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- PDB-3m5n: Crystal structure of HCV NS3/4A protease in complex with N-termin... -

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基本情報

登録情報
データベース: PDB / ID: 3m5n
タイトルCrystal structure of HCV NS3/4A protease in complex with N-terminal product 4B5A
要素
  • NS3/4A
  • SECTTPC peptide
キーワードHYDROLASE/HYDROLASE INHIBITOR / HCV / Hepatitis C Virus / NS3 / protease / drug resistance / serine protease / chimera protein / fusion protein / HYDROLASE-HYDROLASE INHIBITOR complex
機能・相同性
機能・相同性情報


host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
類似検索 - 分子機能
Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily ...Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Trypsin-like serine proteases / Thrombin, subunit H / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
類似検索 - ドメイン・相同性
Genome polyprotein / Genome polyprotein
類似検索 - 構成要素
生物種Hepatitis C virus subtype 1a (C型肝炎ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.9 Å
データ登録者Schiffer, C.A. / Romano, K.P.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / : 2010
タイトル: Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding.
著者: Romano, K.P. / Ali, A. / Royer, W.E. / Schiffer, C.A.
履歴
登録2010年3月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02010年11月24日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22017年8月9日Group: Refinement description / Source and taxonomy / カテゴリ: entity_src_gen / software
改定 1.32017年11月8日Group: Refinement description / カテゴリ: software
改定 1.42024年2月21日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999The cofactor 4A residues 990-1000(GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) in this entry ...The cofactor 4A residues 990-1000(GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) in this entry correspond to residues numbering 1678-1688 of database sequence reference (UNP A8DG50). This peptide is covalently linked to the N-terminus of NS3. C1679S mutation was engineered to prevent disulfide formation. The V1686I and I1687N were engineered to optimize the linker between the cofactor 4A and NS3.

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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: NS3/4A
B: NS3/4A
C: NS3/4A
D: NS3/4A
F: SECTTPC peptide
G: SECTTPC peptide
H: SECTTPC peptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)88,81515
ポリマ-88,1697
非ポリマー6468
8,755486
1
A: NS3/4A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,6493
ポリマ-21,4871
非ポリマー1612
181
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
2
B: NS3/4A
F: SECTTPC peptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)22,3894
ポリマ-22,2272
非ポリマー1612
362
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
3
C: NS3/4A
G: SECTTPC peptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)22,3894
ポリマ-22,2272
非ポリマー1612
362
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
4
D: NS3/4A
H: SECTTPC peptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)22,3894
ポリマ-22,2272
非ポリマー1612
362
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)67.315, 58.894, 98.267
Angle α, β, γ (deg.)90.00, 101.01, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
NS3/4A


分子量: 21487.330 Da / 分子数: 4
断片: NS4A (UNP residues 1678-1688), NS3 (UNP residues 1027-1657)
変異: A1027S, P1028G, I1029D, L1039E, L1040E, I1043Q, I1044E, L1047Q, A1066T, C1073S, C1078L, I1098T, P1112Q, S1165A, C1185S, C1679S, V1686I, I1687N
由来タイプ: 組換発現
詳細: The protein crystallized is a single-chain construct of protease domain of hepatitis C virus NS3/4A, with cofactor 4A covalently linked at the N-terminus.
