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- PDB-4auq: Structure of BIRC7-UbcH5b-Ub complex. -

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基本情報

登録情報
データベース: PDB / ID: 4auq
タイトルStructure of BIRC7-UbcH5b-Ub complex.
要素
  • BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 7
  • POLYUBIQUITIN-C
  • UBIQUITIN-CONJUGATING ENZYME E2 D2
キーワードLIGASE/LIGASE/SIGNALLING PROTEIN / LIGASE-LIGASE-SIGNALLING PROTEIN COMPLEX
機能・相同性
機能・相同性情報


regulation of natural killer cell apoptotic process / (E3-independent) E2 ubiquitin-conjugating enzyme / negative regulation of necroptotic process / lens development in camera-type eye / cysteine-type endopeptidase inhibitor activity / ユビキチン結合酵素 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / ubiquitin conjugating enzyme activity / negative regulation of tumor necrosis factor-mediated signaling pathway / protein autoubiquitination ...regulation of natural killer cell apoptotic process / (E3-independent) E2 ubiquitin-conjugating enzyme / negative regulation of necroptotic process / lens development in camera-type eye / cysteine-type endopeptidase inhibitor activity / ユビキチン結合酵素 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / ubiquitin conjugating enzyme activity / negative regulation of tumor necrosis factor-mediated signaling pathway / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / グリコーゲン合成 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling
類似検索 - 分子機能
BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. ...BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / ユビキチン結合酵素 / Ubiquitin-conjugating (UBC) core domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 薬指 / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / ユビキチン様タンパク質 / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D2 / Baculoviral IAP repeat-containing protein 7
類似検索 - 構成要素
生物種HOMO SAPIENS (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.176 Å
データ登録者Dou, H. / Buetow, L. / Sibbet, G.J. / Cameron, K. / Huang, D.T.
引用ジャーナル: Nat.Struct.Mol.Biol. / 年: 2012
タイトル: Birc7-E2 Ubiquitin Conjugate Structure Reveals the Mechanism of Ubiquitin Transfer by a Ring Dimer.
著者: Dou, H. / Buetow, L. / Sibbet, G.J. / Cameron, K. / Huang, D.T.
履歴
登録2012年5月21日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02012年8月15日Provider: repository / タイプ: Initial release
改定 1.12012年9月26日Group: Database references
改定 1.22019年7月31日Group: Advisory / Data collection / Derived calculations
カテゴリ: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
改定 1.32023年12月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: UBIQUITIN-CONJUGATING ENZYME E2 D2
B: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 7
C: POLYUBIQUITIN-C
D: UBIQUITIN-CONJUGATING ENZYME E2 D2
E: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 7
F: POLYUBIQUITIN-C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)65,34310
ポリマ－65,0816
非ポリマー2624
水2,756153
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-42.5 kcal/mol
Surface area25040 Å2
手法PISA
単位格子
Length a, b, c (Å)100.640, 100.640, 123.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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要素

#1: タンパク質 UBIQUITIN-CONJUGATING ENZYME E2 D2 / UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2 / UBIQUITIN-CONJUGATING ...UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2 / UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2 / UBIQUITIN-PROTEIN LIGASE D2


分子量: 16766.252 Da / 分子数: 2 / 断片: UBCH5B, RESIDUES 1-147 / 変異: YES / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62837, ユビキチンリガーゼ
#2: タンパク質 BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 7 / KIDNEY INHIBITOR OF APOPTOSIS PROTEIN / KIAP / LIVIN / MELANOMA INHIBITOR OF APOPTOSIS PROTEIN / ML- ...KIDNEY INHIBITOR OF APOPTOSIS PROTEIN / KIAP / LIVIN / MELANOMA INHIBITOR OF APOPTOSIS PROTEIN / ML-IAP / RING FINGER PROTEIN 50 / BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 7 30KDA SUBUNIT / TRUNCATED LIVIN / P30-LIVIN / TLIVIN


分子量: 6852.156 Da / 分子数: 2 / 断片: RESIDUES 239-298 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3)
参照: UniProt: Q96CA5, 合成酵素; C-N結合を形成; 酸-D-アミノ酸リガーゼ（ペプチド合成）
#3: タンパク質 POLYUBIQUITIN-C / UBIQUITIN


分子量: 8922.141 Da / 分子数: 2 / 断片: UBIQUITIN, RESIDUES 1-76 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P0CG48
#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 / 式: Zn
#5: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 153 / 由来タイプ: 天然 / 式: H2O
構成要素の詳細ENGINEERED RESIDUE IN CHAIN A, SER 22 TO ARG ENGINEERED RESIDUE IN CHAIN A, ASN 77 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, SER 22 TO ARG ENGINEERED RESIDUE IN CHAIN A, ASN 77 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 85 TO SER ENGINEERED RESIDUE IN CHAIN D, SER 22 TO ARG ENGINEERED RESIDUE IN CHAIN D, ASN 77 TO ALA ENGINEERED RESIDUE IN CHAIN D, CYS 85 TO SER

