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- PDB-7elx: The crystal structure of CTLA-4 and Fab -

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基本情報

登録情報
データベース: PDB / ID: 7elx
タイトルThe crystal structure of CTLA-4 and Fab
要素
  • Cytotoxic T-lymphocyte protein 4
  • heavy chain of Fab
  • light chain of Fab
キーワードAPOPTOSIS / complex
機能・相同性
機能・相同性情報


protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response ...protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response / positive regulation of apoptotic process / immune response / external side of plasma membrane / DNA damage response / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane
類似検索 - 分子機能
Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
Cytotoxic T-lymphocyte protein 4
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.14 Å
データ登録者Yu, X.J. / Wang, L. / Yu, C.F.
引用ジャーナル: To Be Published
タイトル: The crystal structure of CTLA-4 and Fab
著者: Yu, X.J. / Yu, C.F.
履歴
登録2021年4月12日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年6月30日Provider: repository / タイプ: Initial release
改定 1.12023年11月29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 / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
H: heavy chain of Fab
L: light chain of Fab
h: heavy chain of Fab
l: light chain of Fab
c: Cytotoxic T-lymphocyte protein 4
C: Cytotoxic T-lymphocyte protein 4


分子量 (理論値)分子数
合計 (水以外)181,3526
ポリマ－181,3526
非ポリマー00
水11,385632
1
H: heavy chain of Fab
L: light chain of Fab
C: Cytotoxic T-lymphocyte protein 4


分子量 (理論値)分子数
合計 (水以外)90,6763
ポリマ－90,6763
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
h: heavy chain of Fab
l: light chain of Fab
c: Cytotoxic T-lymphocyte protein 4


分子量 (理論値)分子数
合計 (水以外)90,6763
ポリマ－90,6763
非ポリマー00
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)95.923, 196.921, 148.389
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDモデル要素
11h-1-

GLN

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain C and (resid 2 through 15 or resid 17...
21(chain c and (resid 2 through 15 or resid 17...
12(chain H and (resid 1 through 42 or resid 44...
22(chain h and (resid 1 through 42 or resid 44...
13(chain L and (resid 1 through 126 or resid 128...
23(chain l and (resid 1 through 126 or resid 128...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALASERSER(chain C and (resid 2 through 15 or resid 17...CF2 - 152 - 15
121GLYGLYVALVAL(chain C and (resid 2 through 15 or resid 17...CF17 - 7717 - 77
131LEULEUGLYGLY(chain C and (resid 2 through 15 or resid 17...CF79 - 8379 - 83
141ASPASPILEILE(chain C and (resid 2 through 15 or resid 17...CF88 - 11788 - 117
211ALAALASERSER(chain c and (resid 2 through 15 or resid 17...cE2 - 152 - 15
221GLYGLYVALVAL(chain c and (resid 2 through 15 or resid 17...cE17 - 7717 - 77
231LEULEUGLYGLY(chain c and (resid 2 through 15 or resid 17...cE79 - 8379 - 83
241ASPASPILEILE(chain c and (resid 2 through 15 or resid 17...cE88 - 11788 - 117
112GLNGLNGLYGLY(chain H and (resid 1 through 42 or resid 44...HA1 - 4220 - 61
122GLYGLYVALVAL(chain H and (resid 1 through 42 or resid 44...HA44 - 6463 - 83
132GLNGLNPROPRO(chain H and (resid 1 through 42 or resid 44...HA1 - 21820 - 237
142GLNGLNPROPRO(chain H and (resid 1 through 42 or resid 44...HA1 - 21820 - 237
152GLYGLYLYSLYS(chain H and (resid 1 through 42 or resid 44...HA123 - 214142 - 233
162VALVALPROPRO(chain H and (resid 1 through 42 or resid 44...HA216 - 218235 - 237
212GLNGLNGLYGLY(chain h and (resid 1 through 42 or resid 44...hC1 - 4220 - 61
222GLYGLYVALVAL(chain h and (resid 1 through 42 or resid 44...hC44 - 6463 - 83
232GLNGLNPROPRO(chain h and (resid 1 through 42 or resid 44...hC1 - 21820 - 237
242VALVALVALVAL(chain h and (resid 1 through 42 or resid 44...hC221
252VALVALPROPRO(chain h and (resid 1 through 42 or resid 44...hC216 - 218235 - 237
113GLUGLULEULEU(chain L and (resid 1 through 126 or resid 128...LB1 - 12621 - 146
123SERSERARGARG(chain L and (resid 1 through 126 or resid 128...LB128 - 143148 - 163
133ALAALAVALVAL(chain L and (resid 1 through 126 or resid 128...LB145 - 147165 - 167
143TRPTRPSERSER(chain L and (resid 1 through 126 or resid 128...LB149 - 169169 - 189
153ASPASPARGARG(chain L and (resid 1 through 126 or resid 128...LB171 - 212191 - 232
213GLUGLULEULEU(chain l and (resid 1 through 126 or resid 128...lD1 - 12621 - 146
223SERSERARGARG(chain l and (resid 1 through 126 or resid 128...lD128 - 143148 - 163
233ALAALAALAALA(chain l and (resid 1 through 126 or resid 128...lD145165
243TRPTRPSERSER(chain l and (resid 1 through 126 or resid 128...lD149 - 169169 - 189
253ASPASPARGARG(chain l and (resid 1 through 126 or resid 128...lD171 - 212191 - 232

