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- PDB-4p4h: Caught-in-action signaling complex of RIG-I 2CARD domain and MAVS... -

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基本情報

登録情報
データベース: PDB / ID: 4p4h
タイトルCaught-in-action signaling complex of RIG-I 2CARD domain and MAVS CARD domain
要素
  • Mitochondrial antiviral-signaling protein
  • Probable ATP-dependent RNA helicase DDX58
  • Ubiquitin-60S ribosomal protein L40
キーワードSIGNALING PROTEIN / signaling complex
機能・相同性
機能・相同性情報


positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / regulation of type III interferon production / RIG-I signaling pathway / positive regulation of chemokine (C-C motif) ligand 5 production / CARD domain binding / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus ...positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / regulation of type III interferon production / RIG-I signaling pathway / positive regulation of chemokine (C-C motif) ligand 5 production / CARD domain binding / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / peroxisomal membrane / positive regulation of granulocyte macrophage colony-stimulating factor production / cellular response to exogenous dsRNA / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / positive regulation of NLRP3 inflammasome complex assembly / type I interferon-mediated signaling pathway / RSV-host interactions / response to exogenous dsRNA / positive regulation of interferon-alpha production / Peptide chain elongation / TRAF6 mediated NF-kB activation / positive regulation of type I interferon production / 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) / GTP hydrolysis and joining of the 60S ribosomal subunit / bicellular tight junction / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of defense response to virus by host / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / signaling adaptor activity / ubiquitin ligase complex / activation of innate immune response / antiviral innate immune response / 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 / positive regulation of interferon-beta production / regulation of cell migration / 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 / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / 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 / Gap-filling DNA repair synthesis and ligation in GG-NER / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1
類似検索 - 分子機能
IPS1, CARD domain / : / RIG-I, CARD domain repeat 2 / Death Domain, Fas / Death Domain, Fas / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : ...IPS1, CARD domain / : / RIG-I, CARD domain repeat 2 / Death Domain, Fas / Death Domain, Fas / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Death-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / helicase superfamily c-terminal domain / Ubiquitin domain profile. / Ubiquitin-like 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 / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Antiviral innate immune response receptor RIG-I / Ubiquitin-ribosomal protein eL40 fusion protein / Mitochondrial antiviral-signaling protein
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 / 解像度: 3.4 Å
データ登録者Wu, B. / Hur, S.
引用ジャーナル: Mol Cell / 年: 2014
タイトル: Molecular imprinting as a signal-activation mechanism of the viral RNA sensor RIG-I.
著者: Bin Wu / Alys Peisley / David Tetrault / Zongli Li / Edward H Egelman / Katharine E Magor / Thomas Walz / Pawel A Penczek / Sun Hur /
要旨: RIG-I activates interferon signaling pathways by promoting filament formation of the adaptor molecule, MAVS. Assembly of the MAVS filament is mediated by its CARD domain (CARD(MAVS)), and requires ...RIG-I activates interferon signaling pathways by promoting filament formation of the adaptor molecule, MAVS. Assembly of the MAVS filament is mediated by its CARD domain (CARD(MAVS)), and requires its interaction with the tandem CARDs of RIG-I (2CARD(RIG-I)). However, the precise nature of the interaction between 2CARD(RIG-I) and CARD(MAVS), and how this interaction leads to CARD(MAVS) filament assembly, has been unclear. Here we report a 3.6 Å electron microscopy structure of the CARD(MAVS) filament and a 3.4 Å crystal structure of the 2CARD(RIG-I):CARD(MAVS) complex, representing 2CARD(RIG-I) "caught in the act" of nucleating the CARD(MAVS) filament. These structures, together with functional analyses, show that 2CARD(RIG-I) acts as a template for the CARD(MAVS) filament assembly, by forming a helical tetrameric structure and recruiting CARD(MAVS) along its helical trajectory. Our work thus reveals that signal activation by RIG-I occurs by imprinting its helical assembly architecture on MAVS, a previously uncharacterized mechanism of signal transmission.
履歴
登録2014年3月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年7月30日Provider: repository / タイプ: Initial release
改定 1.12014年10月1日Group: Database references
改定 1.22015年1月7日Group: Database references
改定 1.32023年12月27日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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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: Probable ATP-dependent RNA helicase DDX58
B: Probable ATP-dependent RNA helicase DDX58
C: Probable ATP-dependent RNA helicase DDX58
D: Probable ATP-dependent RNA helicase DDX58
E: Probable ATP-dependent RNA helicase DDX58
F: Probable ATP-dependent RNA helicase DDX58
G: Probable ATP-dependent RNA helicase DDX58
H: Probable ATP-dependent RNA helicase DDX58
I: Mitochondrial antiviral-signaling protein
J: Mitochondrial antiviral-signaling protein
K: Mitochondrial antiviral-signaling protein
L: Mitochondrial antiviral-signaling protein
N: Mitochondrial antiviral-signaling protein
O: Mitochondrial antiviral-signaling protein
P: Mitochondrial antiviral-signaling protein
S: Ubiquitin-60S ribosomal protein L40
T: Ubiquitin-60S ribosomal protein L40
U: Ubiquitin-60S ribosomal protein L40
W: Ubiquitin-60S ribosomal protein L40
X: Ubiquitin-60S ribosomal protein L40
M: Mitochondrial antiviral-signaling protein


