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- PDB-2wdt: Crystal structure of Plasmodium falciparum UCHL3 in complex with ... -

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基本情報

登録情報
データベース: PDB / ID: 2wdt
タイトルCrystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME
要素
  • UBIQUITIN
  • UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3
キーワードHYDROLASE/PROTEIN BINDING / HYDROLASE-PROTEIN BINDING COMPLEX / ENZYME-LIGAND COMPLEX / UBIQUITIN ISOPEPTIDASE / UCH-L SUPERFAMILY / CYSTEIN PROTEINASE / PEPTIDASE_C12 / HYDROLASE
機能・相同性
機能・相同性情報


Synthesis of active ubiquitin: roles of E1 and E2 enzymes / UCH proteinases / Neddylation / : / : / protein modification process => GO:0036211 / deNEDDylase activity / protein deneddylation / Peptide chain elongation / Selenocysteine synthesis ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / UCH proteinases / Neddylation / : / : / protein modification process => GO:0036211 / deNEDDylase activity / protein deneddylation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein deubiquitination / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / cytosolic ribosome / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex
類似検索 - 分子機能
Ubiquitin carboxyl-terminal hydrolase, domain 1 / Ubiquitin carboxyl-terminal hydrolase, domain 2 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Actin-binding Protein, T-fimbrin; domain 1 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily ...Ubiquitin carboxyl-terminal hydrolase, domain 1 / Ubiquitin carboxyl-terminal hydrolase, domain 2 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Actin-binding Protein, T-fimbrin; domain 1 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Dna Ligase; domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40 / Ubiquitin carboxyl-terminal hydrolase UCHL3
類似検索 - 構成要素
生物種PLASMODIUM FALCIPARUM (マラリア病原虫)
HOMO SAPIENS (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.3 Å
データ登録者Weihofen, W.A. / Artavanis-Tsakonas, K. / Gaudet, R. / Ploegh, H.L.
引用ジャーナル: J.Biol.Chem. / 年: 2010
タイトル: Characterization and Structural Studies of the Plasmodium Falciparum Ubiquitin and Nedd8 Hydrolase Uchl3.
著者: Artavanis-Tsakonas, K. / Weihofen, W.A. / Antos, J.M. / Coleman, B.I. / Comeaux, C.A. / Duraisingh, M.T. / Gaudet, R. / Ploegh, H.L.
履歴
登録2009年3月26日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02009年12月29日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Advisory / Version format compliance
改定 2.02023年11月15日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
カテゴリ: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
改定 2.12023年12月13日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3
B: UBIQUITIN
C: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3
D: UBIQUITIN
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)71,1696
ポリマ－71,0984
非ポリマー712
水3,405189
1
A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3
D: UBIQUITIN
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,5853
ポリマ－35,5492
非ポリマー351
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-19.9 kcal/mol
Surface area13130 Å2
手法PISA
2
B: UBIQUITIN
C: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,5853
ポリマ－35,5492
非ポリマー351
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-20.5 kcal/mol
Surface area13160 Å2
手法PISA
単位格子
Length a, b, c (Å)134.400, 75.300, 85.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
非結晶学的対称性 (NCS)NCS oper: (Code: given
Matrix: (0.801, -0.599, 0.008), (-0.599, -0.801, -0.005), (0.01, -0.001, -1)
ベクター: -0.1647, -0.9035, -0.3297)

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要素

#1: タンパク質 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3 / UCHL3 / UCH-L3 / UBIQUITIN THIOLESTERASE


分子量: 26930.320 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) PLASMODIUM FALCIPARUM (マラリア病原虫)
株: CLONE 3D7 / 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: Q8IKM8*PLUS, ubiquitinyl hydrolase 1
#2: タンパク質 UBIQUITIN


分子量: 8618.910 Da / 分子数: 2 / Fragment: RESIDUES 1-75 / 由来タイプ: 組換発現
詳細: C-TERMINAL GLY76 OF WILDTYPE UBIQUITIN IS REPLACED BY A VINYL METHYLESTER MOIETY (UBVME)
由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PTYB / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62988, UniProt: P0CG48*PLUS
#3: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cl
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 189 / 由来タイプ: 天然 / 式: H2O
非ポリマーの詳細METHYL 4-AMINOBUTANOATE (GVE): ACTIVE SITE CYS95 OF UCHL3 FORMS A COVALENT BOND TO METHYL 4- ...METHYL 4-AMINOBUTANOATE (GVE): ACTIVE SITE CYS95 OF UCHL3 FORMS A COVALENT BOND TO METHYL 4-AMINOBUTANOATE WHICH IS IN TURN FUSED TO GLY75 OF UBIQUITIN
配列の詳細CDNA OF PLASMODIUM FALCIPARUM UCHL3 WAS GENERATED AS DESCRIBED IN FRICKEL ET AL., CELL. MICROBIOL. ...CDNA OF PLASMODIUM FALCIPARUM UCHL3 WAS GENERATED AS DESCRIBED IN FRICKEL ET AL., CELL. MICROBIOL. 2007, 9, 1601-10. SEQUENCE DIFFERS FROM THE UCHL3 SEQUENCE ANNOTATED IN THE PLASMODIUM DATABASE (PLASMODB ENTRY PF14- 0576).

