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- PDB-6job: Ferritin variant with "GMG" motif -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 6job
タイトルFerritin variant with "GMG" motif
要素Ferritin heavy chain
キーワードOXIDOREDUCTASE / amyloidogenic motifs / protein nanocage / protein surfaces redesign / pH-manipulated / 2D ordered arrays / 3D cubic-like arrays
機能・相同性
機能・相同性情報


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / autophagosome / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Ferritin heavy chain
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / 溶液散乱 / シンクロトロン / 解像度: 2.93 Å
データ登録者Zheng, B.W. / Zhou, K. / Zhang, T. / Lv, C. / Wang, H. / Zhao, G.
資金援助 中国, 1件
組織認可番号国
National Natural Science Foundation of China31730069 中国
引用ジャーナル: To Be Published
タイトル: Self-assembly of protein nanocage into designed 2D and 3D networks by grafting amyloidogenic motifs on the exterior surfaces.
著者: Zheng, B.W. / Zhou, K. / Zhang, T. / Lv, C. / Wang, H. / Zhao, G.
履歴
登録2019年3月20日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02020年3月25日Provider: repository / タイプ: Initial release
改定 1.12024年3月27日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain


分子量 (理論値)分子数
合計 (水以外)255,24912
ポリマ－255,24912
非ポリマー00
水00
1
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain

A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain

G: Ferritin heavy chain
H: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain

G: Ferritin heavy chain
H: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain

E: Ferritin heavy chain
F: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain

E: Ferritin heavy chain
F: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain


分子量 (理論値)分子数
合計 (水以外)510,49824
ポリマ－510,49824
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation3_454-y-1/2,x+1/2,z-1/21
crystal symmetry operation5_455-x-1/2,y+1/2,-z+1/21
crystal symmetry operation4_445y-1/2,-x-1/2,z+1/21
crystal symmetry operation6_554x+1/2,-y+1/2,-z-1/21
Buried area98400 Å2
ΔGint-408 kcal/mol
Surface area143910 Å2
手法PISA
単位格子
Length a, b, c (Å)219.170, 219.170, 147.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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要素

#1: タンパク質
Ferritin heavy chain / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


分子量: 21270.756 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P02794, ferroxidase

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実験情報

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実験

実験
手法使用した結晶の数
X線回折1
溶液散乱

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試料調製

結晶マシュー密度: 3.48 Å3/Da / 溶媒含有率: 64.66 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: sodium citrate tribase dihydrate, 1,6-Hexanediol