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶マシュー密度: 2.41 Å3/Da / 溶媒含有率: 48.96 % / 解説: NONE

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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: Diamond / ビームライン: I04 / 波長: 0.9763
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: 0.9763 Å / 相対比: 1
反射解像度: 2.18→30 Å / Num. obs: 33958 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / 冗長度: 6.7 % / Biso Wilson estimate: 46.81 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.5
反射 シェル解像度: 2.18→2.29 Å / 冗長度: 6.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.3 / % possible all: 99.2

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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
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 3A33 AND 3EB6

3a33

3eb6


解像度: 2.176→29.499 Å / SU ML: 0.79 / σ(F): 1.34 / 位相誤差: 23.89 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2495 1718 5.1 %
Rwork0.2021 --
obs0.2044 33958 99.84 %
溶媒の処理減衰半径: 0.95 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 57.769 Å2 / ksol: 0.342 e/Å3
原子変位パラメータBiso mean: 63.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.4426 Å20 Å20 Å2
2---2.4426 Å20 Å2
3---4.8852 Å2
精密化ステップサイクル: LAST / 解像度: 2.176→29.499 Å
タンパク質核酸リガンド溶媒全体
原子数4199 0 4 153 4356
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0094338
X-RAY DIFFRACTIONf_angle_d1.2395929
X-RAY DIFFRACTIONf_dihedral_angle_d14.8931584
X-RAY DIFFRACTIONf_chiral_restr0.083690
X-RAY DIFFRACTIONf_plane_restr0.008769
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1764-2.24040.41481380.35022602X-RAY DIFFRACTION98
2.2404-2.31270.35021580.32072616X-RAY DIFFRACTION100
2.3127-2.39530.32881400.27492648X-RAY DIFFRACTION100
2.3953-2.49120.27461330.2572658X-RAY DIFFRACTION100
2.4912-2.60450.27821360.23172647X-RAY DIFFRACTION100
2.6045-2.74170.30961260.23972690X-RAY DIFFRACTION100
2.7417-2.91330.29151590.22122644X-RAY DIFFRACTION100
2.9133-3.1380.27761640.21112668X-RAY DIFFRACTION100
3.138-3.45340.26981410.19642690X-RAY DIFFRACTION100
3.4534-3.95210.21251440.19252715X-RAY DIFFRACTION100
3.9521-4.97530.21491500.15152745X-RAY DIFFRACTION100
4.9753-29.50190.20811290.19252917X-RAY DIFFRACTION100
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)
19.5556-0.1331-5.54217.6347-0.04512.21930.02720.5242-1.9287-0.4623-0.5105-0.46260.67090.82130.44910.43650.15860.01680.4223-0.02580.43754.877-31.98499.5367
23.9333-0.4743-2.20413.7341-1.84983.3243-1.37890.77220.1317-0.8036-0.8846-0.18391.2741-0.93610.73190.5462-0.0680.27730.50370.05510.614410.8077-27.455-0.5565
35.27711.4234-3.16474.8904-2.65635.2086-0.25550.51260.15240.00660.0206-0.73740.0460.39760.17370.2230.0004-0.09440.40770.00260.43618.0081-19.24854.4517
43.1971-0.0324-1.00366.5545-6.72338.45280.29080.23431.30670.13160.169-0.0023-1.02730.1634-0.43950.386-0.1114-0.06570.50.10450.559.643-9.76330.0527
56.19943.252-0.26077.6063-3.4944.58420.15420.57581.2035-0.2571-0.25460.3776-0.18230.20170.09560.30050.0532-0.06380.39550.10560.491-0.9818-14.0460.8252
67.80863.9181-3.9629.1974-4.97012.1282-0.38990.32550.4622-0.86161.01250.08290.8062-0.9029-0.66620.35-0.0144-0.06380.456-0.03250.40533.6334-20.0401-4.4178
79.53841.8872-6.56082.04886.02886.64631.68912.3343-1.8049-0.8002-1.31361.87680.8597-2.124-0.65520.7430.0662-0.25661.04840.17681.3569-1.6923-6.7686-8.4414
86.372-1.90131.18348.4859-1.75846.52281.76263.00860.1854-0.9820.62171.9324-1.0447-1.1209-0.69250.6291-0.2097-0.07120.45041.56471.16673.1822-0.6747-14.5519