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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: 3.3 Å3/Da / 溶媒含有率: 63 % / 解説: NONE
結晶化pH: 5.5 / 詳細: 100 MM BIS-TRIS PH 5.5, 200 MM NACL, 25 % PEG 3350

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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: 24-ID-C / 波長: 0.979
検出器タイプ: ADSC CCD / 検出器: CCD / 日付: 2007年6月30日
詳細: TRIPLE STRIPED VERTICAL AND HORIZANTAL FOCUSSING MIRRORS IN KIRKPATRICK- BAEZ GEOMETRY
放射モノクロメーター: CRYOGENICALLY-COOLED DOUBLE CRYSTAL SI(111)
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: 0.979 Å / 相対比: 1
反射解像度: 2.3→30 Å / Num. obs: 39592 / % possible obs: 98.1 % / Observed criterion σ(I): 3 / 冗長度: 5.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8
反射 シェル解像度: 2.3→2.36 Å / 冗長度: 3.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 90.2

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解析

ソフトウェア
名称バージョン分類
REFMAC5.4.0066精密化
XDSデータ削減
XSCALE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 ENTRY 1XD3

1xd3


解像度: 2.3→19.85 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.763 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.192 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-4 AND 227-232 OF CHAINS A AND C ARE DISORDERED RESTRAINTS FOR REFMAC5 FOR METHYL 4- AMINOBUTANOATE WERE GENERATED WITH THE DUNDEE PRODRG DSERVER
Rfactor反射数%反射Selection details
Rfree0.235 1062 2.7 %RANDOM
Rwork0.187 ---
obs0.188 38252 100 %-
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: 1.2 Å
溶媒モデル: BABINET FOR INITIAL AND SIMPLE SCALING FOR FURTHER REFINEMENT
原子変位パラメータBiso mean: 35.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2--3.3 Å20 Å2
3----2.5 Å2
精密化ステップサイクル: LAST / 解像度: 2.3→19.85 Å
タンパク質核酸リガンド溶媒全体
原子数4564 0 2 189 4755
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224655
X-RAY DIFFRACTIONr_bond_other_d0.0010.023166
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9646278
X-RAY DIFFRACTIONr_angle_other_deg0.9083.0017750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9395554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59125.667240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.415850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7511518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02886
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_it0.711.52793
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35424538
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.93231862
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1214.51740
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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: 2.3→2.36 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.255 76 -
Rwork0.216 2746 -
obs--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)
19.56641.44820.188411.2609-2.414513.54620.01760.41590.43510.3581-0.0432-0.0616-1.91040.89380.02560.2105-0.14490.0208-0.23940.0178-0.0912-6.652-9.084-15.72
23.06150.9211-3.35985.4125-1.203411.80330.22220.13270.6233-0.13250.1391-0.3033-1.27510.4585-0.3613-0.1034-0.0742-0.0218-0.10590.034-0.1226-6.34-12.803-12.216
310.46122.5385-0.69884.8313-1.39759.3429-0.3149-0.14650.0679-0.0273-0.0719-0.6370.23190.9370.3867-0.22880.05210.0301-0.1116-0.0068-0.1465-3.539-20.974-9.097