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データ収集

回折平均測定温度: 77.15 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: BL17U1 / 波長: 0.97894 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2018年11月9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: 0.97894 Å / 相対比: 1
反射解像度: 2.93→107.014 Å / Num. obs: 76098 / % possible obs: 98 % / 冗長度: 13.2 % / Net I/σ(I): 7
反射 シェル解像度: 2.97→3.05 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.14_3260: ???)精密化
HKL-2000データ削減
HKL-2000データスケーリング
精密化解像度: 2.93→107.014 Å / SU ML: 0.53 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 47 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3677 3835 5.07 %
Rwork0.284 --
obs0.2882 75679 97.53 %
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: 2.93→107.014 Å
タンパク質核酸リガンド溶媒全体
原子数16956 0 0 0 16956
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01217292
X-RAY DIFFRACTIONf_angle_d1.56923280
X-RAY DIFFRACTIONf_dihedral_angle_d10.48210416
X-RAY DIFFRACTIONf_chiral_restr0.0782460
X-RAY DIFFRACTIONf_plane_restr0.013060
LS精密化 シェル解像度: 2.93→2.9671 Å
Rfactor反射数%反射
Rfree0.4188 145 -
Rwork0.383 --
obs-2704 100 %
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)
10.7573-0.35160.30030.1805-0.810.1086-0.03670.14380.5849-0.0556-0.31280.13360.31630.3474-0.00290.52230.04240.03950.4974-0.10210.5092-50.73630.7091-7.8424
21.3153-0.02830.0167-1.1980.93220.7440.0276-0.02790.305-0.0354-0.12860.0428-0.03890.02960.00190.60880.06680.00640.5218-0.05550.5764-52.12685.5771-7.058
30.7762-1.6754-1.00591.37720.38390.40360.29730.1742-0.26330.2141-0.1013-0.00240.24270.08980.0050.5032-0.0287-0.0490.39550.01230.4259-42.3866-1.1612-13.0718
40.1988-0.13230.90160.1159-1.67130.0109-0.41490.36850.13010.21080.1787-0.07150.154-0.0988-0.00120.57820.0039-0.02770.5803-0.11090.405-41.46948.8027-16.9152
5-0.0450.2563-0.0840.36350.0090.29391.158-0.5929-0.2616-0.26650.11640.57030.1013-0.53330.02160.6758-0.0453-0.08010.5139-0.03250.54-23.612812.4051-0.7481
6-0.09510.1876-0.2920.8363-0.09920.82020.4483-0.2747-0.1089-0.3029-0.2801-0.0350.7968-0.35490.00220.52920.025-0.00730.43820.01060.426-50.7064-0.026711.1404
70.2366-0.27150.429-0.8601-0.07010.17450.17060.07080.1509-0.0964-0.2124-0.20.21040.12420.00140.45660.0531-0.03580.45550.05720.6202-58.20428.24714.0978
82.18490.1757-0.8882.0127-0.65580.3644-0.0886-0.4885-0.05620.09010.0597-0.1336-0.0313-0.14360.00020.58530.06110.01150.53320.00070.4796-57.16390.205114.2426
90.3673-0.17040.6148-0.3814-0.51270.88170.37160.0113-0.5840.039-0.04090.10030.0256-0.2765-0.0010.58590.043-0.06110.5902-0.00570.4904-75.742610.72257.8046
10-0.96480.599-0.18751.38720.37010.5339-0.11480.05110.1386-0.0455-0.0514-0.20960.3748-0.467-0.00030.32060.0264-0.00970.5421-0.03040.6514-104.886853.98-10.8625
11-0.31020.9729-0.04661.0017-0.87190.1453-0.4714-0.11980.15110.30470.1936-0.5663-0.2598-0.2328-0.00010.58440.0718-0.0110.47540.03260.5168-96.337246.4778-3.9183
120.2446-0.3796-1.06760.9071.14570.5836-0.1364-0.35450.04951.0401-0.06950.6647-0.47810.2977-0.00130.44990.013-0.1320.6653-0.00810.6099-109.004148.3593-3.2856
130.6559-0.26260.60120.87610.35790.2954-0.2644-0.10840.0577-0.14230.69570.36650.1896-0.03870.0080.4593-0.09280.02770.47880.05540.5123-104.832444.089-17.6822
140.8410.1403-0.97580.1553-0.82370.2888-0.05260.0482-0.0083-0.4194-0.3855-1.10470.1041-0.3491-0.00220.6761-0.0683-0.01520.62320.0140.4848-95.766140.6865-16.5568
