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- PDB-5vi4: IL-33/ST2/IL-1RAcP ternary complex structure -

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基本情報

登録情報
データベース: PDB / ID: 5vi4
タイトルIL-33/ST2/IL-1RAcP ternary complex structure
要素
  • Interleukin-1 receptor accessory protein
  • Interleukin-1 receptor-like 1
  • Interleukin-33Interleukin 33
キーワードSIGNALING PROTEIN / cytokine (サイトカイン) / cytokine receptor / signaling
機能・相同性
機能・相同性情報


interleukin-33 binding / Interleukin-36 pathway / Interleukin-33 signaling / interleukin-33 receptor binding / negative regulation of macrophage proliferation / positive regulation of CD86 production / positive regulation of CD80 production / positive regulation of cellular defense response / interleukin-33 receptor activity / positive regulation of MHC class I biosynthetic process ...interleukin-33 binding / Interleukin-36 pathway / Interleukin-33 signaling / interleukin-33 receptor binding / negative regulation of macrophage proliferation / positive regulation of CD86 production / positive regulation of CD80 production / positive regulation of cellular defense response / interleukin-33 receptor activity / positive regulation of MHC class I biosynthetic process / negative regulation of T-helper 1 type immune response / negative regulation of immunoglobulin production / interleukin-1 receptor activity / Receptor-type tyrosine-protein phosphatases / trans-synaptic signaling by trans-synaptic complex / microglial cell activation involved in immune response / synaptic membrane adhesion / regulation of postsynaptic density assembly / negative regulation of leukocyte migration / Interleukin-1 signaling / PIP3 activates AKT signaling / microglial cell proliferation / regulation of sensory perception of pain / interleukin-33-mediated signaling pathway / positive regulation of type 2 immune response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of interleukin-5 production / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / Ub-specific processing proteases / macrophage activation involved in immune response / positive regulation of macrophage activation / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / positive regulation of MHC class II biosynthetic process / interleukin-1 receptor binding / positive regulation of synapse assembly / interleukin-1-mediated signaling pathway / positive regulation of interleukin-13 production / positive regulation of oligodendrocyte differentiation / positive regulation of nitric-oxide synthase biosynthetic process / regulation of presynapse assembly / negative regulation of type II interferon production / positive regulation of immunoglobulin production / positive regulation of interleukin-4 production / coreceptor activity / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / 小胞 / cytokine activity / positive regulation of cytokine production / positive regulation of inflammatory response / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of tumor necrosis factor production / 染色体 / positive regulation of NF-kappaB transcription factor activity / defense response to virus / membrane => GO:0016020 / 炎症 / negative regulation of cell population proliferation / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / 自然免疫系 / シナプス / glutamatergic synapse / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / 細胞膜 / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / extracellular region / 核質 / 細胞核 / 細胞膜 / 細胞質基質 / 細胞質
類似検索 - 分子機能
Interleukin-33 / Interleukin 33 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / 免疫グロブリンフォールド / Interleukin-1 receptor family / TIR domain / 免疫グロブリンフォールド / Toll - interleukin 1 - resistance / TIR domain profile. ...Interleukin-33 / Interleukin 33 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / 免疫グロブリンフォールド / Interleukin-1 receptor family / TIR domain / 免疫グロブリンフォールド / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / 免疫グロブリンフォールド / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / 抗体 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / 抗体 / Immunoglobulin-like fold / Immunoglobulin-like / サンドイッチ / Mainly Beta
類似検索 - ドメイン・相同性
Interleukin-1 receptor-like 1 / Interleukin-1 receptor accessory protein / Interleukin-33
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.792 Å
データ登録者Guenther, S. / Sundberg, E.J.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01AR068436 米国
American Asthma Foundation13-0066 米国
引用ジャーナル: Immunity / 年: 2017
タイトル: IL-1 Family Cytokines Use Distinct Molecular Mechanisms to Signal through Their Shared Co-receptor.
著者: Gunther, S. / Deredge, D. / Bowers, A.L. / Luchini, A. / Bonsor, D.A. / Beadenkopf, R. / Liotta, L. / Wintrode, P.L. / Sundberg, E.J.
履歴