由来: (組換発現) Hepatitis C virus subtype 1a (C型肝炎ウイルス)
: genotype 1a BID-V318 / 遺伝子: NS3 / プラスミド: pET28a / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: A8DG50, hepacivirin
#2: タンパク質・ペプチド SECTTPC peptide


分子量: 739.815 Da / 分子数: 3 / 断片: residues 1966-1972 / 由来タイプ: 合成 / 詳細: N-terminal product 4B5A
由来: (合成) Hepatitis C virus subtype 1a (C型肝炎ウイルス)
参照: UniProt: B3TKQ3
#3: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 4 / 由来タイプ: 合成 / : SO4
#4: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / : Zn
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 486 / 由来タイプ: 天然 / : 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: 2.19 Å3/Da / 溶媒含有率: 43.9 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5
詳細: 100mM MES buffer pH 6.5, 4% (w/v) ammonium sulfate, 20-26% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: APS / ビームライン: 14-ID-B / 波長: 1.033 Å
検出器タイプ: MAR CCD 165 mm / 検出器: CCD / 日付: 2009年12月3日
放射モノクロメーター: Si (111) double-crystal monochromator
プロトコル: SINGLE WAVELENGTH / 散乱光タイプ: x-ray
放射波長波長: 1.033 Å / 相対比: 1
反射解像度: 1.9→50 Å / Num. obs: 59622 / % possible obs: 99.4 % / 冗長度: 3.6 % / Rsym value: 0.053 / Net I/σ(I): 12.4
反射 シェル解像度: 1.9→1.97 Å / 冗長度: 3.2 % / Mean I/σ(I) obs: 3.177 / Rsym value: 0.354 / % possible all: 98.9

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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
DENZOデータ削減
SCALEPACKデータスケーリング
PHASER位相決定
REFMAC精密化
PDB_EXTRACT3.1データ抽出
HKL-2000データ削減
HKL-2000データスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 1.9→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.702 / SU ML: 0.107 / SU R Cruickshank DPI: 0.165 / 交差検証法: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.156 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.24018 3010 5.1 %RANDOM
Rwork0.18815 ---
obs0.19073 56564 98.87 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK
原子変位パラメータBiso mean: 29.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å2-0.29 Å2
2---1.39 Å20 Å2
3---0.12 Å2
精密化ステップサイクル: LAST / 解像度: 1.9→50 Å
タンパク質核酸リガンド溶媒全体
原子数5851 0 24 486 6361
拘束条件
Refine-IDタイプDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215966
X-RAY DIFFRACTIONr_bond_other_d0.0010.023901
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.9638130
X-RAY DIFFRACTIONr_angle_other_deg0.91639536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38722.32194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53115900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5611547
X-RAY DIFFRACTIONr_chiral_restr0.0920.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021163
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8261.54026
X-RAY DIFFRACTIONr_mcbond_other0.2341.51668
X-RAY DIFFRACTIONr_mcangle_it1.47526456
X-RAY DIFFRACTIONr_scbond_it2.28331940
X-RAY DIFFRACTIONr_scangle_it3.6784.51674
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS精密化 シェル解像度: 1.9→1.944 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.265 232 -
Rwork0.214 3884 -
obs--92.74 %
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9578-3.6126-0.331313.63741.24850.1185-0.2435-0.0682-0.17440.88080.23420.66960.06990.04070.00920.42970.05180.10260.2677-0.03570.2034-12.39516.729560.4916