150.62570.4366-2.10470.9461-1.61386.20551.42220.37110.35180.4374-0.13960.6789-3.0433-0.44170.50940.16730.3594-0.10940.5373-0.11770.4981-92.087823.7955-0.7482
16-0.3755-0.2565-0.55471.64610.2350.1695-0.1980.035-0.01970.19790.30640.253-0.0373-0.43590.00070.2582-0.0132-0.02330.5284-0.01770.5275-104.803950.724611.094
170.7814-1.15350.2530.8976-0.10.2984-0.42-0.0985-0.0853-0.1272-0.1802-0.89380.02650.1347-0.00010.48130.07640.02490.50240.04170.5242-96.424158.16394.0561
180.0353-0.72930.39790.85560.39170.8805-0.05380.0167-0.10150.2969-0.0906-0.1934-0.0484-0.1062-0.00030.492-0.04280.04410.6653-0.03570.6425-104.446557.235214.1997
19-0.2540.30650.3028-0.0725-0.06780.9732-0.13420.25090.13770.6710.2058-0.2801-0.20860.24940.00040.52880.00390.03040.37510.02390.4111-93.972275.83367.7865
201.0846-0.9782-0.3412-1.24340.97030.77670.9508-0.39010.72840.6681-0.37520.0654-0.63630.28030.13950.5145-0.01330.06240.52730.04320.3623-124.619138.1169-39.0192
211.2148-0.89040.37750.1435-0.8238-0.1917-0.18370.4594-0.40970.10770.10580.15140.3198-0.2212-0.00190.3014-0.1060.01420.3302-0.11260.4524-141.030640.7394-37.6036
221.118-0.3576-0.6731-0.18650.55451.23470.04950.05930.0224-0.1584-0.0244-0.00370.2029-0.1967-00.5263-0.0587-0.01230.5112-0.01060.5413-128.397343.7591-33.5542
230.3894-0.479-1.0258-0.40450.0742-0.3275-0.52250.0650.02280.0490.30990.0906-0.06140.05720.00070.452-0.13370.02450.5750.00920.532-147.364153.848-27.8456
24-0.0297-0.6606-0.10910.585-0.6180.1746-0.3046-0.6581-0.5378-0.12680.0003-0.0598-0.12470.4147-0.00190.4402-0.06150.07780.55320.0280.3494-144.92924.138-34.8875
255.4219-0.82820.45640.2132-0.25660.13821.28052.35181.91370.5441-1.25930.9025-0.4981-1.3167-0.0610.7166-0.1769-0.11650.6488-0.14620.554-122.934630.0604-55.0344
26-0.2410.2342-0.52440.92490.50770.20410.26980.36940.30950.1420.3035-0.0342-0.5852-0.0920.01450.56940.01840.01110.53030.02840.4464-143.01229.4655-45.4937
271.49541.0671-0.75570.3446-0.01772.121-0.0168-0.692-0.7636-0.112-0.25310.6816-0.53120.6635-0.01370.4437-0.00890.09220.46460.02210.7118-140.334225.5825-31.7762
280.9932-0.5797-0.01880.9390.2477-0.4176-0.0922-1.0358-0.1825-0.114-0.1066-0.07490.31750.1474-0.00020.5193-0.00430.04220.58250.03090.4563-139.114115.7727-44.6529
290.1745-0.7955-0.36270.94190.60220.3081-0.39920.1085-0.2951-0.05440.22380.1717-0.0489-0.8036-0.00450.63520.00880.05020.6615-0.01660.8048-157.343119.1589-39.1006
300.46990.355-0.8530.00880.1818-0.00961.20320.84740.2794-0.1202-0.2974-0.5087-0.9103-0.51020.01670.5198-0.05220.04990.7877-0.05450.6118-140.767116.604-56.4572
313.74956.09271.64372.00753.08541.05940.2872-0.7806-0.68061.4786-0.6036-2.0170.6421-0.28380.16780.69360.0248-0.08561.0860.31920.958-123.064314.9937-66.7474
323.60442.31720.65073.37540.15960.29340.7298-1.34590.7427-0.5812-1.93170.4012-0.80810.3557-0.22640.41810.0038-0.00480.672-0.16760.1529-130.489125.2974-65.5008
331.20530.8834-0.9152-0.31810.55950.00370.4020.21350.0785-0.1178-0.24240.03120.17850.26410.01310.49450.0166-0.00140.43010.03670.4678-19.8845-37.877639.0561
341.18860.644-0.46320.1627-0.54190.48340.5531-0.46570.44630.0447-0.4110.14810.3729-0.39450.00080.44940.0570.01450.4484-0.07070.6393-36.2877-40.55637.6634
350.2862-0.32980.3891-0.72170.51012.6507-0.0916-0.1306-0.04660.0040.14880.0183-0.1239-0.02110.00090.4167-0.0824-0.07220.46460.06540.5684-23.6918-43.616733.5758
361.06831.77471.31230.5064-0.0772-0.30360.01290.23510.335-0.06950.03580.1269-0.02750.1697-0.00030.3738-0.001-0.02420.43480.01450.4758-42.6782-53.519627.9144