登録2017年4月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年9月27日Provider: repository / タイプ: Initial release
改定 1.12019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22020年7月29日Group: Data collection / Derived calculations / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.32023年10月4日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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: Interleukin-33
B: Interleukin-1 receptor-like 1
C: Interleukin-1 receptor accessory protein
D: Interleukin-33
E: Interleukin-1 receptor-like 1
F: Interleukin-1 receptor accessory protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)185,6619
ポリマ－184,9986
非ポリマー6643
水0
1
A: Interleukin-33
B: Interleukin-1 receptor-like 1
C: Interleukin-1 receptor accessory protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)92,7204
ポリマ－92,4993
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-11 kcal/mol
Surface area34360 Å2
手法PISA
2
D: Interleukin-33
E: Interleukin-1 receptor-like 1
F: Interleukin-1 receptor accessory protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)92,9415
ポリマ－92,4993
非ポリマー4422
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-9 kcal/mol
Surface area35640 Å2
手法PISA
単位格子
Length a, b, c (Å)106.314, 107.332, 176.036
Angle α, β, γ (deg.)90.000, 107.270, 90.000
Int Tables number5
Space group name H-MI121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain B and (resid 29 through 112 or (resid 113...
21(chain E and (resid 29 through 43 or resid 51...
12(chain A and (resid 114 through 135 or (resid 136...
22(chain D and (resid 114 through 197 or (resid 198...
13(chain C and (resid 23 through 255 or resid 263...
23(chain F and (resid 23 through 254 or resid 261 or resid 263 through 348))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERLYSLYS(chain B and (resid 29 through 112 or (resid 113...BB29 - 1126 - 89
121LYSLYSLYSLYS(chain B and (resid 29 through 112 or (resid 113...BB11390
131SERSERNAGNAG(chain B and (resid 29 through 112 or (resid 113...BB - G29 - 4016
141SERSERNAGNAG(chain B and (resid 29 through 112 or (resid 113...BB - G29 - 4016
151SERSERNAGNAG(chain B and (resid 29 through 112 or (resid 113...BB - G29 - 4016
161SERSERNAGNAG(chain B and (resid 29 through 112 or (resid 113...BB - G29 - 4016
211SERSERPROPRO(chain E and (resid 29 through 43 or resid 51...EE29 - 436 - 20
221PROPROTRPTRP(chain E and (resid 29 through 43 or resid 51...EE51 - 5428 - 31
231ARGARGARGARG(chain E and (resid 29 through 43 or resid 51...EE7047
241SERSERNAGNAG(chain E and (resid 29 through 43 or resid 51...EE - I27 - 4024
251SERSERNAGNAG(chain E and (resid 29 through 43 or resid 51...EE - I27 - 4024
261SERSERNAGNAG(chain E and (resid 29 through 43 or resid 51...EE - I27 - 4024
271SERSERNAGNAG(chain E and (resid 29 through 43 or resid 51...EE - I27 - 4024
112SERSERLEULEU(chain A and (resid 114 through 135 or (resid 136...AA114 - 1356 - 27
122GLUGLUGLUGLU(chain A and (resid 114 through 135 or (resid 136...AA13628
132SERSERLYSLYS(chain A and (resid 114 through 135 or (resid 136...AA114 - 2656 - 157
142SERSERLYSLYS(chain A and (resid 114 through 135 or (resid 136...AA114 - 2656 - 157
152SERSERLYSLYS(chain A and (resid 114 through 135 or (resid 136...AA114 - 2656 - 157
162SERSERLYSLYS(chain A and (resid 114 through 135 or (resid 136...AA114 - 2656 - 157
212SERSERASPASP(chain D and (resid 114 through 197 or (resid 198...DD114 - 1976 - 89
222LYSLYSLYSLYS(chain D and (resid 114 through 197 or (resid 198...DD19890
232SERSERLYSLYS(chain D and (resid 114 through 197 or (resid 198...DD114 - 2656 - 157
242SERSERLYSLYS(chain D and (resid 114 through 197 or (resid 198...DD114 - 2656 - 157
252SERSERLYSLYS(chain D and (resid 114 through 197 or (resid 198...DD114 - 2656 - 157
262SERSERLYSLYS(chain D and (resid 114 through 197 or (resid 198...DD114 - 2656 - 157
113ARGARGGLUGLU(chain C and (resid 23 through 255 or resid 263...CC23 - 2556 - 238
123VALVALLEULEU(chain C and (resid 23 through 255 or resid 263...CC263 - 316246 - 299
133PROPROVALVAL(chain C and (resid 23 through 255 or resid 263...CC323 - 347306 - 330
143LYSLYSLYSLYS(chain C and (resid 23 through 255 or resid 263...CC348331
153ARGARGLYSLYS(chain C and (resid 23 through 255 or resid 263...CC23 - 3486 - 331
163ARGARGLYSLYS(chain C and (resid 23 through 255 or resid 263...CC23 - 3486 - 331
173ARGARGLYSLYS(chain C and (resid 23 through 255 or resid 263...CC23 - 3486 - 331
183ARGARGLYSLYS(chain C and (resid 23 through 255 or resid 263...CC23 - 3486 - 331
213ARGARGTYRTYR(chain F and (resid 23 through 254 or resid 261 or resid 263 through 348))FF23 - 2546 - 237
223GLUGLUGLUGLU(chain F and (resid 23 through 254 or resid 261 or resid 263 through 348))FF261244
233VALVALLYSLYS(chain F and (resid 23 through 254 or resid 261 or resid 263 through 348))FF263 - 348246 - 331