NCSアンサンブル:
ID
1
2
3

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要素

#1: 抗体 heavy chain of Fab


分子量: 51448.055 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
#2: 抗体 light chain of Fab


分子量: 25717.693 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
#3: タンパク質 Cytotoxic T-lymphocyte protein 4 / Cytotoxic T-lymphocyte-associated antigen 4 / CTLA-4


分子量: 13510.340 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CTLA4, CD152 / 発現宿主: Escherichia phage EcSzw-2 (ファージ) / 参照: UniProt: P16410
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 632 / 由来タイプ: 天然 / 式: H2O

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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: 1.93 Å3/Da / 溶媒含有率: 36.33 %
結晶化温度: 285 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: PEG8000 10%, 0.1M Na Citrate 0.1M (NH4)2SO4

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL17U / 波長: 0.9791 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2020年9月16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: 0.9791 Å / 相対比: 1
反射解像度: 2.14→45.64 Å / Num. obs: 76857 / % possible obs: 100 % / 冗長度: 7.8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 27.12
反射 シェル解像度: 2.14→2.18 Å / Rmerge(I) obs: 0.101

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類NB
HKL-2000データ削減
HKL-2000データスケーリング
PHASER位相決定
PHENIX1.18.2_3874精密化
PDB_EXTRACT3.27データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 6rp8