分子量 (理論値)分子数
合計 (水以外)334,39321
ポリマ－334,39321
非ポリマー00
水00
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 area50470 Å2
ΔGint-52 kcal/mol
Surface area99430 Å2
手法PISA
単位格子
Length a, b, c (Å)111.810, 117.330, 257.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A and (resseq 1:188 ) and (not element H)
21chain E and (resseq 1:188 ) and (not element H)
12chain B and (resseq 1:189 ) and (not element H)
22chain F and (resseq 1:189 ) and (not element H)
13chain C and (resseq 1:189 ) and (not element H)
23chain G and (resseq 1:189 ) and (not element H)
14chain D and (resseq 1:188 ) and (not element H)
24chain H and (resseq 1:188 ) and (not element H)
15chain I and (resseq 1:97 ) and (not element H)
25chain M and (resseq 1:97 ) and (not element H)
16chain J and (resseq 1:97 ) and (not element H)
26chain N and (resseq 1:97 ) and (not element H)
17chain K and (resseq 1:78 ) and (not element H)
27chain O and (resseq 1:78 ) and (not element H)
18chain L and (resseq 1:78 ) and (not element H)
28chain P and (resseq 1:78 ) and (not element H)
19chain S and (resseq 1:71 ) and (not element H)
29chain U and (resseq 1:72 ) and (not element H)
39chain W and (resseq 1:71 ) and (not element H)
110chain T and (resseq 1:73 ) and (not element H)
210chain X and (resseq 1:73 ) and (not element H)

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 1:188 ) and (not element H)A0
211chain E and (resseq 1:188 ) and (not element H)E0
112chain B and (resseq 1:189 ) and (not element H)B0
212chain F and (resseq 1:189 ) and (not element H)F0
113chain C and (resseq 1:189 ) and (not element H)C0
213chain G and (resseq 1:189 ) and (not element H)G0
114chain D and (resseq 1:188 ) and (not element H)D0
214chain H and (resseq 1:188 ) and (not element H)H0
115chain I and (resseq 1:97 ) and (not element H)I0
215chain M and (resseq 1:97 ) and (not element H)M0
116chain J and (resseq 1:97 ) and (not element H)J0
216chain N and (resseq 1:97 ) and (not element H)N0
117chain K and (resseq 1:78 ) and (not element H)K0
217chain O and (resseq 1:78 ) and (not element H)O0
118chain L and (resseq 1:78 ) and (not element H)L0
218chain P and (resseq 1:78 ) and (not element H)P0
119chain S and (resseq 1:71 ) and (not element H)S0
219chain U and (resseq 1:72 ) and (not element H)U0
319chain W and (resseq 1:71 ) and (not element H)W0
1110chain T and (resseq 1:73 ) and (not element H)T0
2110chain X and (resseq 1:73 ) and (not element H)X0

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10

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要素

#1: タンパク質
Probable ATP-dependent RNA helicase DDX58 / DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG- ...DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG-1 / Retinoic acid-inducible gene I protein / RIG-I