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質 Interleukin-33 / Interleukin 33 / IL-33


分子量: 17519.279 Da / 分子数: 2 / 変異: C139S, C165S, C231S, C256S / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Il33 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(D3)pLysS / 参照: UniProt: Q8BVZ5
#2: タンパク質 Interleukin-1 receptor-like 1 / Interleukin-33 receptor alpha chain / Lymphocyte antigen 84 / Protein ST2 / Protein T1


分子量: 35509.023 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Il1rl1, Ly84, St2, Ste2 / 細胞株 (発現宿主): HEK293T / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P14719
#3: タンパク質 Interleukin-1 receptor accessory protein / IL-1RAcP / Interleukin-33 receptot beta chain


分子量: 39470.613 Da / 分子数: 2 / 変異: N107Q, N111Q, N196Q,N209Q / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Il1rap / 細胞株 (発現宿主): HEK293T / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q61730
#4: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン / N-アセチルグルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 3 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.59 Å3/Da / 溶媒含有率: 52.55 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6
詳細: 16% PEG 3350, 0.2 M NaMalonate, pH 6, 0.2 M NaThiocyanate

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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: 23-ID-D / 波長: 1.03322 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2016年7月18日
放射モノクロメーター: double crystal monochromator / 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: 1.03322 Å / 相対比: 1
反射解像度: 2.79→29.681 Å / Num. obs: 46553 / % possible obs: 99 % / 冗長度: 6.9 % / Biso Wilson estimate: 65.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.044 / Rrim(I) all: 0.117 / Net I/σ(I): 15
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.79-2.896.81.130.6650.461.22293.9
10.81-29.686.50.0250.9990.0110.02795

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
Aimless0.3.11データスケーリング
PHASER位相決定
PHENIX精密化
PDB_EXTRACT3.22データ抽出
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4KC3, 4YFD