6rp8


解像度: 2.14→44.2 Å / SU ML: 0.23 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 22.57 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2172 1996 2.6 %
Rwork0.1768 74861 -
obs0.1778 76857 99.72 %
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 max: 141.98 Å2 / Biso mean: 48.4125 Å2 / Biso min: 20.63 Å2
精密化ステップサイクル: final / 解像度: 2.14→44.2 Å
タンパク質核酸リガンド溶媒全体
原子数8204 0 0 632 8836
Biso mean---47.99 -
残基数----1077
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11C622X-RAY DIFFRACTION3.551TORSIONAL
12c622X-RAY DIFFRACTION3.551TORSIONAL
21H1220X-RAY DIFFRACTION3.551TORSIONAL
22h1220X-RAY DIFFRACTION3.551TORSIONAL
31L1236X-RAY DIFFRACTION3.551TORSIONAL
32l1236X-RAY DIFFRACTION3.551TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.14-2.20.27291380.22265190532898
2.2-2.260.22121410.214752755416100
2.26-2.320.2981420.203953355477100
2.32-2.40.25491420.195553115453100
2.4-2.480.27451410.195753095450100
2.48-2.580.2341420.195652935435100
2.58-2.70.25651420.193653515493100
2.7-2.840.23681420.183253375479100
2.84-3.020.24661420.188353415483100
3.02-3.260.26251430.18953495492100
3.26-3.580.21651440.171353805524100
3.58-4.10.20641440.162554095553100
4.1-5.170.15931450.138254185563100
5.17-44.20.19451480.18655563571199
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)
13.84271.6594-3.34282.3174-0.24963.5867-0.03870.3152-0.3828-0.48260.2350.34470.454-0.6925-0.20480.43820.0658-0.10870.2294-0.07410.42222.1701-44.6054-19.8164
21.80990.1514-0.24682.3999-0.71152.06520.16470.1392-0.1731-0.1651-0.0867-0.09120.22920.2312-0.0460.4080.1273-0.08450.2975-0.05460.309210.6883-35.6313-20.86
31.78830.7593-0.90152.4759-1.33161.44710.07690.0091-0.1887-0.099-0.061-0.04780.31310.2023-0.02770.41510.1014-0.1280.2895-0.06970.29198.7458-37.6002-18.9429
48.06932.0835-1.39670.98080.03770.6694-0.5556-0.2357-0.8701-0.01760.0063-0.16660.49540.02390.5420.49770.0849-0.02420.2594-0.00660.4404-7.6543-48.6402-10.6372
56.0682-1.43941.31625.6212-2.63763.2032-0.232-0.2972-0.11550.03730.36780.76630.0096-0.4656-0.12590.3123-0.0451-0.02940.2976-0.01380.3603-28.5072-42.9468-9.2239
62.9706-0.224-0.79284.25380.29892.8122-0.0730.296-0.0884-0.4148-0.06950.44550.2615-0.41760.09240.2982-0.0696-0.00630.3309-0.00730.304-25.4337-40.1221-14.6478
72.7342-3.59660.65816.44890.53944.1065-0.09171.2417-0.5166-0.6652-0.26470.42880.3084-0.34740.24380.3823-0.0976-0.01180.4308-0.09120.3511-26.0968-48.6147-17.1964
84.3335-0.01590.48912.13050.03762.25250.1264-0.26910.19270.25460.08410.04880.0760.0672-0.14340.33580.0127-0.01330.2221-0.04730.2575-1.2236-14.0542-13.5712
95.62291.1393-1.94445.5812-0.84181.9448-0.25410.12290.105-0.45390.12440.58110.2347-0.07290.11680.38180.0722-0.09980.2507-0.04050.25390.8332-22.2722-22.4461
102.2482-1.61841.03446.94640.47196.87190.24920.69010.0573-0.57840.052-0.5-0.19150.3541-0.30160.22380.0213-0.02020.2263-0.02910.23672.1862-15.2357-29.6221
118.27820.96963.55592.0896-0.33023.8360.24920.17090.31150.32360.0073-0.04510.24560.1896-0.27210.29910.046-0.0240.2154-0.01320.31972.4059-10.5577-19.4975