21.0950.63850.1942.0472-1.04221.0134-0.07390.1262-0.1603-0.0935-0.0769-0.51180.210.22830.15080.21260.0845-0.04480.1867-0.01730.2536-2.8542-13.092844.2727
34.23350.32036.027319.10971.56798.64710.0171-0.31790.19911.6846-0.35370.65450.1172-0.47960.33660.359-0.04630.07160.1232-0.04650.1302-8.3315-8.877359.2023
43.1335-0.4025-4.28156.87854.416215.7719-0.1221-0.4278-0.33280.82160.0149-0.26610.38581.1310.10720.1736-0.0198-0.10960.16770.04960.17880.1194-4.630555.6195
510.1771-2.8341-6.27338.68441.44259.9451-0.10630.10670.10770.4005-0.003-0.05750.1175-0.18650.10930.027-0.0147-0.02290.07810.01950.0763-7.9599-5.092947.1936
60.9786-0.1320.58182.12890.42542.08550.0156-0.00510.03590.0649-0.0655-0.1563-0.09690.02580.04990.0281-0.0145-0.00850.0740.01150.0844-6.59811.929244.265
71.8525-0.7182.04983.6005-1.03645.2290.04120.12110.08480.0124-0.1003-0.3587-0.20850.33740.0590.0394-0.0296-0.02430.07690.00190.1071-3.4787.090645.6992
82.61961.07040.91893.52541.0150.8876-0.11960.38610.1172-0.20660.0307-0.50370.35660.30450.08890.47260.11310.18280.33820.09010.2004-0.088-4.375830.954
95.592-2.9159-0.24866.5114-8.762523.8211-0.0827-0.2901-0.1316-0.18260.19450.43850.3188-0.2069-0.11190.1058-0.02180.0040.0597-0.01390.1007-11.1068-11.761138.6325
103.5952-2.65431.988912.4626-1.24788.6117-0.11820.43070.2352-0.97470.0206-0.25470.3291-0.13380.09750.1371-0.08060.00640.13760.00150.0357-12.868-5.043225.8427
115.24327.2474-3.0210.4954-5.37427.9043-0.53560.145-0.4831-0.88310.1533-0.44220.25390.12780.38240.2252-0.0598-0.05130.2348-0.03950.3046-19.2347-11.610728.2651
1215.922111.068311.497813.87275.274111.61010.7201-0.3267-0.66080.1267-0.01520.00490.6818-0.5308-0.70490.1103-0.0764-0.030.174-0.01540.1908-19.2418-10.428638.4312
132.90560.3174-3.291.8470.53295.1403-0.1899-0.0936-0.1361-0.35340.0879-0.23510.35080.35990.1020.17090.02880.05040.15010.01750.1125-5.1676-5.13531.3548
1429.32318.13368.63024.55622.54472.5503-0.3587-0.37590.7473-0.30270.1130.4308-0.1236-0.10240.24580.0681-0.0308-0.04340.22040.01670.1548-18.4047-1.633734.2656
1516.45598.9083-6.78447.6278-3.50422.8112-0.52090.70360.0136-0.51130.48460.3890.1821-0.27930.03640.1559-0.05-0.08090.22440.01240.1737-25.6265-7.306930.2786
1613.358310.70843.049112.04450.81153.4372-0.15580.61040.4172-0.25710.25670.0553-0.253-0.0913-0.10090.16750.00660.00940.22360.04130.1495-8.88263.12530.1727
175.8348.18582.567515.71170.27183.764-0.66160.90370.2591-0.65340.24290.1205-0.63481.25730.41870.3274-0.1889-0.01930.42710.09370.3082-2.19849.696333.7809
181.0449-3.91921.287414.7056-4.81561.6369-0.0645-0.04190.0860.13340.1439-0.36060.078-0.0255-0.07940.40850.1086-0.24780.3166-0.0510.478127.6367-34.46860.2299
190.82390.493-0.26472.98150.31463.1777-0.12270.06470.0937-0.03440.12880.4321-0.3957-0.4599-0.00610.09260.0405-0.00730.12160.00710.151217.1399-15.163143.172
202.38891.1732-0.39317.0302-5.31478.8733-0.0374-0.1743-0.14820.5343-0.11990.044-0.07140.09170.15730.13610.02370.02050.0309-0.01490.087921.3216-15.231354.3065
2110.25391.05410.20657.4286-3.42747.26620.055-0.1976-0.06870.5921-0.2077-0.0129-0.3119-0.14860.15260.1749-0.01640.05440.07220.00260.030619.472-24.732959.5076
228.3328-3.1222-1.74091.3304-1.924343.62520.2005-0.3161-0.10420.01030.25690.114-1.0421-1.2764-0.45740.14520.01970.0920.27840.04170.403511.4742-19.294247.0609
