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- PDB-5foa: Crystal Structure of Human Complement C3b in complex with DAF (CCP2-4) -

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基本情報

登録情報
データベース: PDB / ID: 5foa
タイトルCrystal Structure of Human Complement C3b in complex with DAF (CCP2-4)
要素
  • COMPLEMENT C3 BETA CHAIN
  • COMPLEMENT C3B ALPHA CHAIN
  • DECAY ACCELERATING FACTOR, CD55
キーワードLIPID BINDING / COMPLEMENT SYSTEM / IMMUNE SYSTEM / PLASMA PROTEIN / REGULATORS OF COMPLEMENT ACTIVITY / DECAY-ACCELERATING ACTIVITY
機能・相同性
機能・相同性情報


regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / regulation of complement-dependent cytotoxicity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / regulation of complement activation ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / regulation of complement-dependent cytotoxicity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / regulation of complement activation / complement-mediated synapse pruning / Alternative complement activation / respiratory burst / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of type IIa hypersensitivity / positive regulation of CD4-positive, alpha-beta T cell proliferation / complement receptor mediated signaling pathway / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement activation / complement activation, alternative pathway / Class B/2 (Secretin family receptors) / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / B cell activation / positive regulation of vascular endothelial growth factor production / ficolin-1-rich granule membrane / complement activation, classical pathway / Purinergic signaling in leishmaniasis infection / transport vesicle / side of membrane / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane / Peptide ligand-binding receptors / secretory granule membrane / Regulation of Complement cascade / response to bacterium / Post-translational protein phosphorylation / fatty acid metabolic process / positive regulation of T cell cytokine production / positive regulation of receptor-mediated endocytosis / positive regulation of protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / positive regulation of cytosolic calcium ion concentration / virus receptor activity / blood microparticle / secretory granule lumen / G alpha (i) signalling events / immune response / G protein-coupled receptor signaling pathway / inflammatory response / membrane raft / receptor ligand activity / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / innate immune response / lipid binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
類似検索 - 分子機能
: / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 ...: / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / : / Anaphylatoxin domain signature. / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
Complement C3 / Complement decay-accelerating factor
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: 4.188 Å
データ登録者Forneris, F. / Wu, J. / Xue, X. / Gros, P.
引用ジャーナル: Embo J. / 年: 2016
タイトル: Regulators of Complement Activity Mediate Inhibitory Mechanisms Through a Common C3B-Binding Mode.
著者: Forneris, F. / Wu, J. / Xue, X. / Ricklin, D. / Lin, Z. / Sfyroera, G. / Tzekou, A. / Volokhina, E. / Granneman, J.C. / Hauhart, R. / Bertram, P. / Liszewski, M.K. / Atkinson, J.P. / Lambris, J.D. / Gros, P.
履歴
登録2015年11月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02016年4月6日Provider: repository / タイプ: Initial release
改定 1.12016年6月1日Group: Database references
改定 1.22024年1月10日Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
改定 1.32024年11月6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: COMPLEMENT C3 BETA CHAIN
B: COMPLEMENT C3B ALPHA CHAIN
C: COMPLEMENT C3 BETA CHAIN
D: COMPLEMENT C3B ALPHA CHAIN
E: DECAY ACCELERATING FACTOR, CD55
F: DECAY ACCELERATING FACTOR, CD55


分子量 (理論値)分子数
合計 (水以外)393,5176
ポリマ－393,5176
非ポリマー00
水00
1
A: COMPLEMENT C3 BETA CHAIN
B: COMPLEMENT C3B ALPHA CHAIN
E: DECAY ACCELERATING FACTOR, CD55


分子量 (理論値)分子数
合計 (水以外)196,7583
ポリマ－196,7583
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area13970 Å2
ΔGint-80 kcal/mol
Surface area96000 Å2
手法PQS
2
C: COMPLEMENT C3 BETA CHAIN
D: COMPLEMENT C3B ALPHA CHAIN
F: DECAY ACCELERATING FACTOR, CD55