371.42030.46220.0851-0.30650.6640.66710.02360.44560.4957-0.0939-0.112-0.20550.33870.17-0.00110.5185-0.0587-0.02230.39340.12130.481-36.2994-24.999638.599
380.7622-0.10810.8029-0.5982-0.00220.13920.522-0.43370.46410.0149-0.32720.01851.0572-0.43260.00260.70970.0015-0.12470.52640.0260.4827-39.0975-29.140344.9411
39-0.07680.30360.11520.1780.94430.7574-0.1438-0.2406-0.4284-0.38930.18160.0305-0.48250.19810.00960.5972-0.0479-0.08260.6215-0.02670.8708-29.3564-24.418236.8713
402.53550.56380.12240.78510.8868-0.1970.22390.18760.058-0.1613-0.1588-0.15610.0541-0.07640.0010.43610.0099-0.0060.46170.05540.4321-40.8295-16.258146.9095
410.3722-0.35180.00590.30960.45920.11740.28070.8991-0.5254-0.7679-0.243-1.23740.0031-0.11920.00080.45810.0243-0.02130.61330.09370.5014-23.4734-22.040466.0343
420.83590.05610.99970.49060.49020.53160.13530.06690.09460.4799-0.40810.0137-0.32230.2-0.00120.44180.03560.05180.3859-0.05770.3321-129.825378.3012-38.5714
430.1659-0.71781.0285-0.1543-1.90270.21950.14750.0301-0.189-0.00550.21310.0577-0.1713-0.2286-0.00150.63520.0565-0.0210.5979-0.0130.6172-133.80574.7038-42.477
440.7520.5674-0.46241.0413-0.3599-0.6845-0.0952-0.059-0.08570.18790.0013-0.38190.1789-0.0508-0.00060.5015-0.00210.00310.45830.03310.4708-122.311676.9486-45.4914
450.0796-0.20840.24791.37320.46110.6872-0.60850.2195-0.19611.85930.70150.44370.00080.05490.02020.46560.021-0.06840.4194-0.05290.402-126.826991.0369-65.8065
460.05481.1595-1.18710.4212-0.0298-0.0266-0.0557-0.0788-0.27990.41960.23010.1821-0.0377-0.22610.00670.4685-0.0477-0.040.355-0.06440.4062-142.657592.1166-38.1053
471.21010.38610.05970.6798-0.1777-0.3372-0.163-0.0058-0.01880.09520.29540.1304-0.14430.02560.00050.53650.00130.0110.511-0.09140.3926-143.507682.4984-38.7952
480.1210.94350.82080.73290.86340.07860.17240.21520.1370.1335-0.4373-0.4385-0.07610.29830.00210.32560.08730.110.5612-0.0270.4974-149.636488.4351-29.0542
49-0.60780.34990.41730.4328-2.29270.14770.06850.0267-0.0388-0.2519-0.0852-0.13920.03220.20380.00010.62060.028-0.01970.4710.0250.5631-157.520677.832-31.7995
50-0.6617-1.1694-1.0178-0.09491.06791.2480.0108-0.1840.0717-0.3593-0.06670.0579-0.32870.01020.00060.5707-0.0008-0.0940.40170.00560.5388-89.4477-36.153538.6676
510.283-0.03191.438-0.05581.8649-0.2070.0139-0.05370.07380.67140.2536-0.03350.78950.37880.00420.6267-0.05490.06240.63840.01020.4619-85.3509-39.019844.9808
521.0996-0.111-1.19420.3350.54280.4712-0.08870.46060.0884-0.07050.10110.3671-0.0313-0.0442-0.02410.29920.0472-0.01440.4722-0.02270.5443-90.0965-29.325237.0748
530.69461.05520.39051.62231.0979-0.9294-0.1839-0.0317-0.0202-0.07820.12390.30360.22210.02020.00070.6413-0.01050.01420.4957-0.01990.4757-98.2699-40.742346.9329
540.48620.4142-0.56580.29320.07820.3415-0.4476-0.27131.2456-1.16590.6992-0.51680.16520.37230.01420.6517-0.0194-0.03090.4340.07260.6273-92.3668-23.497465.9841
551.0704-0.3440.41430.4468-0.0109-0.3169-0.2868-0.0703-0.0433-0.31370.17120.5705-0.2190.1542-0.00150.3662-0.04090.09060.32880.03580.3407-76.702-26.672336.4043
560.5855-0.4224-2.87070.83580.56250.9579-0.11350.3692-0.2939-0.01820.07010.1893-0.38820.1922-0.00280.5221-0.004-0.10760.4451-0.03180.498-75.5906-28.807240.8367
570.3396-1.6037-0.41041.55790.13390.6311-0.0922-0.28150.0394-0.26080.3306-0.028-0.04450.13760.0020.4998-0.0203-0.00370.46050.00820.5545-68.4572-24.242532.5974
58-0.4453-0.38110.55710.58641.5556-0.9180.0929-0.1742-0.0599-0.0455-0.09430.4619-0.15670.22150.00030.6305-0.0217-0.01480.4785-0.05280.5688-61.0315-42.419627.7892