4kc3

4yfd


解像度: 2.792→29.681 Å / SU ML: 0.39 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.56
Rfactor反射数%反射
Rfree0.2672 2337 5.02 %
Rwork0.2121 --
obs0.2149 46538 99.02 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 179.57 Å2 / Biso mean: 75.843 Å2 / Biso min: 25.69 Å2
精密化ステップサイクル: final / 解像度: 2.792→29.681 Å
タンパク質核酸リガンド溶媒全体
原子数11262 0 42 0 11304
Biso mean--82.46 --
残基数----1405
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0111598
X-RAY DIFFRACTIONf_angle_d1.18515736
X-RAY DIFFRACTIONf_chiral_restr0.0661730
X-RAY DIFFRACTIONf_plane_restr0.0092004
X-RAY DIFFRACTIONf_dihedral_angle_d6.4376914
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11B2065X-RAY DIFFRACTION11.707TORSIONAL
12E2065X-RAY DIFFRACTION11.707TORSIONAL
21A1312X-RAY DIFFRACTION11.707TORSIONAL
22D1312X-RAY DIFFRACTION11.707TORSIONAL
31C2862X-RAY DIFFRACTION11.707TORSIONAL
32F2862X-RAY DIFFRACTION11.707TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7919-2.84890.35951340.29792348248291
2.8489-2.91080.33351350.28092573270899
2.9108-2.97840.34531380.27122608274699
2.9784-3.05280.31781360.25826062742100
3.0528-3.13530.29981380.25562601273999
3.1353-3.22740.27631370.25362592272999
3.2274-3.33150.30381370.23862606274399
3.3315-3.45040.26471360.22262608274499
3.4504-3.58830.25761360.21032579271599
3.5883-3.75130.29411390.214626312770100
3.7513-3.94870.28241370.201826102747100
3.9487-4.19540.22391370.191526112748100
4.1954-4.51830.23931380.1726092747100
4.5183-4.97110.21441370.166526282765100
4.9711-5.6860.25651410.188326492790100
5.686-7.14730.29241370.2226482785100
7.1473-29.68230.26051440.231726942838100
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)
12.3768-2.21612.78287.5652-3.41083.4691-0.35740.09710.1548-0.4660.4881-0.74660.06390.9312-0.07580.42130.14370.12520.7496-0.16050.479535.638144.0741-27.0184
23.34154.62981.09946.45391.05964.56930.08771.34530.28841.03420.3110.572-0.68271.10470.00380.8384-0.01890.03430.7975-0.02060.735342.056755.7697-28.2922
35.5268-5.38915.91585.2328-5.76846.3413-0.33680.42620.46570.68590.6411-0.5853-0.63941.0068-0.54830.71870.041-0.02670.77930.0470.640337.092548.4181-38.4764
45.24011.074-4.68112.5244-1.48724.2383-0.05641.1977-0.47470.2068-0.04180.45360.3031-0.07810.22750.5260.06760.10780.6663-0.00880.585632.144934.561-14.7221
50.515-0.76981.14057.35012.02425.08920.10570.10210.17520.4451-0.0892-1.2882-0.57610.8346-0.020.3767-0.0002-0.09470.79060.07210.654438.910544.229-16.319
68.6862.7024-0.94466.6692-0.83063.1554-0.09250.0834-0.52960.2080.4143-1.1413-0.45981.10090.00750.37040.0123-0.0320.70810.02440.523134.786644.4555-17.3403
72.19710.4988-0.56569.5083-6.51774.51810.3357-0.34870.6910.6628-0.16420.6849-0.88070.687-0.31160.50980.0403-0.03180.6109-0.12980.565630.704952.6947-16.3441
85.8066-4.7658-6.95664.23996.4129.7483-0.50790.1173-0.05290.149-0.00751.18310.0058-0.26690.4280.36080.01660.02740.5415-0.02410.576824.444247.5699-23.3406