分子量 (理論値)分子数
合計 (水以外)196,7583
ポリマ－196,7583
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14990 Å2
ΔGint-79 kcal/mol
Surface area94280 Å2
手法PQS
単位格子
Length a, b, c (Å)117.429, 142.378, 323.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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要素

#1: タンパク質 COMPLEMENT C3 BETA CHAIN / C3 AND PZP-LIKE ALPHA-2-MACROGLOBULIN DOMAIN-CONTAINING PRO


分子量: 71393.320 Da / 分子数: 2 / 断片: UNP RESIDUES 23-667 / 由来タイプ: 天然 / 詳細: PURIFIED FROM HUMAN PLASMA / 由来: (天然) HOMO SAPIENS (ヒト) / 参照: UniProt: P01024
#2: タンパク質 COMPLEMENT C3B ALPHA CHAIN / C3 AND PZP-LIKE ALPHA-2-MACROGLOBULIN DOMAIN-CONTAINING PRO


分子量: 104074.148 Da / 分子数: 2 / 断片: UNP RESIDUES 749-1663 / 由来タイプ: 天然 / 詳細: PURIFIED FROM HUMAN PLASMA / 由来: (天然) HOMO SAPIENS (ヒト) / 参照: UniProt: P01024
#3: タンパク質 DECAY ACCELERATING FACTOR, CD55 / DECAY ACCELERATING FACTOR /


分子量: 21290.883 Da / 分子数: 2 / 断片: CCP DOMAINS 2-4, UNP RESIDUES 97-285 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 細胞株 (発現宿主): HEK293 / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: P08174
Has protein modificationY
配列の詳細RESIDUES GS AT N-TERMINUS AND AAA AT C-TERMINUS ARE ADDED BY CLONING. RESIDUE 1013 HAS BEEN ...RESIDUES GS AT N-TERMINUS AND AAA AT C-TERMINUS ARE ADDED BY CLONING. RESIDUE 1013 HAS BEEN CONVERTED FROM GLN TO GLU IN CONVERSION OF C3 PROTEIN TO C3B

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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: 3.49 Å3/Da / 溶媒含有率: 64.8 % / 解説: NONE
結晶化詳細: 60MM MGCL2 30MM BIS-TRIS PH 5.5 6.5% PEG 3350 3% MESO-ERHYTROL

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: ID14-4 / 波長: 0.975
検出器タイプ: DECTRUS PILATUS / 検出器: PIXEL
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: 0.975 Å / 相対比: 1
反射解像度: 4.2→117.83 Å / Num. obs: 39033 / % possible obs: 96.5 % / Observed criterion σ(I): 1.5 / 冗長度: 4.1 % / Biso Wilson estimate: 133.88 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.3
反射 シェル解像度: 4.2→4.43 Å / 冗長度: 3.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.3 / % possible all: 92.6

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
iMOSFLMデータ削減
SCALAデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRIES 2I07, 1OK3

