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- PDB-6oel: Engineered Fab bound to IL-4 receptor -

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基本情報

登録情報
データベース: PDB / ID: 6oel
タイトルEngineered Fab bound to IL-4 receptor
要素
  • (engineered Fab ...) x 2
  • Cytokine receptor common subunit gamma
  • Interleukin-4 receptor subunit alpha
  • engineered Interleukin-4, RGA variant
キーワードIMMUNE SYSTEM / cytokine receptor / fab
機能・相同性
機能・相同性情報


interleukin-4 receptor activity / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / negative regulation of complement-dependent cytotoxicity / negative regulation of T-helper 1 cell differentiation / T-helper 1 cell differentiation ...interleukin-4 receptor activity / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / negative regulation of complement-dependent cytotoxicity / negative regulation of T-helper 1 cell differentiation / T-helper 1 cell differentiation / positive regulation of cellular respiration / production of molecular mediator involved in inflammatory response / Interleukin-18 signaling / regulation of isotype switching / positive regulation of T cell differentiation in thymus / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / lymphocyte differentiation / positive regulation of T-helper 2 cell differentiation / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-7-mediated signaling pathway / positive regulation of T-helper 2 cell cytokine production / dendritic cell differentiation / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / neuroinflammatory response / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of mast cell degranulation / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / positive regulation of interleukin-13 production / macrophage activation / positive regulation of amyloid-beta clearance / myeloid dendritic cell differentiation / interleukin-15-mediated signaling pathway / positive regulation of MHC class II biosynthetic process / cellular homeostasis / positive regulation of macrophage activation / STAT3 nuclear events downstream of ALK signaling / Interleukin-15 signaling / cytokine receptor activity / Interleukin-2 signaling / negative regulation of cellular response to transforming growth factor beta stimulus / type 2 immune response / T-helper 2 cell differentiation / positive regulation of T cell differentiation / positive regulation of B cell differentiation / positive regulation of immunoglobulin production / positive regulation of myoblast fusion / defense response to protozoan / cytokine binding / negative regulation of osteoclast differentiation / positive regulation of ATP biosynthetic process / immunoglobulin mediated immune response / positive regulation of interleukin-10 production / positive regulation of macroautophagy / negative regulation of tumor necrosis factor production / Interleukin receptor SHC signaling / cell surface receptor signaling pathway via JAK-STAT / regulation of immune response / negative regulation of endothelial cell apoptotic process / cholesterol metabolic process / coreceptor activity / positive regulation of chemokine production / positive regulation of B cell proliferation / positive regulation of T cell proliferation / Interleukin-7 signaling / positive regulation of phagocytosis / T cell activation / B cell differentiation / cytokine activity / growth factor activity / positive regulation of receptor-mediated endocytosis / negative regulation of inflammatory response / centriolar satellite / cytokine-mediated signaling pathway / T cell differentiation in thymus / positive regulation of cold-induced thermogenesis / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / gene expression / receptor complex / endosome / immune response / positive regulation of cell migration / external side of plasma membrane / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / membrane
類似検索 - 分子機能
Interleukin-4 receptor alpha, N-terminal / Interleukin-4 receptor alpha chain, N-terminal / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Interleukin-4 / Interleukin 4 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site ...Interleukin-4 receptor alpha, N-terminal / Interleukin-4 receptor alpha chain, N-terminal / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Interleukin-4 / Interleukin 4 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
NITRATE ION / Interleukin-4 / Interleukin-4 receptor subunit alpha / Cytokine receptor common subunit gamma
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: 3.1 Å
データ登録者Jude, K.M. / Moraga, I. / Spangler, J.B. / Garcia, K.C.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI51321 米国
引用ジャーナル: J.Biol.Chem. / 年: 2019
タイトル: A strategy for the selection of monovalent antibodies that span protein dimer interfaces.
著者: Spangler, J.B. / Moraga, I. / Jude, K.M. / Savvides, C.S. / Garcia, K.C.
履歴
登録2019年3月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年8月7日Provider: repository / タイプ: Initial release
改定 1.12019年8月21日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
改定 1.22019年10月2日Group: Data collection / Database references / カテゴリ: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.32019年12月18日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12023年10月11日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
改定 2.22024年10月9日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: engineered Interleukin-4, RGA variant
B: Interleukin-4 receptor subunit alpha
C: Cytokine receptor common subunit gamma
H: engineered Fab heavy chain
L: engineered Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)111,32312
ポリマ－109,7875
非ポリマー1,5357
水36020
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-25 kcal/mol
Surface area41400 Å2
単位格子
Length a, b, c (Å)328.100, 328.100, 328.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Space group name HallF4d23