236.7682-3.04784.50428.7778-1.64778.0669-0.0830.0769-0.14420.5924-0.0491-0.33780.10660.34990.13210.0541-0.00170.00160.104800.107125.182-22.954548.6533
240.3199-0.18850.03352.3718-0.45021.76630.00970.0021-0.0573-0.0071-0.03420.13910.1521-0.06350.02450.0162-0.01860.00830.0812-0.00450.096221.3289-30.074643.8239
252.0309-1.8821-2.85786.43355.53259.7882-0.01620.1784-0.11490.2604-0.29130.56080.2061-0.63390.30750.028-0.02820.04610.0944-0.00030.137415.7793-34.444949.5646
262.2821-2.5237-0.98154.5937-0.52795.09490.07690.0551-0.1114-0.294-0.09790.19010.0932-0.07840.0210.0536-0.02580.01610.0623-0.0160.086822.2173-35.360641.5599
272.1850.4116-1.40112.6045-3.66748.4342-0.0761-0.0783-0.09650.14060.1120.33-0.3947-0.5664-0.03590.0448-0.0013-0.01230.2407-0.040.248610.4115-25.407337.4436
283.16550.62032.97493.07792.583611.0848-0.09710.3073-0.0865-0.25150.17450.0469-0.40020.2098-0.07740.0762-0.03070.01090.0770.01650.083323.2158-18.31830.6405
292.34240.658-3.00267.6565-0.565.4589-0.2790.3895-0.0958-0.58350.1834-0.38960.24760.0720.09560.0976-0.07010.01040.274-0.0370.068227.4987-22.542625.9241
305.39734.6934.16828.31050.58047.0929-0.27150.17730.299-0.0344-0.18290.1427-0.27430.20340.45440.0416-0.02260.02180.15670.03260.119734.3847-16.165231.444
311.58530.5221.88061.5833-0.78023.8062-0.15350.07450.0307-0.14660.05680.0647-0.1704-0.05630.09670.08780.0078-0.02220.1558-0.04860.11822.1817-22.315332.9559
3221.76717.9119-2.7985.85260.07382.6479-0.27760.129-1.1234-0.21860.0206-1.10070.28020.20030.25690.05730.01340.08780.19140.03450.382239.0022-23.876132.4833
3313.64127.28941.5586.1931.13470.2439-0.57120.661-0.1832-0.75910.5244-0.3132-0.11060.10060.04680.1388-0.05050.08420.2409-0.01540.239831.4855-25.320830.1929
345.54023.2121-5.44468.9233-7.07917.541-0.2680.6002-0.5819-0.8020.12680.40360.6428-0.52590.14130.2432-0.1418-0.02530.2956-0.07030.247717.2134-36.063632.4522
350.88711.3028-2.40371.9305-3.42667.51230.18110.0074-0.14410.16550.0394-0.2857-0.58580.09-0.22050.48100.13870.2784-0.03640.43912.7408-24.9746-12.2685
362.91570.7362-2.29728.2268-3.48938.0001-0.01440.2739-0.0709-0.1510.12790.39850.0896-0.2996-0.11350.0954-0.0001-0.06580.0793-0.01160.1287-5.1508-38.8538-1.6196
372.9993-1.3352-2.251718.2937-3.83068.46310.2678-0.1941-0.30050.3768-0.00431.43590.1643-0.857-0.26350.2816-0.09060.04970.27880.01960.2637-8.8367-47.893610.8545
381.4378-1.09451.6365.7479-2.66110.2890.1404-0.10910.1039-0.49110.28770.35320.1091-0.0983-0.42810.1331-0.0194-0.01740.03350.00280.1413-4.2459-46.2326-1.2241
396.9066-0.7597-1.61318.812-1.83516.5856-0.04170.30320.005-0.96770.04770.00150.4738-0.0569-0.0060.2566-0.0153-0.03060.07730.02060.0124-4.443-36.2182-11.535
4012.38582.3322-4.36767.662.900817.2510.0012-0.1670.0614-0.3805-0.07270.52630.6474-2.18280.07150.159-0.1063-0.01090.36790.03520.2564-12.6788-40.41551.428
419.16692.9865-7.4528.8739-4.37059.47460.0736-0.11960.3064-0.4234-0.1459-0.26520.19710.30640.07230.09790.0275-0.02150.0727-0.00360.0950.6348-36.5123-0.4044
420.18860.15150.54451.8606-1.19533.12970.0012-0.020.03930.00570.02740.1485-0.0123-0.1246-0.02860.07540.0112-0.00320.0628-0.00690.1075-2.7303-29.96943.9685