128.2209-0.9129-0.20614.64450.13112.62910.12890.1663-0.4046-0.04320.14850.54050.2149-0.0838-0.24370.2953-0.0182-0.01750.2016-0.03890.2222-6.222-18.0731-22.1709
133.67690.5681-1.22910.4004-0.13360.81180.1103-0.08070.08630.13970.08610.0860.1174-0.024-0.17650.31520.0293-0.04380.2451-0.00150.3033-6.0927-20.5024-14.1335
141.94-0.1171-1.66285.1-2.88484.1751-0.09960.0169-0.1203-0.08660.00960.40950.4064-0.13150.08760.2737-0.0483-0.020.32370.00860.3559-27.6313-34.6388-2.4792
156.45732.1627-5.03842.6371-1.48863.94890.1134-0.78070.02150.3005-0.2040.0652-0.27240.32130.12070.3845-0.0216-0.01250.3767-0.01470.3393-22.3374-33.64035.1079
161.73731.1596-2.20955.0012-2.70773.9029-0.022-0.07850.11630.30230.07450.36140.0904-0.1994-0.08480.2605-0.071-0.01030.35320.00480.369-28.053-31.7553-0.8889
174.3316-1.2524-2.92121.7070.84734.6978-0.3268-0.1381-0.44650.5230.10480.0750.7020.17510.23240.4962-0.0514-0.01280.2844-0.00170.3823-2.3253-30.117217.5758
183.8894-0.31341.78782.6470.25512.68750.0330.3238-0.22760.07550.08550.08870.2283-0.1277-0.10590.4648-0.01850.02620.2335-0.04790.2834-4.8841-21.50311.0413
194.94070.0316-2.78761.26840.23064.8443-0.10280.3106-0.4489-0.4471-0.04390.30250.8696-0.61090.1620.6193-0.0589-0.04240.2573-0.08050.3099-7.4689-27.98628.7956
202.6352-1.0706-0.58454.11552.32181.26510.05580.0365-0.24890.00340.0221-0.04640.227-0.1364-0.06670.4149-0.018-0.0010.22380.01520.2765-1.5187-24.186814.5223
213.48560.06012.69281.0943-0.6032.55270.46020.1495-0.20040.05940.1547-0.44090.81560.314-0.52690.52250.0557-0.08540.2626-0.10610.357515.0336-34.64977.6354
223.3019-0.69980.88824.1767-0.03213.11840.16830.16060.03530.19640.1651-0.76680.29610.4829-0.29470.39330.0952-0.06570.4756-0.15240.492329.6532-29.00116.3762
234.4872-0.1571-0.75332.0834-0.77790.47470.5201-0.2306-0.21221.0527-0.0561-1.21331.04560.9958-0.38530.67350.2096-0.29870.659-0.18640.894437.455-26.929522.6489
248.71473.79444.16773.72751.58345.04540.1285-0.5829-0.4130.37740.1995-1.1980.0710.2532-0.36690.38630.125-0.1180.5049-0.15950.644529.9511-36.947220.2791
256.48680.15932.66232.1457-0.20014.29070.0950.5169-0.0747-0.23570.067-0.2237-0.04460.2826-0.12710.3039-0.00990.03840.213-0.03820.2556.7764-1.409714.0548
267.3996-2.4685-1.27986.68150.08373.3947-0.5217-0.2131-0.11860.46980.4410.09090.23080.00810.04410.3955-0.0247-0.02610.2278-0.01130.25392.5869-10.695320.8652
273.57411.83263.91827.77111.5594.27940.0316-0.67240.13880.8916-0.2740.6462-0.0156-0.56280.25060.3813-0.05180.00750.31570.02680.3183-0.8577-4.468828.085
285.6353-1.04184.09952.26630.20527.9093-0.0967-0.04230.4004-0.04120.0344-0.1619-0.14630.12780.08320.29950.0001-0.02570.2566-0.02030.27691.6371.367918.978
296.097-0.08451.29352.1717-1.48661.79610.0059-0.1744-0.23550.1880.1089-0.22240.13580.2101-0.10060.39480.05590.01510.2273-0.00860.31489.3832-6.516423.1941
300.31310.58040.38151.22450.31341.0533-0.18050.2831-0.2059-0.24230.2932-0.66450.12910.4858-0.09660.36480.01870.13770.434-0.18270.56523.0176-16.485113.3678
311.0282-2.3505-1.19415.81122.64312.3449-0.07130.4882-0.0114-0.65320.3392-0.9416-0.21020.5818-0.19180.4169-0.04570.14350.7768-0.19020.798734.1712-15.36810.1848