92.58750.91910.55883.97390.9620.9507-0.16940.61650.0848-0.67330.3389-0.1655-0.9370.6086-0.23530.7463-0.26540.14881.22130.22530.586834.086467.4802-42.2665
103.49171.8837-0.11348.9401-1.05825.8833-0.08410.49440.037-0.5935-0.2020.0171-0.1040.35220.29640.3634-0.0242-0.03440.61810.08230.261319.085952.8059-40.9535
116.0823-4.49471.07938.1138-0.17971.9223-0.0977-0.0617-0.31810.4050.4515-0.1220.70.9719-0.30880.5820.2591-0.07590.6576-0.14410.507832.896919.7957-18.6885
126.50043.4372-1.17595.4874-1.05683.8157-0.1990.40910.0117-0.43130.18970.717-0.019-0.38440.03420.47220.0473-0.03710.38340.03390.493-23.108942.973-9.7921
133.9069-3.6066-0.37235.49870.98871.0017-0.00590.194-0.1081-0.0605-0.01410.4043-0.088-0.12390.04610.2921-0.0367-0.05070.27560.020.32560.544849.1121-21.8382
144.1103-1.44451.97083.2898-2.13874.04450.0138-0.2493-0.3040.43870.237-0.09960.7221-0.0938-0.20320.84620.124-0.13650.4531-0.01560.499914.77211.7296-18.8613
154.44150.31952.39593.7018-0.17221.31350.3334-0.24670.5570.8889-0.3385-0.5186-0.94090.80890.35970.4584-0.1152-0.05830.5303-0.07050.482211.029731.9011-59.3671
162.6801-4.1015-2.17768.10131.66763.1502-0.15180.1449-0.10150.27090.0272-1.78270.95861.1841-0.00120.70170.1798-0.04460.7053-0.00980.78999.043816.392-54.4168
175.90423.5457-5.86617.001-2.87885.8850.7214-0.37090.3444-1.3569-0.2397-1.03920.46420.3097-0.52140.7260.2026-0.09470.67740.11960.61098.929520.0178-44.1907
182.6996-0.81841.41544.583-2.01188.06280.345-0.2508-0.08080.33920.0453-0.2493-0.71870.9425-0.23080.4628-0.2008-0.07880.66460.04550.464812.678731.9608-62.7052
193.97314.03013.78654.12524.1556.1689-1.0830.15560.9391-0.17450.25471.0109-0.3346-1.64670.4660.865-0.1389-0.28750.60570.15950.7142-3.23437.6913-73.1409
208.0357-2.03661.52716.44072.47047.6302-0.01970.9581-0.2576-0.5661-0.492-0.88410.17291.090.55060.3144-0.11110.11780.69560.07690.657311.565325.1984-67.3097
215.77534.2071-3.56393.7093-2.0872.61-0.44262.47861.6499-1.04321.3826-0.7256-0.13361.5214-1.11310.9660.10570.13871.60990.17251.127317.881219.9819-67.7333
226.2578-6.1372-0.67916.01020.50027.25231.18880.73871.4017-1.2626-0.5778-1.15420.01530.1018-0.76170.4712-0.04430.02940.4563-0.05420.60076.9827.3592-69.2765
235.4248-2.9349-4.44243.14822.27873.6090.0007-0.3292-0.2678-0.07160.6881-0.17410.02620.1843-0.63690.5298-0.040.01390.3949-0.02820.4157-0.791527.4525-61.9096
248.9322-0.73831.46139.3014-5.85964.2984-0.15710.325-1.2118-0.82040.561-0.56051.7541-0.2603-0.39030.6136-0.07590.00290.4384-0.19920.53783.199516.9995-67.2992
258.35244.43855.09776.53184.69454.18110.0750.7249-0.78050.00720.36270.3228-0.1677-0.4129-0.32670.3455-0.1696-0.08090.53190.0240.5645-2.918121.9698-60.2924
262.33252.0570.88163.89471.09064.68520.5557-0.0351-0.6278-0.14780.0286-0.37921.24091.1023-0.39530.66710.2234-0.2160.64410.07170.74149.22760.0043-44.139
277.9498-6.25498.064.7708-6.27848.4979-0.7457-0.65030.43331.00370.0992-0.2002-1.0862-0.42140.37890.5153-0.023-0.03450.5680.03440.4217-1.810119.7316-37.7128