2i07

1ok3


解像度: 4.188→110.39 Å / SU ML: 0.64 / σ(F): 1.34 / 位相誤差: 32.64 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3073 1953 5 %
Rwork0.2695 --
obs0.2714 38966 95.55 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 192 Å2
精密化ステップサイクル: LAST / 解像度: 4.188→110.39 Å
タンパク質核酸リガンド溶媒全体
原子数27275 0 0 0 27275
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01527873
X-RAY DIFFRACTIONf_angle_d2.06537776
X-RAY DIFFRACTIONf_dihedral_angle_d15.45610420
X-RAY DIFFRACTIONf_chiral_restr0.0914259
X-RAY DIFFRACTIONf_plane_restr0.0134896
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.188-4.29280.36541390.33922197X-RAY DIFFRACTION83
4.2928-4.40880.36781460.31672490X-RAY DIFFRACTION93
4.4088-4.53860.33841190.29452580X-RAY DIFFRACTION93
4.5386-4.6850.32831270.29022540X-RAY DIFFRACTION94
4.685-4.85250.32831500.26672589X-RAY DIFFRACTION95
4.8525-5.04680.33881380.27262625X-RAY DIFFRACTION96
5.0468-5.27650.31931350.26592675X-RAY DIFFRACTION97
5.2765-5.55460.30481240.28292677X-RAY DIFFRACTION97
5.5546-5.90260.35861500.29352731X-RAY DIFFRACTION99
5.9026-6.35830.32771280.29452734X-RAY DIFFRACTION99
6.3583-6.99810.30231430.29122747X-RAY DIFFRACTION99
6.9981-8.01050.30191460.27192780X-RAY DIFFRACTION99
8.0105-10.09130.25531530.21272783X-RAY DIFFRACTION99
10.0913-110.42810.2721550.25012865X-RAY DIFFRACTION96
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.0001-0.00320.00540.00180.00070.0033-0.05180.0855-0.0614-0.0098-0.0101-0.00570.03210.0137-0.00041.3530.1517-0.21441.1707-0.03421.3675116.1321-15.212519.5735
20.00390.0010.00070.00840.00150.00050.04310.0208-0.0112-0.02080.028-0.0023-0.0313-0.0567-0.00021.58070.11920.19141.567-0.12261.2507110.4725-4.344115.8248
30.00710.0002-0.00110.00340.0017-0.00110.01810.00550.05830.00610.01260.05420.0333-0.0018-0.00011.6796-0.14040.16961.62740.02251.7955124.3951-10.300513.7614
40.0957-0.0584-0.03790.07150.00880.02120.0125-0.040.0836-0.0890.0731-0.0320.1260.0040.01010.5410.1582-0.020.52080.20730.4065100.385518.991530.6761
50.0148-0.0101-0.02010.03530.01230.0241-0.0287-0.0269-0.05680.0338-0.04650.0060.0237-0.0038-0.00180.60610.07220.02480.54750.2070.292982.133946.659442.8769
60.003-0.0007-0.00580.00940.00270.0025-0.0458-0.01710.0302-0.0053-0.0165-0.0326-0.0121-0.0358-0.00010.7257-0.20640.24430.7964-0.06410.931279.642760.017645.6015
70.0281-0.0104-0.01050.0087-0.0110.02090.06420.0154-0.01460.03260.0561-0.0199-0.024-0.01820.10240.1625-0.2579-0.12540.3033-0.1785-0.035889.888649.471746.6329
80.0012-0.0026-0.00690.00270.01160.0035-0.09260.0244-0.0640.0325-0.12140.06650.018-0.13400.6193-0.11830.26430.44710.11790.568108.5137-12.405565.0569
90.00330.00950.01010.00470.0057-0-0.0949-0.01930.03440.08490.0085-0.052-0.0038-0.03870.00030.36790.2566-0.07980.4080.09180.5638112.8649-9.967667.7392
100.00360.0025-0.00650.01350.00760.0247-0.0928-0.0611-0.050.12030.03870.03040.0484-0.07240.04430.51110.2372-0.17710.58850.32150.4954124.510322.762168.4787
110.0242-0.035-0.09390.02030.00560.1689-0.19720.0782-0.0092-0.03360.0117-0.09760.02380.1596-0.13290.0606-0.1404-0.00890.1447-0.07490.4759135.187730.256244.7706