分子量: 24014.543 Da / 分子数: 8 / 変異: E52A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DDX58 / プラスミド: pET47b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Bl21(DE3) / 参照: UniProt: O95786, RNA helicase
#2: タンパク質
Mitochondrial antiviral-signaling protein / MAVS / CARD adapter inducing interferon beta / Cardif / Interferon beta promoter stimulator protein ...MAVS / CARD adapter inducing interferon beta / Cardif / Interferon beta promoter stimulator protein 1 / IPS-1 / Putative NF-kappa-B-activating protein 031N / Virus-induced-signaling adapter / VISA


分子量: 12292.028 Da / 分子数: 8 / 変異: D23K, E26K, E80K / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IPS1, KIAA1271, MAVS, pstS, VISA / プラスミド: pET47b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Bl21(DE3) / 参照: UniProt: Q7Z434
#3: タンパク質
Ubiquitin-60S ribosomal protein L40 / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1


分子量: 8788.049 Da / 分子数: 5 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBA52, UBCEP2 / プラスミド: pET47b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62987

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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: 2.53 Å3/Da / 溶媒含有率: 51.3 % / 解説: hexagonal rods
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 / 詳細: Tri-Li Citrate, PEG 3350, Cr(III) Cl3

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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: 21-ID-F / 波長: 1 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2013年12月13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: 1 Å / 相対比: 1
反射解像度: 3.4→46.8 Å / Num. obs: 89450 / % possible obs: 99.1 % / 冗長度: 3.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.28
反射 シェル解像度: 3.4→3.438 Å / 冗長度: 3.2 % / Rmerge(I) obs: 1.315 / Mean I/σ(I) obs: 1.26 / % possible all: 97.8

