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- PDB-6hpr: Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a n... -

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基本情報

登録情報
データベース: PDB / ID: 6hpr
タイトルCrystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub
要素
  • Baculoviral IAP repeat-containing protein 2
  • Polyubiquitin-B
  • Ubiquitin-conjugating enzyme E2 D2
キーワードLIGASE / Ubiquitin / E3 / cIAP1 / UbcH5B / ubiquitin ligase
機能・相同性
機能・相同性情報


negative regulation of ripoptosome assembly involved in necroptotic process / FBXO family protein binding / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / positive regulation of protein K63-linked ubiquitination / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / CD40 receptor complex ...negative regulation of ripoptosome assembly involved in necroptotic process / FBXO family protein binding / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / positive regulation of protein K63-linked ubiquitination / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / CD40 receptor complex / (E3-independent) E2 ubiquitin-conjugating enzyme / negative regulation of necroptotic process / XY body / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / non-canonical NF-kappaB signal transduction / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / TNFR1-induced proapoptotic signaling / fat pad development / RIPK1-mediated regulated necrosis / mitochondrion transport along microtubule / regulation of reactive oxygen species metabolic process / E2 ubiquitin-conjugating enzyme / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / female gonad development / seminiferous tubule development / male meiosis I / necroptotic process / ubiquitin conjugating enzyme activity / regulation of cell differentiation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to cAMP / canonical NF-kappaB signal transduction / protein K48-linked ubiquitination / protein autoubiquitination / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / 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 / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / placenta development / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / ubiquitin binding / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy
類似検索 - 分子機能
BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / : / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat ...BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / : / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Herpes Virus-1 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Death-like domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Polyubiquitin-B / Ubiquitin-conjugating enzyme E2 D2 / Baculoviral IAP repeat-containing protein 2
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: 1.7 Å
データ登録者Patel, A. / Huang, D.T.
資金援助 英国, 1件
組織認可番号国
Cancer Research UKA23278 英国
引用ジャーナル: J. Biol. Chem. / 年: 2019
タイトル: Structural insights into non-covalent ubiquitin activation of the cIAP1-UbcH5B∼ubiquitin complex.
著者: Patel, A. / Sibbet, G.J. / Huang, D.T.
履歴
登録2018年9月21日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02018年12月12日Provider: repository / タイプ: Initial release
改定 1.12018年12月19日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
改定 1.22018年12月26日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
改定 1.32019年3月6日Group: Data collection / Database references
カテゴリ: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
改定 1.42019年5月8日Group: Advisory / Data collection / Derived calculations
カテゴリ: diffrn_source / pdbx_validate_close_contact ...diffrn_source / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
改定 1.52019年7月10日Group: Data collection / カテゴリ: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
改定 1.62024年1月24日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Baculoviral IAP repeat-containing protein 2
B: Polyubiquitin-B
C: Ubiquitin-conjugating enzyme E2 D2
D: Polyubiquitin-B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,0626
ポリマ－41,9314
非ポリマー1312
水3,999222
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
  • 根拠: surface plasmon resonance, Other biochemical assays, NMR
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-19 kcal/mol
Surface area16870 Å2
手法PISA
単位格子
Length a, b, c (Å)79.190, 53.600, 78.540
Angle α, β, γ (deg.)90.00, 107.57, 90.00
Int Tables number5
Space group name H-MC121

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要素

#1: タンパク質 Baculoviral IAP repeat-containing protein 2 / Cellular inhibitor of apoptosis 1 / C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / ...Cellular inhibitor of apoptosis 1 / C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / hIAP2 / RING finger protein 48 / RING-type E3 ubiquitin transferase BIRC2 / TNFR2-TRAF-signaling complex protein 2


分子量: 7305.725 Da / 分子数: 1 / 由来タイプ: 組換発現
詳細: cIAP1 residues 556-C with N-terminal GS resulted from TEV cleavage
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BIRC2, API1, MIHB, RNF48 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q13490, RING-type E3 ubiquitin transferase
#2: タンパク質 Polyubiquitin-B


分子量: 8922.141 Da / 分子数: 2 / 由来タイプ: 組換発現
詳細: Ubiquitin residues 1-76 contains N-terminal GSGGS after TEV cleavage. Chain D Gly76 forms isopeptide linkage with Chain C Lys85.
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0CG47
#3: タンパク質 Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


分子量: 16781.264 Da / 分子数: 1 / 由来タイプ: 組換発現
詳細: UbcH5B residues 1-147. Cys85 is mutated to Lys and forms isopeptide linkage with ubiquitin's Gly76 in chain D.
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#4: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 天然 / 式: Zn
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 222 / 由来タイプ: 天然 / 式: 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: 1.89 Å3/Da / 溶媒含有率: 34.94 %
結晶化温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.2 M ammonium fluoride and 15% (w/v) 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: Diamond / ビームライン: I03 / 波長: 0.9763 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2014年5月27日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9763 Å / 相対比: 1
反射解像度: 1.7→23.52 Å / Num. obs: 34206 / % possible obs: 98.8 % / 冗長度: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.04 / Rrim(I) all: 0.075 / Net I/σ(I): 13.8
反射 シェル解像度: 1.7→1.74 Å / 冗長度: 2.7 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2 / CC1/2: 0.632 / % possible all: 94.7