120.0410.029-0.01830.0118-0.01710.03630.00970.09510.01250.01980.0096-0.0779-0.10110.14180.00850.2423-0.13750.02270.4306-0.16180.2322141.663122.875337.5658
130.03030.00630.00230.00260.00120.00870.03250.0192-0.029-0.0250.07260.0642-0.00520.04590.0020.98690.12650.0980.7724-0.130.4616124.96395.102430.7819
140.01480.00130.01210.01960.01390.0026-0.08120.0648-0.0641-0.0458-0.06230.0104-0.01660.1162-0.00020.43540.0869-0.02190.498-0.14780.6916125.5567-5.027733.682
150.0516-0.01240.04090.0260.05140.0470.13080.1099-0.2479-0.07580.1001-0.05010.26640.02660.1981-0.23920.059-0.3561-0.0868-0.00550.0082113.69163.14749.0096
160.00770.0183-0.0190.0776-0.0227-0.007-0.01050.01380.03910.1008-0.1093-0.1008-0.2413-0.1984-0.0301-0.0563-0.0830.1150.06960.03560.3933123.747251.641255.5132
170.01270.07710.07740.08610.04140.0862-0.1144-0.0055-0.147-0.04650.0965-0.04720.27850.1324-0.0611.22080.0836-0.22920.6320.17770.4339134.8675-10.796690.7414
180.12880.06460.12320.1068-0.0130.3018-0.32430.17040.0941-0.0946-0.0646-0.3652-0.4213-0.187-0.21760.6214-0.4134-0.22690.20430.02020.5598147.964771.326664.8383
190.0752-0.0043-0.0628-0.00890.02990.0272-0.0398-0.1811-0.15160.06770.0029-0.0222-0.10190.14050.0710.17570.25180.38560.33170.08040.150196.871780.092928.5889
200.0551-0.02190.0003-0.001-0.00310.0297-0.023-0.25870.00320.20120.0441-0.1850.00090.07610.0987-0.2189-0.05190.07810.1780.28040.004886.928543.95054.6913
210.16330.011-0.1424-0.02110.03510.19720.1860.01590.3226-0.07090.268-0.0415-0.36710.01631.0317-0.52170.21120.5634-0.24210.1978-0.1941103.336667.60824.2226
22-0.003-0.0034-0.00160.0020.00330.0054-0.01260.00640.0534-0.0508-0.07170.008-0.0302-0.013-0.00030.97020.24590.11360.6985-0.03910.244986.886178.777154.2952
230.0097-0.0036-0.0010.0047-0.00290.0065-0.02430.0068-0.01080.01640.011-0.0331-0.01550.050300.80090.04480.14880.74870.20720.497997.313471.038752.8176
240.0257-0.00430.00610.0023-0.00180.00430.03340.03740.00980.00660.04280.01630.00210.00730.00040.98640.31480.00780.7780.15940.845183.832373.031345.3178
250.0191-0.017-0.00340.0142-0.00260.00030.0120.0175-0.0072-0.0398-0.0323-0.0084-0.0956-0.04380.00080.5601-0.03860.16710.53860.13430.5613106.912152.89563.582
260.01560.00340.00490.00450.00640.00410.04780.0135-0.05170.0505-0.0237-0.0320.0423-0.021-0.00550.61920.3161-0.22650.39-0.05950.1908103.598245.459471.1397
270.00810.00160.00530.0242-0.00890.01230.0309-0.0003-0.03920.04990.0364-0.01570.06030.04940.00030.8290.104-0.11530.89930.09220.8875107.505653.056573.3535
280.0044-0.0087-0.00170.0135-0.00240.0104-0.00230.01980.04320.05730.01630.0008-0.01340.02440.00021.41670.20640.22171.19710.04611.1311119.526521.783888.4836
290.0025-0.0018-0.00190.001700.0038-0.0309-0.012-0.02140.0044-0.064-0.0051-0.0151-0.00070.00031.54560.1843-0.08731.35650.16991.2464121.22298.287890.8347
300.00110.0004-0.00110.0105-0.00110.0024-0.0172-0.0092-0.04130.0058-0.0225-0.01470.04990.00910.00011.21390.15590.09371.07660.02981.0572108.612724.02583.663