43.7231.4047-4.57110.43432.055911.37750.11890.3075-0.2648-0.62760.05460.76380.7771-0.1898-0.1735-0.0439-0.0365-0.0623-0.03590.0031-0.2116-12.63-23.353-18.358
53.67860.3271-0.99352.7042-1.219311.046-0.07620.60310.5265-0.47950.17170.1219-0.7621-0.4629-0.0954-0.0408-0.0030.0003-0.07940.0745-0.1221-11.088-14.663-18.741
69.40373.4933-6.87042.4657-5.542515.6772-0.3526-0.0672-0.149-0.2169-0.4834-0.41010.86921.52880.836-0.19860.14660.0504-0.20820.0066-0.1468-9.832-26.8950.194
710.3909-3.35440.75822.6254-1.71583.011-0.1447-0.0174-0.57720.21590.4081-0.08730.66840.0368-0.2634-0.0189-0.10860.043-0.0987-0.0181-0.0703-22.692-56.383-12.439
83.05550.46090.64825.31-1.966510.36750.03010.0655-0.464-0.25480.19720.0021.1365-0.326-0.2273-0.1106-0.07540.0541-0.1821-0.0152-0.1086-20.3-53.813-16.244
92.6931-2.2519-0.28287.7871-2.53610.1571-0.06410.2721-0.1412-0.3732-0.2868-0.5010.60390.72090.351-0.1446-0.02380.0502-0.04480.0184-0.0715-13.17-49.188-19.531
105.25852.87070.03927.9916-2.679911.84530.0990.04310.47210.2895-0.1090.1557-1.09350.22740.01-0.0526-0.04470.0296-0.1373-0.0425-0.1248-18.38-41.562-10.324
115.81022.4656-0.57297.2915-4.524610.107-0.0084-0.3689-0.09410.42650.21050.17460.0485-1.0473-0.2022-0.2149-0.04660.0202-0.1442-0.015-0.2278-22.513-49.126-9.556
126.5981-3.9051.97136.368-7.856711.6211-0.3782-0.19480.19410.0068-0.4309-0.33450.34521.70410.809-0.1758-0.0686-0.0011-0.06090.0257-0.1282-14.509-40.523-28.682
1311.8389-2.73025.43598.06613.22497.61290.18130.4632-0.1261-0.3692-0.263-0.0261-0.38490.87490.0817-0.1588-0.05-0.0158-0.06820.0133-0.1377-6.697-33.6-40.506
149.66171.1735-2.832610.15317.49996.9767-0.0881-0.3858-0.04420.81150.4091-0.51440.4018-0.0599-0.3210.02520.0175-0.0417-0.0537-0.0259-0.1777-15.852-33.34-27.691
152.2850.98760.13975.1673-1.26813.43030.1105-0.10350.11450.2690.1750.4569-0.4286-0.8713-0.2856-0.16010.02160.05310.0754-0.0102-0.2326-26.768-32.835-30.686
161.14120.72370.70751.9733-1.17763.92280.0841-0.1117-0.19050.0478-0.04760.1478-0.4262-0.3394-0.03650.01450.04330.01030.01840.0081-0.0785-22.171-28.283-42.257
174.778-0.15431.64963.28022.14599.3221-0.03420.03760.5575-0.1855-0.01520.1157-1.4584-0.36870.04940.21230.10360.0212-0.1621-0.0052-0.0543-21.083-17.315-43.845
1812.1475-0.016610.14366.6404-2.76979.6139-0.37580.65970.38260.172-0.1274-0.1232-0.7270.69490.50310.04180.0114-0.0011-0.02190.0035-0.0624-16.839-25.601-51.898
199.5869-2.70984.88738.2622-6.4425.90780.05360.27980.7107-0.0289-0.451-0.309-0.35760.8340.39750.0909-0.04640.0066-0.03480.0191-0.0253-8.689-24.561-40.435
208.1085-8.9388-1.591410.13320.88163.0418-0.4579-0.6516-0.06651.06210.6861-0.46480.29220.099-0.2281-0.0203-0.0534-0.04040.06750.040.0117-4.239-39.077-33.553
218.8942-0.5453-0.65052.4730.14635.1472-0.0570.0262-0.3865-0.03910.11460.49710.0586-0.9918-0.0576-0.044-0.03250.02590.12550.0307-0.0944-28.131-35.657-40.752
224.34180.5089-3.04654.8191-2.34199.74010.00720.0273-0.1459-0.07660.14060.46870.0221-1.5047-0.1479-0.2241-0.1224-0.04440.2605-0.0162-0.107-33.81-39.098-39.429
239.1850.50719.696111.4379-5.632113.82270.32690.3162-1.1734-0.74030.19720.11751.0074-0.1251-0.52410.0663-0.10550.0295-0.0169-0.0456-0.0404-25.403-51.811-36.741