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要素

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タンパク質 , 3種, 3分子 ABC

#1: タンパク質 engineered Interleukin-4, RGA variant / IL-4 / B-cell stimulatory factor 1 / BSF-1 / Binetrakin / Lymphocyte stimulatory factor 1 / Pitrakinra


分子量: 14981.291 Da / 分子数: 1 / 断片: UNP residues 25-153 / 変異: K117R,T118V,R121Q,E122S,Y124W,S125F,S128G,S129A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IL4 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P05112
#2: タンパク質 Interleukin-4 receptor subunit alpha / IL-4RA


分子量: 22964.746 Da / 分子数: 1 / 断片: UNP residues 27-224 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IL4R, IL4RA, 582J2.1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P24394
#3: タンパク質 Cytokine receptor common subunit gamma / Interleukin-2 receptor subunit gamma / IL-2RG / gammaC / p64


分子量: 22816.475 Da / 分子数: 1 / 断片: UNP residues 61-249 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IL2RG / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P31785

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抗体 , 2種, 2分子 HL

#4: 抗体 engineered Fab heavy chain


分子量: 24630.568 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Trichoplusia ni (イラクサキンウワバ)
#5: 抗体 engineered Fab light chain


分子量: 24394.037 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Trichoplusia ni (イラクサキンウワバ)

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糖 , 2種, 6分子

#6: 多糖 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 367.349 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: 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


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 5 / 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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非ポリマー , 2種, 21分子

#8: 化合物 ChemComp-NO3 / NITRATE ION


分子量: 62.005 Da / 分子数: 1 / 由来タイプ: 天然 / 式: NO3
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 20 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.35 Å3/Da / 溶媒含有率: 63.3 %
結晶化温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.5
詳細: 22.5% PurePEG (Microlytic), 0.1 M sodium citrate, pH 5.5, 0.6 M ammonium nitrate

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: ALS / ビームライン: 8.2.1 / 波長: 0.999939 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2015年2月8日
放射モノクロメーター: double crystal Si(111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.999939 Å / 相対比: 1
反射解像度: 3.104→63.143 Å / Num. obs: 26526 / % possible obs: 100 % / 冗長度: 17.7 % / Biso Wilson estimate: 69.82 Å2 / CC1/2: 0.997 / Rsym value: 0.275 / Net I/σ(I): 14.87
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Mean I/σ(I) obsNum. unique obsCC1/2Rsym value% possible all
9.26-82.01514.9765.99120110.03599.3
6.57-9.2616.942.6619860.9990.059100
5.37-6.5717.5326.1924990.9980.114100
4.65-5.3717.922428990.9970.132100
4.16-4.6518.117.2532630.9950.206100
3.8-4.1617.997.9835740.9710.51397.1
3.52-3.818.14.2838810.9030.94499.9
3.29-3.5218.262.1741460.7421.896100
3.104-3.2917.351.0843950.4033.572100

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15.2_3472精密化
XDSNovember 3, 2014データ削減
XDSNovember 3, 2014データスケーリング
PHASER2.5.7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 3BPL & 3SOB