310.0034-0.00360.00310.0105-0.01040.00960.0052-0.00750.0016-0.00010.0002-0.0062-0.0070.0118-0.00031.43360.03060.16911.50570.20661.4565114.27489.288992.6761
320.0771-0.0706-0.0020.0664-0.0120.10560.11530.1016-0.0486-0.0245-0.01050.0310.1722-0.05320.1812-0.03470.2794-0.22540.350.19760.444899.090727.640315.0449
330.24830.289-0.16960.1946-0.15720.28240.10370.04730.06980.00350.1679-0.1069-0.0797-0.38890.52580.3620.69150.43090.13280.10730.133575.442565.52429.1251
340.05740.0290.09770.067-0.00810.10050.16280.14620.35020.07410.12940.19620.2023-0.19480.15990.68920.16580.56690.6780.21280.790961.382779.470339.8987
350.2502-0.12390.04830.2156-0.03090.1415-0.00310.126-0.42470.17620.21870.31670.13580.06420.28690.1649-0.00650.128-0.07650.23070.281769.57650.46128.7661
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'F' AND (RESID 97 THROUGH 123 )
2X-RAY DIFFRACTION2CHAIN 'F' AND (RESID 124 THROUGH 144 )
3X-RAY DIFFRACTION3CHAIN 'F' AND (RESID 145 THROUGH 157 )
4X-RAY DIFFRACTION4CHAIN 'F' AND (RESID 158 THROUGH 222 )
5X-RAY DIFFRACTION5CHAIN 'F' AND (RESID 223 THROUGH 247 )
6X-RAY DIFFRACTION6CHAIN 'F' AND (RESID 248 THROUGH 263 )
7X-RAY DIFFRACTION7CHAIN 'F' AND (RESID 264 THROUGH 285 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 23 THROUGH 76 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 77 THROUGH 124 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 125 THROUGH 210 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 211 THROUGH 277 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 278 THROUGH 369 )
13X-RAY DIFFRACTION13CHAIN 'A' AND (RESID 370 THROUGH 411 )
14X-RAY DIFFRACTION14CHAIN 'A' AND (RESID 412 THROUGH 469 )
15X-RAY DIFFRACTION15CHAIN 'A' AND (RESID 470 THROUGH 664 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 752 THROUGH 932 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 932 THROUGH 1360 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 1361 THROUGH 1663 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 23 THROUGH 134 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 135 THROUGH 322 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 323 THROUGH 664 )
22X-RAY DIFFRACTION22CHAIN 'E' AND (RESID 97 THROUGH 123 )
23X-RAY DIFFRACTION23CHAIN 'E' AND (RESID 124 THROUGH 144 )
24X-RAY DIFFRACTION24CHAIN 'E' AND (RESID 145 THROUGH 157 )
25X-RAY DIFFRACTION25CHAIN 'E' AND (RESID 158 THROUGH 171 )
26X-RAY DIFFRACTION26CHAIN 'E' AND (RESID 172 THROUGH 206 )
27X-RAY DIFFRACTION27CHAIN 'E' AND (RESID 207 THROUGH 222 )
28X-RAY DIFFRACTION28CHAIN 'E' AND (RESID 223 THROUGH 247 )
29X-RAY DIFFRACTION29CHAIN 'E' AND (RESID 248 THROUGH 263 )
30X-RAY DIFFRACTION30CHAIN 'E' AND (RESID 264 THROUGH 276 )
31X-RAY DIFFRACTION31CHAIN 'E' AND (RESID 277 THROUGH 285 )
32X-RAY DIFFRACTION32CHAIN 'D' AND (RESID 752 THROUGH 853 )
33X-RAY DIFFRACTION33CHAIN 'D' AND (RESID 854 THROUGH 1152 )
34X-RAY DIFFRACTION34CHAIN 'D' AND (RESID 1153 THROUGH 1349 )
35X-RAY DIFFRACTION35CHAIN 'D' AND (RESID 1350 THROUGH 1663 )

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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