134 }F120 - 134
41X-RAY DIFFRACTION43{ F|135 - F|145 }F135 - 145
42X-RAY DIFFRACTION44{ F|146 - F|157 }F146 - 157
43X-RAY DIFFRACTION45{ F|158 - F|203 }F158 - 203
44X-RAY DIFFRACTION46{ F|204 - F|215 }F204 - 215
45X-RAY DIFFRACTION47{ G|1 - G|18 }G1 - 18
46X-RAY DIFFRACTION48{ G|19 - G|61 }G19 - 61
47X-RAY DIFFRACTION49{ G|62 - G|102 }G62 - 102
48X-RAY DIFFRACTION50{ G|103 - G|113 }G103 - 113
49X-RAY DIFFRACTION51{ G|114 - G|128 }G114 - 128
50X-RAY DIFFRACTION52{ G|129 - G|150 }G129 - 150
51X-RAY DIFFRACTION53{ G|151 - G|163 }G151 - 163
52X-RAY DIFFRACTION54{ G|164 - G|174 }G164 - 174
53X-RAY DIFFRACTION55{ G|175 - G|198 }G175 - 198
54X-RAY DIFFRACTION56{ G|199 - G|214 }G199 - 214
55X-RAY DIFFRACTION57{ H|1 - H|82 }H1 - 82
56X-RAY DIFFRACTION59{ H|125 - H|143 }H125 - 143
57X-RAY DIFFRACTION60{ H|144 - H|215 }H144 - 215
58X-RAY DIFFRACTION61{ L|1 - L|25 }L1 - 25
59X-RAY DIFFRACTION62{ L|26 - L|48 }L26 - 48
60X-RAY DIFFRACTION63{ L|49 - L|69 }L49 - 69
61X-RAY DIFFRACTION64{ L|70 - L|83 }L70 - 83
62X-RAY DIFFRACTION65{ L|84 - L|101 }L84 - 101
63X-RAY DIFFRACTION66{ L|102 - L|113 }L102 - 113
64X-RAY DIFFRACTION67{ L|114 - L|128 }L114 - 128
65X-RAY DIFFRACTION68{ L|129 - L|150 }L129 - 150
66X-RAY DIFFRACTION69{ L|151 - L|163 }L151 - 163
67X-RAY DIFFRACTION70{ L|164 - L|174 }L164 - 174
68X-RAY DIFFRACTION71{ L|175 - L|188 }L175 - 188
69X-RAY DIFFRACTION72{ L|189 - L|198 }L189 - 198
70X-RAY DIFFRACTION73{ L|199 - L|214 }L199 - 214

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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