284.6628-4.20490.4577.7541-0.16675.4897-0.0273-0.1671-0.26490.5179-0.04420.34150.2073-0.29650.14280.3342-0.06760.00170.36980.05520.3844-9.958715.0218-42.8192
295.29664.6314-1.25127.214-0.93173.786-0.05590.0528-0.0572-0.1255-0.0611-0.074-0.96530.80060.07570.6336-0.1842-0.10620.5686-0.0110.32937.430150.2917-65.9803
306.3715-1.86210.41178.7081-2.3854.80630.1509-0.24280.26780.6680.05940.9149-0.2317-0.5734-0.13770.5573-0.0646-0.070.4432-0.02480.6397-52.729127.1917-74.4861
310.861.5701-0.20883.98350.37510.9076-0.05470.10460.3301-0.30370.15140.3378-0.32140.0429-0.07680.50830.0478-0.06250.32980.05280.5536-20.476138.6159-64.3257
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 114 through 134 )A114 - 134
2X-RAY DIFFRACTION2chain 'A' and (resid 135 through 145 )A135 - 145
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 155 )A146 - 155
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 172 )A156 - 172
5X-RAY DIFFRACTION5chain 'A' and (resid 173 through 201 )A173 - 201
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 231 )A202 - 231
7X-RAY DIFFRACTION7chain 'A' and (resid 232 through 250 )A232 - 250
8X-RAY DIFFRACTION8chain 'A' and (resid 251 through 265 )A251 - 265
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 120 )B29 - 120
10X-RAY DIFFRACTION10chain 'B' and (resid 121 through 209 )B121 - 209
11X-RAY DIFFRACTION11chain 'B' and (resid 210 through 322 )B210 - 322
12X-RAY DIFFRACTION12chain 'C' and (resid 23 through 144 )C23 - 144
13X-RAY DIFFRACTION13chain 'C' and (resid 145 through 234 )C145 - 234
14X-RAY DIFFRACTION14chain 'C' and (resid 235 through 348 )C235 - 348
15X-RAY DIFFRACTION15chain 'D' and (resid 114 through 125 )D114 - 125
16X-RAY DIFFRACTION16chain 'D' and (resid 126 through 145 )D126 - 145
17X-RAY DIFFRACTION17chain 'D' and (resid 146 through 154 )D146 - 154
18X-RAY DIFFRACTION18chain 'D' and (resid 155 through 162 )D155 - 162
19X-RAY DIFFRACTION19chain 'D' and (resid 163 through 172 )D163 - 172
20X-RAY DIFFRACTION20chain 'D' and (resid 173 through 201 )D173 - 201
21X-RAY DIFFRACTION21chain 'D' and (resid 202 through 212 )D202 - 212
22X-RAY DIFFRACTION22chain 'D' and (resid 213 through 221 )D213 - 221
23X-RAY DIFFRACTION23chain 'D' and (resid 222 through 231 )D222 - 231
24X-RAY DIFFRACTION24chain 'D' and (resid 232 through 250 )D232 - 250
25X-RAY DIFFRACTION25chain 'D' and (resid 251 through 265 )D251 - 265
26X-RAY DIFFRACTION26chain 'E' and (resid 27 through 111 )E27 - 111
27X-RAY DIFFRACTION27chain 'E' and (resid 112 through 135 )E112 - 135
28X-RAY DIFFRACTION28chain 'E' and (resid 136 through 209 )E136 - 209
29X-RAY DIFFRACTION29chain 'E' and (resid 210 through 322 )E210 - 322
30X-RAY DIFFRACTION30chain 'F' and (resid 23 through 132 )F23 - 132
31X-RAY DIFFRACTION31chain 'F' and (resid 133 through 348 )F133 - 348

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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