3bpl

3sob


解像度: 3.1→63.14 Å / SU ML: 0.3704 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.8768
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.2556 1327 5 %random selection
Rwork0.1988 25199 --
obs0.2016 26526 95.08 %-
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
原子変位パラメータBiso mean: 77.12 Å2
精密化ステップサイクル: LAST / 解像度: 3.1→63.14 Å
タンパク質核酸リガンド溶媒全体
原子数7091 0 98 20 7209
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00277376
X-RAY DIFFRACTIONf_angle_d0.553110086
X-RAY DIFFRACTIONf_chiral_restr0.04071162
X-RAY DIFFRACTIONf_plane_restr0.00441275
X-RAY DIFFRACTIONf_dihedral_angle_d11.3814322
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.230.3982870.31311648X-RAY DIFFRACTION56.98
3.23-3.380.31661490.26122832X-RAY DIFFRACTION98.42
3.38-3.550.31011520.23032885X-RAY DIFFRACTION99.97
3.55-3.780.29481510.21322887X-RAY DIFFRACTION100
3.78-4.070.26871530.19992909X-RAY DIFFRACTION100
4.07-4.480.2091540.15912929X-RAY DIFFRACTION100
4.48-5.120.20371560.16022945X-RAY DIFFRACTION99.9
5.12-6.450.27691580.19522991X-RAY DIFFRACTION100
6.45-63.160.23051670.20373173X-RAY DIFFRACTION99.67
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)
17.883193034484.635325751890.6562427138757.415900887085.48376294788.158075347540.206662579729-0.3577696213611.35088886614-0.496022155079-0.37342320050.157641342558-0.0619746876422-0.5080386725680.5511794897320.5218558043280.1068204826070.2426858345750.4393945481950.2010233053910.702002310665-55.1948581284-18.4035486604-45.1123667038
22.664505575493.520951561232.07752151236.044719586915.743640073768.081827475730.1709395413460.6335476693330.989591747116-0.6137025070240.385381376704-0.673269176138-1.056285701740.267975924729-0.4964218756610.6560644455940.07092467011770.3010284207430.8701992473290.221124540050.924990355991-41.4590536812-15.8511611519-54.0520581434
38.089384849630.8650134372342.262635996836.88629394051-1.091904174162.518284783950.1542815070210.5197617332340.130621536196-0.3254603689660.16564548911-0.246216669571-0.4399398319710.378817623535-0.3055451484070.4191594177450.1055183569610.1909099767790.5123814966410.01928497862130.467407945334-43.6989338221-25.1395738912-51.2529557999
47.79203068345-4.0227095349-0.6110802539013.634651257510.3096677452787.745273870490.3472898181340.2406977523291.12221026932-0.0148852238312-0.0500327199077-0.0122756664015-1.504912429430.0386973028927-0.4094715841580.8102035646960.007071838067120.2490718334990.4400706495320.2378171450880.807405421897-49.8605225049-11.9216265415-50.7302934314
56.288486381357.60797388875.89597798529.410151016917.36971942378.920287723490.5483803862390.0400669890109-0.8603399919070.856471526216-0.1373531954170.02437310497530.597167383552-0.349097649162-0.7999077165790.3982960520520.2158165160640.1853587703120.6010628652340.1887159234310.850690512221-66.684897976-42.7430095064-42.2351934841
62.13719397118-1.711892296170.356196201526.30597843366-1.898972007844.161432118970.1527285052710.106867490743-0.165733272282-0.10523039840.0641545833740.8015939464940.230773654982-0.258967931123-0.2568494210580.3485745889230.05265692641210.07924098522090.4800641808910.05898902708630.570270089365-61.5255407481-45.9713335566-45.2794754471
75.66204914327-1.57343996702-4.034828146342.136123931392.536903017489.077776069820.0837898896842-0.3629126625710.7421065632960.0172236355716-0.0035301452194-0.621403006209-0.5089385303190.61252857176-0.1065540043370.339167771596-0.0099933369468-0.0349158844130.2898290472090.003130714323280.602658559082-65.6327691862-23.6364748467-19.6690832847
85.06955490489-1.2808341883-3.11815673893.354572535571.148901362566.669716267360.196694079141-0.1858131364810.33925220705-0.2197712177730.268535750766-0.141855779020.543914892568-0.426630569730.001599234259370.2788895242120.08851593667230.04308803677150.3291465910050.001200853571650.715504711983-67.9047694079-28.5409960642-21.417508194
92.395240333-2.128976850444.032619964042.16443730956-3.138424178927.47039170563-0.1397485290060.8337185718260.750500683965-0.727789882212-0.24855183799-2.08284489635-1.210614964181.487474620850.4652520507381.97301148102-0.05880109253950.8948272449310.8997464019960.1864535083622.21637833905-53.21026829287.76366635807-42.1154305591
105.405763846942.422453227873.007682143924.85344501530.711376917191.767380844791.192652839440.4248309217520.0427682123084-1.434809853240.728512346419-1.01686326233-2.297132682761.47181357807-0.7711597293091.76760355266-0.1218614083090.9317257875741.175764976410.05962808536131.58332754691-44.62656572667.11916331383-53.5838497628
118.09108416831-1.67286257723-1.204123165133.05712636783-1.726592620454.747197009880.6351493199320.448217693181.824147664580.1393512172750.821364076886-0.433628738976-1.60528034975-0.924808908124-1.387101911961.80021656880.035487548480.4782169102260.7647940780580.1223167399561.48184355334-49.662307357715.0200968639-50.1180132834