326.69480.4713-4.09450.54230.17994.2201-0.39461.7172-0.4633-0.38310.197-1.3973-0.03130.13780.04890.678-0.04360.23360.9705-0.15040.872334.3967-18.20041.2079
335.0999-3.7606-3.14616.08592.92164.8152-0.19130.6046-0.3421-0.35710.1729-0.79670.29640.36940.12280.4334-0.03090.11130.585-0.17530.675332.6633-20.719811.0754
341.4793-1.2134-1.67111.3910.50974.0430.19541.3325-0.2532-0.5408-0.0828-1.0833-0.2730.5169-0.34480.5085-0.07920.35961.0985-0.31361.187642.7775-14.40537.2005
356.4893-0.1668-4.30642.10461.80834.24140.2560.65520.4055-0.40890.0773-0.1151-0.1956-0.3596-0.26740.59350.0623-0.10040.5190.00870.4359-19.7083-2.151413.6431
362.7907-1.53780.0313.51281.19484.34260.0040.0709-0.2088-0.3212-0.10570.3322-0.2593-0.95490.07920.3666-0.0007-0.11350.4221-0.04650.4447-28.9743-5.35621.8814
373.6733-1.2933-0.92745.91132.51869.049-0.1087-0.2455-0.021-0.13840.2596-0.2804-0.3226-0.0228-0.20150.3493-0.07890.07180.43940.00910.4406-20.5596-13.667623.8895
386.13391.19821.34035.72182.11262.7235-0.00151.1541-0.213-0.33030.4010.91.2704-0.9922-0.42140.7421-0.24030.00550.9706-0.02070.7309-31.5262-17.672918.5379
392.624-0.1881.95662.5068-1.06142.0454-0.0898-0.2327-0.36490.07150.22370.52770.1632-1.855-0.02510.4409-0.0333-0.0730.7875-0.08060.5828-30.543-9.744327.1423
400.9931-0.6607-1.47782.51672.92438.15090.0982-0.12740.3686-0.31170.00540.0721-0.5169-0.1522-0.05540.3032-0.0657-0.03530.3708-0.03570.3755-18.3941-10.264916.0347
412.2223.04070.25365.6519-1.30692.17550.6737-1.0452-0.13370.8823-0.15630.4668-1.08020.3083-0.37970.76970.1033-0.05150.6345-0.0430.4916-26.7717-2.046635.0326
425.34690.2401-3.973.4587-0.86645.11290.4394-0.89910.20030.4519-0.41190.1951-0.68980.2305-0.00420.5575-0.0952-0.08910.6286-0.05790.57323.799-13.9448-19.0894
433.5510.1027-0.02294.9645-3.17725.9077-0.13310.08120.27570.003-0.0667-0.3354-0.18210.19050.30490.3350.0662-0.02290.3872-0.05160.505827.6813-17.2892-30.3642
446.8432-2.63163.29062.648-2.61882.9408-0.1829-0.6877-0.85680.11160.4862-0.2056-0.54580.1624-0.10890.49860.15340.02910.65010.00440.538724.8575-25.5736-31.364
455.8668-1.92490.94096.587-3.85373.28540.1021-0.2583-0.6845-0.1038-0.4462-1.41920.84881.52880.53510.81960.22690.10911.32570.21921.000135.1319-27.4285-29.8721
464.5731-0.6852.81142.5191-0.85888.07850.01580.37110.4218-0.1008-0.528-0.10990.11730.90970.50290.32340.0694-0.0250.71070.09160.608531.5557-18.6059-35.7252
471.29631.0528-2.59772.8807-1.3995.34850.2278-0.12620.07010.2568-0.2087-0.2194-0.07860.40860.07680.28630.0891-0.10380.4342-0.00720.368122.4571-21.6456-22.7866
487.3728-2.23543.66175.18710.75582.59270.0890.63720.3551-0.7584-0.498-1.3539-1.0216-0.20490.48730.55770.05870.1290.51090.13440.702526.1178-9.6445-41.1144
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )H1 - 17
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 60 )H18 - 60
3X-RAY DIFFRACTION3chain 'H' and (resid 61 through 111 )H61 - 111
4X-RAY DIFFRACTION4chain 'H' and (resid 112 through 124 )H112 - 124