432.83691.32722.2663.42751.09234.4844-0.0671-0.0520.26540.0535-0.0460.3974-0.1853-0.27450.1130.07980.0426-0.02120.05630.01170.1184-5.8401-24.7772.4459
444.0645-1.31362.22134.0929-3.95166.6856-0.0711-0.54180.20640.26230.26230.28750.288-0.8695-0.19120.1761-0.03480.05650.238-0.02150.153-9.3395-35.959717.2903
453.3423-3.9851-3.38759.01425.827514.88550.08960.1104-0.106-0.1523-0.1004-0.18560.06310.47780.01080.09530.0002-0.03080.0614-0.00650.13911.6125-43.66649.6903
463.89861.49011.65594.7965-1.24473.6020.0416-0.32910.19320.4956-0.0504-0.0427-0.22940.09030.00880.14140.01120.00140.124-0.02670.0552.8891-37.719622.5921
473.1882-2.12811.49365.222-1.03485.89480.2188-0.115-0.13530.04380.0189-0.06560.29650.5008-0.23760.03940.018-0.04520.12610.00070.10229.6723-41.595516.5464
480.5505-0.9239-0.91484.6111-1.48564.6335-0.02080.0383-0.03510.35760.1440.1865-0.2348-0.3985-0.12320.0903-0.0085-0.00330.1890.00810.1131-4.3168-36.810916.9279
499.2124-3.99921.10846.18630.18231.7472-0.23930.15810.80970.3862-0.0076-0.7757-0.26420.45170.24690.1461-0.0206-0.0690.21090.03620.194413.0622-35.288715.3117
5012.0972-6.08492.35527.2519-1.07971.9472-0.1768-0.5260.23060.24650.2447-0.3546-0.27240.1891-0.06790.1244-0.0041-0.01880.1578-0.01560.06516.1446-33.525618.2282
5112.8741-5.62825.530728.2703-7.00443.2019-0.7303-0.10150.88111.12060.45710.2991-0.5183-0.18440.27320.63430.3736-0.03740.4212-0.16480.334-6.991-22.726315.4095
527.07334.28429.7684.03886.754413.98660.27210.594-0.31990.4694-0.01290.24120.61060.5795-0.25920.4877-0.0759-0.08240.30880.00930.29430.0573-6.6188-11.9738
531.9338-1.3099-0.06112.1992-1.06440.9864-0.0648-0.20930.29850.1301-0.066-0.4408-0.16650.23620.13080.2156-0.08770.04580.1867-0.03340.182840.723513.25884.5045
540.17781.630.900315.85016.47298.7302-0.0301-0.0130.0185-0.6235-0.1120.08130.176-0.26650.14210.25510.00770.01860.1650.01490.08435.3169.608-9.5495
554.4834-1.3207-2.1342.36474.029211.24880.02550.08460.0978-0.46860.1698-0.2953-0.21960.9317-0.19530.36040.01950.08080.24650.02250.18242.68783.8225-8.7044
568.51322.76445.65948.85770.175.8875-0.11280.1986-0.0717-0.1385-0.09-0.4724-0.22430.40650.20280.089-0.00060.04370.10640.01530.094239.54296.99352.4258
577.2921-2.07163.24455.7148-1.14195.69360.2269-0.0143-0.4271-0.2761-0.0184-0.00450.0719-0.1802-0.20850.1005-0.00480.01760.0696-0.00450.048335.82072.24414.3007
580.0302-0.06730.27472.3723-0.12252.65570.0090.01960.0085-0.1647-0.0894-0.22140.1240.17690.08040.13810.02570.02630.08350.00580.093637.271-3.35280.6172
594.73931.2956-4.95273.8081-1.52227.9418-0.0389-0.0662-0.0213-0.0437-0.0166-0.27220.46050.1120.05550.13490.02950.01510.0366-0.0070.049437.4313-8.22844.001
6015.980417.6577-4.76633.60458.956515.7942-0.81990.4901-0.1928-1.14461.4042-0.7177-0.26770.8851-0.58430.4966-0.13020.08390.5210.04910.432949.0760.58041.4941
613.8144-2.10640.07374.25621.49834.0577-0.2177-0.4438-0.16530.35440.1044-0.3013-0.080.40220.11330.09830.0018-0.07240.17870.10450.127442.79033.888321.0984
625.2769-0.46581.5536.744-1.993416.7709-0.1191-0.15990.2338-0.0510.05050.1212-0.6736-0.04080.06860.11240.0137-0.00680.0617-0.01550.053233.430212.700412.2854
632.78681.6538-2.354412.24171.71686.0144-0.0476-0.4393-0.10650.4788-0.15280.37990.4162-0.07370.20050.10150.01860.01270.18230.03370.044930.7894.027923.9247