123.438285456011.9390769221-3.369978152312.37551855956-1.813095063556.612675725090.49653723077-0.1020778481030.910237705098-0.2849651534370.0584355987302-0.437175620368-0.9938124018310.121089614216-0.608114851280.87699440030.0235309646220.4021954257360.434980151217-0.02425737989231.22940998679-63.4613930451-4.01071102355-29.7449976512
137.219525540271.64170346665-1.491022848614.810926375190.9313947020722.01643876252-0.3584316814620.5393936640530.579577889542-0.8589009241960.1457095957151.290517159850.315167030358-0.247968112832-0.08790256098520.4545570623660.151876848508-0.03208167514780.16751168486-0.1213439520460.548635773429-106.709589749-29.5004436599-16.7255078008
143.3481237527-0.663528736014-0.3466714564043.42236290594-0.2568565151072.63532606670.09809968890850.4020297248790.442800155439-0.449286955698-0.09075419563790.1307205447970.280257681701-0.60695562775-0.01289620754440.3521879217720.1604245093240.01050147996150.00916679927042-0.118570556250.378061375363-96.8393157441-27.7255014473-14.73325573
154.86144936696-1.49726672555-0.6942591851224.220179509720.9509235146571.28654016124-0.0145191142625-0.140128583607-0.1534295453050.1510676358510.04662503248950.391004948769-0.0867926580230.1633098093250.03284768345490.2888956294460.06913168046310.08285518120950.150733874636-0.07002226904420.323145643618-96.7079008015-32.4006690837-10.8735948858
164.97878594961-2.271351043141.354573650942.987069762990.1071267313681.75880218662-0.5366736077531.076003350870.345892865807-0.7607618157750.1032331043860.521677506855-0.163884057134-0.5169767474580.2873786418590.6374012724380.0128840038765-0.3537842403640.391392370171-0.02358072906830.988703212709-118.991221984-13.9864194226-21.7536767041
175.43602667581-2.792409677270.7614342771233.856504466651.120433240543.94454591309-0.124271049171-0.5374554381080.3384537417790.2735424434220.225066603283-0.0964104613577-0.05690148024590.221837496973-0.08092151409930.317724008473-0.03536740877550.03220777723410.174006587599-0.09710658871130.415244984134-92.2891989801-9.20482215008-2.44184113263
189.29593285322-2.637141371772.504363653075.149916713910.7055779824288.765302724760.248979736451.34412360760.178717833789-0.783880764666-0.21384460987-0.0134571145905-0.254177809860.0494662104193-0.009886619566540.454904211055-0.003250011317440.016623493570.218649919325-0.10800269290.459664923837-91.7424236746-9.48669922156-15.1904866524
192.62195745255-1.07041361027-0.1253839387353.864776850140.0377865226771.134444772720.0214570155305-0.267015911154-0.0633536427494-0.4762808135090.1942493074710.5165850252640.198041719722-0.160121124522-0.03840058562680.4046259212940.064256278766-0.1137986461660.126370086273-0.2035168742470.349588391904-94.5793846876-11.9152589252-7.13939655718
201.246471588660.516784198079-0.9053284039690.188544028167-0.3710983389910.59922061575-0.3326691282890.6341519607120.626168116036-0.260608892029-0.06638375625621.25387227587-0.467594603841-0.6603986604850.148772983760.4383384856570.0970053458625-0.2945971453480.32339944848-0.001810265668181.63596779418-122.545384413-2.6413462092-15.9134843482
211.533771362880.069473267210.6300288424631.034646285280.5414595712991.58236527586-0.1915980407230.1753180817780.2034564776860.381524638514-0.2788961786131.77266640140.2190019028140.0875560601164-0.07407138194230.6694594828740.0185744759136-0.02701905496460.102857921934-0.2412366295041.87455650987-123.985698446-1.60654960818-10.9980677072
220.7113511220630.24350978321-0.5790053332080.110914421771-0.2084870072530.4802012363650.0532338525431-0.07154141978090.9947977364710.404123741845-0.4359249071791.75248759706-0.254129111101-0.7733601602850.3537167480120.5772371402720.01198971488990.01207722755020.52001311782-0.2973643135182.57202719993-133.262666433-0.0287949786943-13.1762778735
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 105 )
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 129 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 15 )
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 94 )
7X-RAY DIFFRACTION7chain 'B' and (resid 95 through 170 )
8X-RAY DIFFRACTION8chain 'B' and (resid 171 through 199 )
9X-RAY DIFFRACTION9chain 'C' and (resid 39 through 50 )
10X-RAY DIFFRACTION10chain 'C' and (resid 51 through 73 )
11X-RAY DIFFRACTION11chain 'C' and (resid 74 through 99 )
12X-RAY DIFFRACTION12chain 'C' and (resid 100 through 227 )
13X-RAY DIFFRACTION13chain 'H' and (resid 1 through 18 )
14X-RAY DIFFRACTION14chain 'H' and (resid 19 through 49 )
15X-RAY DIFFRACTION15chain 'H' and (resid 50 through 108 )
16X-RAY DIFFRACTION16chain 'H' and (resid 109 through 229 )
17X-RAY DIFFRACTION17chain 'L' and (resid 1 through 44 )
18X-RAY DIFFRACTION18chain 'L' and (resid 45 through 75 )
19X-RAY DIFFRACTION19chain 'L' and (resid 92 through 121 )
20X-RAY DIFFRACTION20chain 'L' and (resid 122 through 148 )
21X-RAY DIFFRACTION21chain 'L' and (resid 149 through 192 )
22X-RAY DIFFRACTION22chain 'L' and (resid 193 through 233 )

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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