5X-RAY DIFFRACTION5chain 'H' and (resid 125 through 150 )H125 - 150
6X-RAY DIFFRACTION6chain 'H' and (resid 151 through 198 )H151 - 198
7X-RAY DIFFRACTION7chain 'H' and (resid 199 through 218 )H199 - 218
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 30 )L1 - 30
9X-RAY DIFFRACTION9chain 'L' and (resid 31 through 49 )L31 - 49
10X-RAY DIFFRACTION10chain 'L' and (resid 50 through 62 )L50 - 62
11X-RAY DIFFRACTION11chain 'L' and (resid 63 through 76 )L63 - 76
12X-RAY DIFFRACTION12chain 'L' and (resid 77 through 91 )L77 - 91
13X-RAY DIFFRACTION13chain 'L' and (resid 92 through 114 )L92 - 114
14X-RAY DIFFRACTION14chain 'L' and (resid 115 through 151 )L115 - 151
15X-RAY DIFFRACTION15chain 'L' and (resid 152 through 164 )L152 - 164
16X-RAY DIFFRACTION16chain 'L' and (resid 165 through 212 )L165 - 212
17X-RAY DIFFRACTION17chain 'h' and (resid 1 through 33 )h1 - 33
18X-RAY DIFFRACTION18chain 'h' and (resid 34 through 60 )h34 - 60
19X-RAY DIFFRACTION19chain 'h' and (resid 61 through 76 )h61 - 76
20X-RAY DIFFRACTION20chain 'h' and (resid 77 through 111 )h77 - 111
21X-RAY DIFFRACTION21chain 'h' and (resid 112 through 124 )h112 - 124
22X-RAY DIFFRACTION22chain 'h' and (resid 125 through 180 )h125 - 180
23X-RAY DIFFRACTION23chain 'h' and (resid 181 through 198 )h181 - 198
24X-RAY DIFFRACTION24chain 'h' and (resid 199 through 218 )h199 - 218
25X-RAY DIFFRACTION25chain 'l' and (resid 1 through 30 )l1 - 30
26X-RAY DIFFRACTION26chain 'l' and (resid 31 through 49 )l31 - 49
27X-RAY DIFFRACTION27chain 'l' and (resid 50 through 62 )l50 - 62
28X-RAY DIFFRACTION28chain 'l' and (resid 63 through 76 )l63 - 76
29X-RAY DIFFRACTION29chain 'l' and (resid 77 through 91 )l77 - 91
30X-RAY DIFFRACTION30chain 'l' and (resid 92 through 129 )l92 - 129
31X-RAY DIFFRACTION31chain 'l' and (resid 130 through 151 )l130 - 151
32X-RAY DIFFRACTION32chain 'l' and (resid 152 through 164 )l152 - 164
33X-RAY DIFFRACTION33chain 'l' and (resid 165 through 189 )l165 - 189
34X-RAY DIFFRACTION34chain 'l' and (resid 190 through 212 )l190 - 212
35X-RAY DIFFRACTION35chain 'c' and (resid 1 through 7 )c1 - 7
36X-RAY DIFFRACTION36chain 'c' and (resid 8 through 32 )c8 - 32
37X-RAY DIFFRACTION37chain 'c' and (resid 33 through 55 )c33 - 55
38X-RAY DIFFRACTION38chain 'c' and (resid 56 through 67 )c56 - 67
39X-RAY DIFFRACTION39chain 'c' and (resid 68 through 89 )c68 - 89
40X-RAY DIFFRACTION40chain 'c' and (resid 90 through 111 )c90 - 111
41X-RAY DIFFRACTION41chain 'c' and (resid 112 through 117 )c112 - 117
42X-RAY DIFFRACTION42chain 'C' and (resid 1 through 7 )C1 - 7
43X-RAY DIFFRACTION43chain 'C' and (resid 8 through 44 )C8 - 44
44X-RAY DIFFRACTION44chain 'C' and (resid 45 through 55 )C45 - 55
45X-RAY DIFFRACTION45chain 'C' and (resid 56 through 67 )C56 - 67
46X-RAY DIFFRACTION46chain 'C' and (resid 68 through 89 )C68 - 89
47X-RAY DIFFRACTION47chain 'C' and (resid 90 through 111 )C90 - 111
48X-RAY DIFFRACTION48chain 'C' and (resid 112 through 117 )C112 - 117

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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