94.2063-1.34883.03385.7611-3.65437.99730.27630.68471.2194-0.9572-0.4741-0.92810.2031.3661-0.00920.5371-0.2410.03711.07230.37170.851915.1279-6.0816-11.9135
106.9294-2.6726-0.21362.02112.47366.1656-0.942-0.5366-0.1357-2.0720.7429-2.1954-0.88321.13440.02390.73190.0917-0.15510.5871-0.25051.1424-1.8536-45.94293.7762
118.87222.36862.44573.66591.44539.91340.0033-0.39280.04490.0837-0.0938-0.00720.4671-0.31570.09890.34910.019-0.07020.2217-0.01350.2409-12.0591-34.91228.4664
129.46757.0765-2.69752.57990.81677.60720.15170.15770.54510.232-0.21840.4274-0.2894-0.60540.10250.33060.0154-0.05350.30910.00040.323-18.263-32.53995.4831
138.326-0.45240.73557.0701-2.28156.8746-0.18570.1315-1.25220.04050.07370.03360.90710.0084-0.0480.52560.043-0.07030.42880.00010.6669-1.2572-36.9018-11.573
146.02521.1915-3.86561.8771-1.80127.0354-0.29620.6126-0.3932-0.28420.1378-0.05140.1279-1.21150.17730.3873-0.0644-0.16910.54280.07220.4984-8.5847-30.2216-14.151
159.47543.08146.56617.40343.66376.8260.20261.8519-0.1174-1.09890.3061-0.2321-1.87580.1925-0.54030.57260.0639-0.05931.04540.01920.4789-0.3386-22.2432-16.8569
166.23033.4522-2.40752.0556-5.0758.6148-0.25412.1841-0.1062-1.4361-0.3091-2.06861.00410.3290.59980.54040.00350.1560.7956-0.03460.7913.4644-29.9384-21.3168
171.82212.98580.67785.37132.59555.62790.14580.3873-0.23531.13280.1607-1.47980.1212-0.2129-0.41230.52730.1009-0.24980.48180.06890.58-0.7495-28.3149-8.1354
188.4778-1.92241.78632.00770.78772.027-0.56990.96620.54890.79070.42450.7298-2.2092-0.29150.17380.84430.1113-0.12720.83250.3420.9575-7.1569-15.1329-6.4303
192.3957-1.04881.36142.6729-1.49046.89430.0782-0.28990.11170.39750.1055-1.51370.16320.8390.00340.3662-0.0498-0.04820.43310.02080.4632-15.8407-66.4334-2.4302
2010.11413.0207-2.43293.3541-5.08538.7215-0.1702-0.3265-0.77540.614-0.6039-0.78730.43060.7650.67490.48890.01690.02190.3066-0.00890.484-21.204-75.69870.6273
213.20652.3656-1.05186.0514-2.2031.65410.1212-0.2604-0.1920.844-0.06530.2721-0.1276-0.225-0.06710.4049-0.04970.12240.3503-0.08230.359-30.5164-74.52023.4763
224.07553.9049-1.67156.4206-2.73110.97980.2922-0.47820.71120.451-0.06721.2714-0.03890.0309-0.18230.39920.00120.1690.3456-0.05660.4893-35.7422-68.05233.1655
232.55246.1535-6.30632.3468-6.70782.26520.3513-1.26840.03840.7884-0.89130.8290.03670.36930.34340.6306-0.06870.15070.4806-0.06330.4899-29.2776-70.03649.7142
242.32492.73752.94683.67394.81216.41930.3287-1.30360.88480.49780.19091.9628-1.14-1.2118-0.45270.774-0.04420.34761.01910.23410.8659-44.2763-70.528210.5063
256.9495-2.00330.10933.4591-0.83345.1972-0.2578-1.0125-0.20541.58020.47191.3602-0.0693-0.723-0.24150.8448-0.020.37160.48980.02090.7168-42.3982-82.816615.8176
261.43471.0986-0.30430.9528-0.37440.13120.9653-1.07220.08930.793-1.19320.137-0.132-0.58320.44820.8949-0.0948-0.40790.7461-0.20071.024-7.2672-53.6697.1479
277.3093.07170.16988.36890.58845.2957-0.1099-0.0239-0.03760.1456-0.1154-0.9807-0.35250.81380.18790.2911-0.0459-0.04830.39-0.04230.418-15.9194-53.0967-1.8971
282.3995-1.9103-2.70972.39372.02498.6121-0.08530.04060.0290.1653-0.26870.37410.0046-0.29350.36360.3299-0.0656-0.01880.2914-0.04870.2533-23.6501-46.5752-0.6112
292.2536-3.937-1.31892.16546.37177.6303-0.62240.54850.23530.23410.08920.43880.3351-0.97070.51390.3364-0.08370.01570.438-0.0290.4274-30.6179-49.46042.7888
304.34043.5672-1.04922.3168-1.20932.3799-0.55420.0333-1.3243-0.94130.161-0.2378-0.09260.54110.43010.6688-0.2046-0.14970.43240.13480.6298-18.4793-39.5872-2.2582