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10_2142: ???)精密化
xia2データ削減
xia2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: 3EB6, 3ZNI

3eb6

3zni


解像度: 1.7→23.515 Å / SU ML: 0.19 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 20.46
Rfactor反射数%反射
Rfree0.1972 1744 5.1 %
Rwork0.1704 --
obs0.1718 34206 98.64 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 1.7→23.515 Å
タンパク質核酸リガンド溶媒全体
原子数2784 0 2 222 3008
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0072851
X-RAY DIFFRACTIONf_angle_d0.9223880
X-RAY DIFFRACTIONf_dihedral_angle_d16.1671758
X-RAY DIFFRACTIONf_chiral_restr0.06457
X-RAY DIFFRACTIONf_plane_restr0.006500
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.29951400.25582578X-RAY DIFFRACTION95
1.75-1.80650.26091330.22872663X-RAY DIFFRACTION98
1.8065-1.8710.23711520.20612681X-RAY DIFFRACTION98
1.871-1.94590.22371490.20072688X-RAY DIFFRACTION99
1.9459-2.03440.23431480.1952686X-RAY DIFFRACTION99
2.0344-2.14160.21231340.18012728X-RAY DIFFRACTION99
2.1416-2.27570.24431490.16892700X-RAY DIFFRACTION99
2.2757-2.45120.22031340.1752737X-RAY DIFFRACTION99
2.4512-2.69760.19131540.16942723X-RAY DIFFRACTION99
2.6976-3.08720.18731420.16662741X-RAY DIFFRACTION100
3.0872-3.88670.17971640.15352732X-RAY DIFFRACTION100
3.8867-23.51760.15211450.14652805X-RAY DIFFRACTION99
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)
12.37813.39362.59356.84874.58593.2009-0.76051.0463-0.4041-0.44660.9886-0.5349-1.09940.7152-0.16030.7581-0.26830.08820.4848-0.12440.3938-8.30434.688733.4518
25.00420.5566-1.60294.1905-1.52524.5867-0.0265-0.0785-0.0134-0.03050.00640.316-0.0268-0.45850.01960.1156-0.0287-0.00350.1787-0.02490.0971-11.3224-15.576828.6709
37.8282-7.53593.04032.1048-4.58042.1223-0.6008-0.12580.46540.84430.334-0.3488-0.17820.20090.17090.31350.0302-0.06250.321-0.09130.41537.035515.83622.0174
42.0362-0.53851.99922.0224-0.00924.0627-0.3089-0.57271.2232-0.03240.496-0.7479-0.6120.2218-0.16920.3354-0.02760.03280.2593-0.11080.63819.290822.737814.5544
55.12874.99461.29946.1381-0.02134.5975-0.3624-0.48850.2254-0.59080.2441-1.4109-0.42291.01170.08920.2541-0.09580.08230.3249-0.12230.623416.490315.445511.9651
65.8583-1.5190.25812.0432-0.15363.41480.16690.31790.465-1.07130.0669-0.1921-0.43860.1665-0.20.2937-0.05480.04560.1708-0.00280.2784.695314.40117.0938
74.65561.7546-2.08924.28510.28722.00530.2988-0.09450.6198-0.07250.16750.2707-0.4507-0.54-0.5360.18040.06150.020.2632-0.0130.2757-2.146815.93213.1253
85.418-2.5476-0.55565.82270.64992.66110.0079-0.24270.7364-0.22920.2695-1.0683-0.00770.9336-0.26060.2044-0.0042-0.02110.3988-0.10180.414715.29810.435814.283
98.81483.9388-1.78072.0526-0.76548.4831-0.2078-0.36021.16980.69090.14790.9979-0.6643-0.44310.15740.26340.0879-0.01690.1816-0.02220.3281-7.13581.169817.6806
102.1046-3.90737.58617.6492-2.34355.98210.2133-0.21990.56270.3748-0.2412-0.31980.4386-0.28990.09220.1709-0.03930.01390.32680.03690.18412.0663.63413.827
112.0416-0.71956.62152.8349-0.79217.4844-0.44180.13650.7384-0.04330.01090.1356-0.1443-0.04830.48890.1628-0.0119-0.0120.1093-0.01480.1403-0.40270.34988.3637
122.0345-4.6766-3.44139.8284-1.55544.2868-0.2428-0.60440.11170.38510.1203-0.4264-0.23120.42920.14910.1337-0.0263-0.03420.1993-0.00670.157421.0745-1.171914.0071
138.07717.4184-2.10649.4101-1.02292.1728-0.46980.3050.3598-0.7590.28150.2214-0.0027-0.09070.18860.1448-0.0001-0.00420.070.01070.09325.8132-1.78156.4637
143.7499-2.6436-2.69295.8448-3.03692.041-0.19750.3935-0.4692-0.1055-0.00530.48090.3547-0.66010.13380.1495-0.05060.00650.1877-0.03240.1368-7.7191-10.586611.6642