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 86 )
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 126 )
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 157 )
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 176 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 41 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 76 )
8X-RAY DIFFRACTION8chain 'B' and (resid 77 through 137 )
9X-RAY DIFFRACTION9chain 'B' and (resid 138 through 176 )
10X-RAY DIFFRACTION10chain 'C' and (resid 5 through 41 )
11X-RAY DIFFRACTION11chain 'C' and (resid 42 through 76 )
12X-RAY DIFFRACTION12chain 'C' and (resid 77 through 95 )
13X-RAY DIFFRACTION13chain 'C' and (resid 96 through 126 )
14X-RAY DIFFRACTION14chain 'C' and (resid 127 through 158 )
15X-RAY DIFFRACTION15chain 'C' and (resid 159 through 176 )
16X-RAY DIFFRACTION16chain 'D' and (resid 5 through 41 )
17X-RAY DIFFRACTION17chain 'D' and (resid 42 through 76 )
18X-RAY DIFFRACTION18chain 'D' and (resid 77 through 137 )
19X-RAY DIFFRACTION19chain 'D' and (resid 138 through 176 )
20X-RAY DIFFRACTION20chain 'E' and (resid 5 through 38 )
21X-RAY DIFFRACTION21chain 'E' and (resid 39 through 76 )
22X-RAY DIFFRACTION22chain 'E' and (resid 77 through 137 )
23X-RAY DIFFRACTION23chain 'E' and (resid 138 through 176 )
24X-RAY DIFFRACTION24chain 'F' and (resid 5 through 40 )
25X-RAY DIFFRACTION25chain 'F' and (resid 41 through 48 )
26X-RAY DIFFRACTION26chain 'F' and (resid 49 through 75 )
27X-RAY DIFFRACTION27chain 'F' and (resid 76 through 90 )
28X-RAY DIFFRACTION28chain 'F' and (resid 91 through 123 )
29X-RAY DIFFRACTION29chain 'F' and (resid 124 through 137 )
30X-RAY DIFFRACTION30chain 'F' and (resid 138 through 157 )
31X-RAY DIFFRACTION31chain 'F' and (resid 158 through 164 )
32X-RAY DIFFRACTION32chain 'F' and (resid 165 through 176 )
33X-RAY DIFFRACTION33chain 'G' and (resid 5 through 38 )
34X-RAY DIFFRACTION34chain 'G' and (resid 39 through 76 )
35X-RAY DIFFRACTION35chain 'G' and (resid 77 through 137 )
36X-RAY DIFFRACTION36chain 'G' and (resid 138 through 176 )
37X-RAY DIFFRACTION37chain 'H' and (resid 5 through 48 )
38X-RAY DIFFRACTION38chain 'H' and (resid 49 through 76 )
39X-RAY DIFFRACTION39chain 'H' and (resid 77 through 95 )
40X-RAY DIFFRACTION40chain 'H' and (resid 96 through 157 )
41X-RAY DIFFRACTION41chain 'H' and (resid 158 through 176 )
42X-RAY DIFFRACTION42chain 'I' and (resid 5 through 48 )
43X-RAY DIFFRACTION43chain 'I' and (resid 49 through 81 )
44X-RAY DIFFRACTION44chain 'I' and (resid 82 through 157 )
45X-RAY DIFFRACTION45chain 'I' and (resid 158 through 176 )
46X-RAY DIFFRACTION46chain 'J' and (resid 5 through 41 )
47X-RAY DIFFRACTION47chain 'J' and (resid 42 through 86 )
48X-RAY DIFFRACTION48chain 'J' and (resid 87 through 126 )
49X-RAY DIFFRACTION49chain 'J' and (resid 127 through 176 )
50X-RAY DIFFRACTION50chain 'K' and (resid 5 through 48 )
51X-RAY DIFFRACTION51chain 'K' and (resid 49 through 76 )
52X-RAY DIFFRACTION52chain 'K' and (resid 77 through 95 )
53X-RAY DIFFRACTION53chain 'K' and (resid 96 through 157 )
54X-RAY DIFFRACTION54chain 'K' and (resid 158 through 176 )
55X-RAY DIFFRACTION55chain 'L' and (resid 5 through 48 )
56X-RAY DIFFRACTION56chain 'L' and (resid 49 through 86 )
57X-RAY DIFFRACTION57chain 'L' and (resid 87 through 137 )
58X-RAY DIFFRACTION58chain 'L' and (resid 138 through 176 )

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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