316.5402-0.6843-0.83695.4009-0.63790.20920.3069-0.9530.27410.84550.9542-0.50990.61280.9987-0.9881.96570.0756-0.17281.4820.05570.3402-16.2234-60.557620.0462
327.63652.14050.40542.01772.12742.018-0.23720.4073-0.18030.77631.2518-0.72861.5796-0.2713-0.88961.1026-0.18890.00921.92-0.44620.6885-17.7072-57.757813.4073
334.137-0.8218-1.90330.13310.36460.8673-0.0657-1.9107-0.79510.5881.0387-0.49730.55230.5656-0.18082.10931.14070.4123.3116-0.102-0.7163-22.6435-57.53530.5307
348.40021.45244.56662.01-6.45027.1594-0.8676-0.29890.15522.3913-0.14520.0728-0.4391-0.69140.77461.3677-0.27550.1781.0358-0.15080.7091-25.0312-52.019119.9631
357.03263.86080.64192.2114-0.09334.18980.42541.2794-0.06921.0533-0.54530.8404-0.15850.27230.01191.1897-0.03750.29590.69430.05010.8255-29.8389-56.312114.9318
365.20735.29023.97225.99632.44167.08581.70390.67440.0495-0.85860.2126-2.15410.03470.1731-1.56551.29910.6050.23851.4289-0.15571.4716-28.5867-68.732918.6713
379.18888.5444-3.36262.00564.24731.99370.3316-2.2988-0.46481.3228-1.4948-0.69180.0553-0.31381.05461.5311-0.21230.08891.39050.22551.0037-29.6351-63.280426.9559
380.50790.391-1.50865.9121-0.61615.0946-0.3316-0.30431.0750.3573-0.3753-0.28510.0684-0.49060.09450.6519-0.27780.17671.1826-0.32781.198-26.2652-63.345116.669
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:15)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 16:25)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 26:65)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 66:74)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 75:98)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 99:111)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 112:120)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 121:130)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 131:147)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 242:249)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 250:278)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 279:298)
13X-RAY DIFFRACTION13CHAIN C AND (RESSEQ 0:17)
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 18:44)
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 45:54)
16X-RAY DIFFRACTION16CHAIN C AND (RESSEQ 55:65)
17X-RAY DIFFRACTION17CHAIN C AND (RESSEQ 66:71)
18X-RAY DIFFRACTION18CHAIN C AND (RESSEQ 72:76)
19X-RAY DIFFRACTION19CHAIN D AND (RESSEQ 2:15)
20X-RAY DIFFRACTION20CHAIN D AND (RESSEQ 16:38)
21X-RAY DIFFRACTION21CHAIN D AND (RESSEQ 39:74)
22X-RAY DIFFRACTION22CHAIN D AND (RESSEQ 75:98)
23X-RAY DIFFRACTION23CHAIN D AND (RESSEQ 99:111)
24X-RAY DIFFRACTION24CHAIN D AND (RESSEQ 112:120)
25X-RAY DIFFRACTION25CHAIN D AND (RESSEQ 121:147)
26X-RAY DIFFRACTION26CHAIN E AND (RESSEQ 242:249)
27X-RAY DIFFRACTION27CHAIN E AND (RESSEQ 250:261)
28X-RAY DIFFRACTION28CHAIN E AND (RESSEQ 262:278)
29X-RAY DIFFRACTION29CHAIN E AND (RESSEQ 279:290)
30X-RAY DIFFRACTION30CHAIN E AND (RESSEQ 291:298)
31X-RAY DIFFRACTION31CHAIN F AND (RESSEQ 2:6)
32X-RAY DIFFRACTION32CHAIN F AND (RESSEQ 7:15)
33X-RAY DIFFRACTION33CHAIN F AND (RESSEQ 16:22)
34X-RAY DIFFRACTION34CHAIN F AND (RESSEQ 23:34)
35X-RAY DIFFRACTION35CHAIN F AND (RESSEQ 35:44)
36X-RAY DIFFRACTION36CHAIN F AND (RESSEQ 45:49)
37X-RAY DIFFRACTION37CHAIN F AND (RESSEQ 50:59)
38X-RAY DIFFRACTION38CHAIN F AND (RESSEQ 60:76)

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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