159.7785-3.56071.64832.1501-0.33990.33460.07420.49770.1611-0.0979-0.2101-0.2341-0.0001-0.00290.12630.1731-0.016-0.01010.14910.00250.117111.5442-6.13573.8525
164.2667-0.1472-2.20570.7850.07012.06030.01670.0889-0.1268-0.0644-0.0507-0.0108-0.0074-0.11360.02770.14230.0054-0.02070.07330.01210.08136.6881-11.446112.3047
177.5817-0.30540.47631.81470.77343.4644-0.00150.0999-0.77640.1248-0.00340.01860.38620.0304-0.01190.17640.01080.01910.0927-0.01780.175921.0971-17.79718.3946
188.6721-6.66833.41487.6831-5.02315.4945-0.10180.27470.6281-0.0614-0.1-0.7275-0.18920.23580.17690.1267-0.03830.02670.1387-0.0170.14724.6545-4.52335.4611
192.10623.17998.33855.42262.89169.3064-0.4005-0.98250.6050.1379-0.02930.0391-0.4866-0.43940.37680.1767-0.00370.02230.362-0.12490.19927.1575-3.177833.9148
208.1227-2.85834.36682.4952-0.88852.6294-0.4292-0.73610.44390.18530.0547-0.1191-0.628-0.56990.34860.2239-0.03240.01110.4701-0.10560.20168.0933-3.703237.5422
213.8833.63113.17882.00242.00958.9525-0.1991-0.3699-0.19890.58890.7506-0.70460.16940.4177-0.59750.16660.0107-0.01010.2829-0.04750.262120.1035-8.009938.6956
229.26671.069-3.87674.97011.20749.17320.0312-0.9443-0.40730.3746-0.25750.08580.4861-0.12480.24040.209-0.0709-0.03620.270.03410.11119.5931-13.179435.9903
233.94442.3161-1.87614.3453-1.23974.50170.0301-0.4195-0.12310.0486-0.17780.02690.0350.06180.14050.1143-0.0183-0.00130.18510.00320.10037.8959-14.677727.994
246.978-3.87237.06057.1078-6.392.06440.20630.212-0.2514-0.4462-0.2431-0.24430.3550.4034-0.01440.20620.01410.04310.19130.00380.157818.666-9.193326.6194
256.03392.3452.60145.44792.13743.944-0.0749-0.57460.7050.0224-0.1048-0.1018-0.32840.01290.19310.1598-0.03640.01450.154-0.03640.165514.9378-3.259329.9188
268.1604-8.8541.98539.91312.00772.0006-0.40890.1979-0.32980.39640.10130.3491.5685-0.53920.46190.2055-0.04480.03280.0794-0.03160.11399.4386-17.674917.0306
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 556 through 569 )
2X-RAY DIFFRACTION2chain 'A' and (resid 570 through 618 )
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 17 )
4X-RAY DIFFRACTION4chain 'B' and (resid 18 through 34 )
5X-RAY DIFFRACTION5chain 'B' and (resid 35 through 44 )
6X-RAY DIFFRACTION6chain 'B' and (resid 45 through 56 )
7X-RAY DIFFRACTION7chain 'B' and (resid 57 through 65 )
8X-RAY DIFFRACTION8chain 'B' and (resid 66 through 74 )
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 15 )
10X-RAY DIFFRACTION10chain 'C' and (resid 16 through 28 )
11X-RAY DIFFRACTION11chain 'C' and (resid 29 through 38 )
12X-RAY DIFFRACTION12chain 'C' and (resid 39 through 48 )
13X-RAY DIFFRACTION13chain 'C' and (resid 49 through 55 )
14X-RAY DIFFRACTION14chain 'C' and (resid 56 through 65 )
15X-RAY DIFFRACTION15chain 'C' and (resid 66 through 74 )
16X-RAY DIFFRACTION16chain 'C' and (resid 75 through 110 )
17X-RAY DIFFRACTION17chain 'C' and (resid 111 through 130 )
18X-RAY DIFFRACTION18chain 'C' and (resid 131 through 147 )
19X-RAY DIFFRACTION19chain 'D' and (resid -1 through 11 )
20X-RAY DIFFRACTION20chain 'D' and (resid 12 through 17 )
21X-RAY DIFFRACTION21chain 'D' and (resid 18 through 22 )
22X-RAY DIFFRACTION22chain 'D' and (resid 23 through 34 )
23X-RAY DIFFRACTION23chain 'D' and (resid 35 through 44 )
24X-RAY DIFFRACTION24chain 'D' and (resid 45 through 56 )
25X-RAY DIFFRACTION25chain 'D' and (resid 57 through 71 )
26X-RAY DIFFRACTION26chain 'D' and (resid 72 through 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