643.8021-1.897-0.34265.51041.5464.5560.1046-0.07580.38710.007-0.2670.1425-0.3473-0.40690.16240.04840.0454-0.00460.1546-0.02980.095124.330611.622715.688
655.61430.23734.94640.2062-0.42246.4929-0.1347-0.17780.2488-0.0145-0.1241-0.0272-0.05950.1010.25880.1110.0124-0.01770.18440.03350.1337.83666.7416.0446
663.4347-2.6607-0.49183.59140.52722.4716-0.05640.3772-0.2920.1916-0.13870.31470.0424-0.17640.19510.0736-0.0063-0.00310.11010.01190.080626.97773.878416.4666
679.4916-4.98840.01645.520.40363.66-0.1856-0.4473-0.13790.2790.21650.14560.2587-0.2764-0.03090.11530.0174-0.00350.09750.02610.014730.80690.578518.6355
683.6999-5.4769-6.89118.97429.614813.2329-0.5992-0.153-0.19331.1019-0.1411-0.34580.82490.49350.74020.3850.0302-0.14240.30150.18590.525341.3732-9.461414.0013
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A986 - 991
2X-RAY DIFFRACTION2A992 - 1010
3X-RAY DIFFRACTION3A1011 - 1018
4X-RAY DIFFRACTION4A1019 - 1030
5X-RAY DIFFRACTION5A1031 - 1041
6X-RAY DIFFRACTION6A1042 - 1065
7X-RAY DIFFRACTION7A1066 - 1087
8X-RAY DIFFRACTION8A1088 - 1105
9X-RAY DIFFRACTION9A1106 - 1111
10X-RAY DIFFRACTION10A1112 - 1123
11X-RAY DIFFRACTION11A1124 - 1131
12X-RAY DIFFRACTION12A1132 - 1137
13X-RAY DIFFRACTION13A1138 - 1153
14X-RAY DIFFRACTION14A1154 - 1159
15X-RAY DIFFRACTION15A1160 - 1167
16X-RAY DIFFRACTION16A1168 - 1173
17X-RAY DIFFRACTION17A1174 - 1179
18X-RAY DIFFRACTION18B986 - 991
19X-RAY DIFFRACTION19B992 - 1006
20X-RAY DIFFRACTION20B1007 - 1015
21X-RAY DIFFRACTION21B1016 - 1026
22X-RAY DIFFRACTION22B1027 - 1032
23X-RAY DIFFRACTION23B1033 - 1042
24X-RAY DIFFRACTION24B1043 - 1064
25X-RAY DIFFRACTION25B1065 - 1077
26X-RAY DIFFRACTION26B1078 - 1086
27X-RAY DIFFRACTION27B1087 - 1098
28X-RAY DIFFRACTION28B1099 - 1111
29X-RAY DIFFRACTION29B1112 - 1123
30X-RAY DIFFRACTION30B1124 - 1134
31X-RAY DIFFRACTION31B1135 - 1154
32X-RAY DIFFRACTION32B1155 - 1162
33X-RAY DIFFRACTION33B1163 - 1171
34X-RAY DIFFRACTION34B1172 - 1179
35X-RAY DIFFRACTION35C986 - 991
36X-RAY DIFFRACTION36C992 - 997
37X-RAY DIFFRACTION37C998 - 1004
38X-RAY DIFFRACTION38C1005 - 1013
39X-RAY DIFFRACTION39C1014 - 1026
40X-RAY DIFFRACTION40C1027 - 1032
41X-RAY DIFFRACTION41C1033 - 1041
42X-RAY DIFFRACTION42C1042 - 1065
43X-RAY DIFFRACTION43C1066 - 1087
44X-RAY DIFFRACTION44C1088 - 1105
45X-RAY DIFFRACTION45C1106 - 1111
46X-RAY DIFFRACTION46C1112 - 1122
47X-RAY DIFFRACTION47C1123 - 1137
48X-RAY DIFFRACTION48C1138 - 1153
49X-RAY DIFFRACTION49C1154 - 1162
50X-RAY DIFFRACTION50C1163 - 1172
51X-RAY DIFFRACTION51C1173 - 1179
52X-RAY DIFFRACTION52D986 - 991
53X-RAY DIFFRACTION53D992 - 1008
54X-RAY DIFFRACTION54D1009 - 1019
55X-RAY DIFFRACTION55D1020 - 1029
56X-RAY DIFFRACTION56D1030 - 1038
57X-RAY DIFFRACTION57D1039 - 1050
58X-RAY DIFFRACTION58D1051 - 1068
59X-RAY DIFFRACTION59D1069 - 1085
60X-RAY DIFFRACTION60D1086 - 1091
61X-RAY DIFFRACTION61D1092 - 1104
62X-RAY DIFFRACTION62D1105 - 1113
63X-RAY DIFFRACTION63D1114 - 1124
64X-RAY DIFFRACTION64D1125 - 1137
65X-RAY DIFFRACTION65D1138 - 1148
66X-RAY DIFFRACTION66D1149 - 1163
67X-RAY DIFFRACTION67D1164 - 1173
68X-RAY DIFFRACTION68D1174 - 1179

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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