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解析

ソフトウェア名称: PHENIX / バージョン: (phenix.refine: 1.8.4_1496) / 分類: 精密化
精密化解像度: 3.4→46.8 Å / SU ML: 0.48 / 交差検証法: FREE R-VALUE / σ(F): 1 / 位相誤差: 25.17 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2397 4448 4.97 %
Rwork0.1911 --
obs0.1936 89450 99.37 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 3.4→46.8 Å
タンパク質核酸リガンド溶媒全体
原子数21711 0 0 0 21711
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01122154
X-RAY DIFFRACTIONf_angle_d1.26829912
X-RAY DIFFRACTIONf_dihedral_angle_d16.988420
X-RAY DIFFRACTIONf_chiral_restr0.0513300
X-RAY DIFFRACTIONf_plane_restr0.0073792
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A1549X-RAY DIFFRACTIONPOSITIONAL0.079
12E1549X-RAY DIFFRACTIONPOSITIONAL0.079
21B1555X-RAY DIFFRACTIONPOSITIONAL0.054
22F1555X-RAY DIFFRACTIONPOSITIONAL0.054
31C1563X-RAY DIFFRACTIONPOSITIONAL0.068
32G1563X-RAY DIFFRACTIONPOSITIONAL0.068
41D1562X-RAY DIFFRACTIONPOSITIONAL0.058
42H1562X-RAY DIFFRACTIONPOSITIONAL0.058
51I789X-RAY DIFFRACTIONPOSITIONAL0.108
52M789X-RAY DIFFRACTIONPOSITIONAL0.108
61J796X-RAY DIFFRACTIONPOSITIONAL0.058
62N796X-RAY DIFFRACTIONPOSITIONAL0.058
71K648X-RAY DIFFRACTIONPOSITIONAL0.057
72O648X-RAY DIFFRACTIONPOSITIONAL0.057
81L648X-RAY DIFFRACTIONPOSITIONAL0.07
82P648X-RAY DIFFRACTIONPOSITIONAL0.07
91S555X-RAY DIFFRACTIONPOSITIONAL0.065
92U555X-RAY DIFFRACTIONPOSITIONAL0.065
93W555X-RAY DIFFRACTIONPOSITIONAL0.039
101T582X-RAY DIFFRACTIONPOSITIONAL0.042
102X582X-RAY DIFFRACTIONPOSITIONAL0.042
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.43870.32921800.32012825X-RAY DIFFRACTION100
3.4387-3.47910.38451320.32522875X-RAY DIFFRACTION100
3.4791-3.52160.36221370.30832867X-RAY DIFFRACTION100
3.5216-3.56610.37011350.30942835X-RAY DIFFRACTION100
3.5661-3.6130.3331290.29752884X-RAY DIFFRACTION100
3.613-3.66250.31281540.28782860X-RAY DIFFRACTION100
3.6625-3.71480.26571640.26152797X-RAY DIFFRACTION100
3.7148-3.77020.29461510.26032888X-RAY DIFFRACTION100
3.7702-3.82910.31941710.2582817X-RAY DIFFRACTION100
3.8291-3.89190.32421480.24692810X-RAY DIFFRACTION100
3.8919-3.95890.31441590.25122836X-RAY DIFFRACTION100
3.9589-4.03090.2431300.24272847X-RAY DIFFRACTION100
4.0309-4.10840.29441550.21972844X-RAY DIFFRACTION100
4.1084-4.19220.26481500.20482846X-RAY DIFFRACTION100
4.1922-4.28330.23881510.19912827X-RAY DIFFRACTION100
4.2833-4.38280.23071530.20032842X-RAY DIFFRACTION100
4.3828-4.49240.25391330.1912888X-RAY DIFFRACTION100
4.4924-4.61370.21881500.18172811X-RAY DIFFRACTION100
4.6137-4.74940.23511350.17722874X-RAY DIFFRACTION100
4.7494-4.90250.26551360.17832846X-RAY DIFFRACTION100
4.9025-5.07750.26551710.18342841X-RAY DIFFRACTION100
5.0775-5.28060.20891640.17412799X-RAY DIFFRACTION100
5.2806-5.52050.2411640.18522837X-RAY DIFFRACTION100
5.5205-5.81110.30361130.19022882X-RAY DIFFRACTION100
5.8111-6.17440.26181400.19312842X-RAY DIFFRACTION100
6.1744-6.64990.28111390.18792841X-RAY DIFFRACTION100
6.6499-7.31690.25221610.15832818X-RAY DIFFRACTION99
7.3169-8.37040.17591380.11812809X-RAY DIFFRACTION99
8.3704-10.52610.12551470.11382804X-RAY DIFFRACTION98
10.5261-46.84990.17141580.14092610X-RAY DIFFRACTION92
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)
18.7594-0.0185-4.17334.0451-1.20375.17960.05440.64250.4905-0.48190.2980.63120.4384-0.7592-0.31360.5468-0.1147-0.18840.55950.07290.7858-26.9914-12.62688.7553
23.8182.5338-1.68625.4702-1.48043.0891-0.3105-0.4548-0.702-0.2195-0.2447-0.77560.60210.54860.47380.60350.26630.01730.78910.00190.73743.387-17.393915.7396
34.47760.30060.03814.6551-1.81283.45020.2425-1.0091-0.10670.7717-0.4771-0.6845-0.44240.78190.20030.5207-0.2233-0.0741.0257-0.11550.79851.067912.597725.3593