240.9174-0.31360.63119.8411.39692.67250.0079-0.12960.25220.6580.2435-0.6711-0.0104-0.3634-0.2514-0.093-0.05530.04010.1217-0.0174-0.1261-24.085-36.965-29.166
2512.0867-0.728-0.06734.61331.71130.6382-0.0297-0.40690.19980.2818-0.1358-0.22150.2069-0.14030.1656-0.05950.0352-0.0189-0.0634-0.0092-0.0362-7.763-36.72512.406
266.9763-1.23732.74210.03292.25445.54850.05210.61860.1107-0.2893-0.01-0.2682-0.04030.2995-0.0421-0.09980.00710.0385-0.0487-0.0332-0.0877-15.178-31.73-0.757
272.84670.1929-0.23464.7446-0.59632.49930.02170.09770.0704-0.22120.03760.1512-0.128-0.485-0.0593-0.17630.0829-0.0258-0.0393-0.0362-0.2259-23.956-25.6531.743
281.2397-0.7721-0.5041.5737-0.71073.98790.0484-0.0961-0.21620.0564-0.0405-0.0845-0.0132-0.3407-0.0079-0.0560.0347-0.01450.0111-0.0031-0.0287-23.311-31.90813.835
292.90410.64062.04364.31332.76259.45110.1043-0.2645-0.31520.2313-0.1780.31860.8892-1.28520.0738-0.0651-0.1203-0.00530.0676-0.0115-0.015-29.036-41.28215.367
3010.32010.8074-6.38643.20783.14168.1907-0.2753-0.5022-0.50140.2818-0.0540.01350.3230.19710.32930.03770.0079-0.0295-0.04630.0044-0.0139-20.77-37.26123.357
318.63410.6212-5.78114.6167-4.85648.1836-0.3015-0.207-0.45340.1591-0.0987-0.12370.3820.27420.4002-0.00220.02180.0011-0.0528-0.03930.0524-14.596-42.94911.981
3211.42522.48981.30240.69830.67641.1384-0.07360.91730.1335-0.22450.2211-0.0953-0.14990.2137-0.1476-0.01420.05140.03140.00690.02110.0399-2.535-34.0535.29
332.2422-3.13740.67014.6018-0.44231.35870.0229-0.07270.17060.12610.0470.0391-0.3537-0.1572-0.06990.01360.0936-0.02620.05440.0009-0.0316-23.665-22.40712.274
344.22880.13270.41732.6307-0.88273.0850.02140.03190.37810.198-0.0041-0.0094-0.4947-0.2674-0.01740.03210.17240.0119-0.0828-0.0603-0.0705-26.061-16.29110.909
3513.92630.2509-11.379810.1455-0.387710.39020.5607-0.66241.23550.397-0.2323-0.8389-1.10140.5423-0.32840.1004-0.0123-0.0652-0.033-0.02330.0584-11.748-11.1418.048
3610.75318.08852.67376.63531.97382.0379-0.1517-0.0116-0.1728-0.2460.068-0.1462-0.1562-0.16570.0837-0.01190.05360.0013-0.018-0.0053-0.042-19.545-23.9240.624
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 5
2X-RAY DIFFRACTION2B6 - 22
3X-RAY DIFFRACTION3B23 - 44
4X-RAY DIFFRACTION4B45 - 55
5X-RAY DIFFRACTION5B56 - 70
6X-RAY DIFFRACTION6B71 - 75
7X-RAY DIFFRACTION7D1 - 5
8X-RAY DIFFRACTION8D6 - 22
9X-RAY DIFFRACTION9D23 - 44
10X-RAY DIFFRACTION10D45 - 55
11X-RAY DIFFRACTION11D56 - 70
12X-RAY DIFFRACTION12D71 - 75
13X-RAY DIFFRACTION13A5 - 9
14X-RAY DIFFRACTION14A10 - 16
15X-RAY DIFFRACTION15A17 - 80
16X-RAY DIFFRACTION16A81 - 108
17X-RAY DIFFRACTION17A109 - 128
18X-RAY DIFFRACTION18A129 - 135
19X-RAY DIFFRACTION19A136 - 147
20X-RAY DIFFRACTION20A148 - 161
21X-RAY DIFFRACTION21A162 - 180
22X-RAY DIFFRACTION22A181 - 206
23X-RAY DIFFRACTION23A207 - 216
24X-RAY DIFFRACTION24A217 - 226
25X-RAY DIFFRACTION25C5 - 9
26X-RAY DIFFRACTION26C10 - 16
27X-RAY DIFFRACTION27C17 - 80
28X-RAY DIFFRACTION28C81 - 108
29X-RAY DIFFRACTION29C109 - 128
30X-RAY DIFFRACTION30C129 - 135
31X-RAY DIFFRACTION31C136 - 147
32X-RAY DIFFRACTION32C148 - 161
33X-RAY DIFFRACTION33C162 - 180
34X-RAY DIFFRACTION34C181 - 206
35X-RAY DIFFRACTION35C207 - 216
36X-RAY DIFFRACTION36C217 - 226

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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