43.8861-0.5051-1.88482.5716-0.77215.80090.14380.32160.4049-0.09770.18080.7857-0.0302-0.5297-0.29480.3664-0.0896-0.07160.5713-0.051.0278-23.282111.9995.4324
52.880.6627-0.19136.9025-1.2176.27910.1847-0.32860.29260.61910.3277-0.414-0.53010.9511-0.40290.6126-0.0042-0.13040.8406-0.26360.8042-15.0981-2.934854.543
62.97680.2341-0.39433.8124-2.04784.02180.1436-0.1402-0.70620.1148-0.0601-0.62821.07251.1918-0.02431.07760.4491-0.30.9898-0.1680.9495-11.5272-33.042846.2456
74.7423-0.0724-1.17393.49652.20156.574-0.11950.0551-0.42790.18920.05420.07370.8229-0.24350.1140.7643-0.0734-0.11950.42440.01730.5913-42.1362-29.613638.5634
83.9022-0.21210.32055.3136-1.1287.8103-0.0788-0.41650.55480.7931-0.00410.0709-0.609-0.41840.13510.6640.1081-0.08250.5862-0.20670.6334-39.4966-6.060659.3613
95.3183-1.5404-0.67955.1566-0.56297.9176-0.07330.0374-0.2081-0.13890.1748-0.10620.90870.1417-0.05430.58620.01570.09810.4866-0.05940.51635.1511-10.9467-11.708
104.92563.87180.33188.06613.46865.72470.3817-0.64770.00890.6597-0.3411-0.56920.38820.13590.06350.3658-0.0096-0.09830.77310.11061.004920.185415.34215.1638
116.6633-4.7677-2.83036.28862.02253.78610.1518-0.2081.1268-0.17960.2273-0.6004-0.23840.0607-0.42410.3752-0.04630.02430.62210.03541.1369-8.335431.5617-5.9395
124.7525-0.02732.63747.0032.42387.54140.21790.8383-0.1698-1.26730.00780.25530.6377-0.3673-0.25721.0266-0.1082-0.04891.10230.06380.4896-6.87364.4672-28.8559
130.9239-0.7724-0.75982.3175-1.18833.2831-0.0554-0.8429-0.56531.1470.6151-0.80371.26190.8253-0.42372.480.5408-0.72421.38750.03211.2007-16.1367-35.654873.8269
143.11840.18990.79020.4107-0.3520.88751.3524-0.3825-1.8841.4437-0.2701-0.13651.5968-0.7923-0.57962.6553-0.6161-0.40530.90110.39281.4663-43.6345-49.542758.1713
152.58890.3637-0.48320.25620.20545.04890.3446-2.30710.97520.438-0.78910.60120.7262-2.46540.21511.3876-0.65730.46142.4043-0.69931.2378-58.8845-20.52371.4354
161.75650.047-1.91930.9538-0.69912.83590.2343-0.6422-0.15610.94370.233-0.17191.2168-0.1976-0.44922.56580.0582-0.30681.62770.12190.7812-30.5347-24.031992.5215
176.7168-2.50250.04417.0155-3.05412.327-0.4411-0.75590.68821.11710.01230.7898-1.0964-0.48040.60240.9318-0.09340.15540.8881-0.36381.2416-21.29136.355223.3076
186.56591.0972-0.57922.7162-0.53360.99560.21860.18172.2732-1.04750.62612.6809-0.1612-0.3725-0.42470.6543-0.0676-0.07861.15470.49912.9505-49.89616.463413.0592
198.42760.36160.30155.31461.55763.29210.544-0.87210.19531.2025-0.0365-2.06120.64971.6125-0.33451.39110.434-0.56552.3485-0.16741.66410.9984-20.956162.1166
209.45911.4029-0.57345.8120.99277.6124-0.5632-0.3151.3121-0.8746-0.37511.0884-0.7981-1.88920.82151.05260.4391-0.25251.4298-0.29461.3172-64.7904-6.368342.7107
219.5019-3.0171.69895.7922-4.02376.07430.0387-0.69560.84090.140.5460.2114-1.44480.0067-0.27461.5510.04930.13340.6113-0.11780.891-33.538520.408452.9529
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A')
2X-RAY DIFFRACTION2(chain 'B')
3X-RAY DIFFRACTION3(chain 'C')
4X-RAY DIFFRACTION4(chain 'D')
5X-RAY DIFFRACTION5(chain 'E')
6X-RAY DIFFRACTION6(chain 'F')
7X-RAY DIFFRACTION7(chain 'G')
8X-RAY DIFFRACTION8(chain 'H')
9X-RAY DIFFRACTION9(chain 'I')
10X-RAY DIFFRACTION10(chain 'J')
11X-RAY DIFFRACTION11(chain 'K')
12X-RAY DIFFRACTION12(chain 'L')
13X-RAY DIFFRACTION13(chain 'M')
14X-RAY DIFFRACTION14(chain 'N')
15X-RAY DIFFRACTION15(chain 'O')
16X-RAY DIFFRACTION16(chain 'P')
17X-RAY DIFFRACTION17(chain 'S')
18X-RAY DIFFRACTION18(chain 'T')
19X-RAY DIFFRACTION19(chain 'U')
20X-RAY DIFFRACTION20(chain 'W')
21X-RAY DIFFRACTION21(chain 'X')

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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