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- PDB-3sn6: Crystal structure of the beta2 adrenergic receptor-Gs protein complex -

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基本情報

登録情報
データベース: PDB / ID: 3sn6
タイトルCrystal structure of the beta2 adrenergic receptor-Gs protein complex
要素
  • (Guanine nucleotide-binding protein ...) x 3
  • Camelid antibody VHH fragment
  • Endolysin,Beta-2 adrenergic receptor
キーワードSIGNALING PROTEIN/Hydrolase / seven transmembrane receptor / nanobody / G protein-coupled receptor / GPCR / signal transduction / G protein signaling / SIGNALING PROTEIN-Hydrolase complex
機能・相同性
機能・相同性情報


sensory perception of chemical stimulus / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 ...sensory perception of chemical stimulus / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Adrenaline,noradrenaline inhibits insulin secretion / beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / ADP signalling through P2Y purinoceptor 12 / positive regulation of mini excitatory postsynaptic potential / G alpha (q) signalling events / positive regulation of cAMP-dependent protein kinase activity / positive regulation of AMPA receptor activity / norepinephrine binding / positive regulation of autophagosome maturation / Thrombin signalling through proteinase activated receptors (PARs) / heat generation / Adrenoceptors / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / G alpha (i) signalling events / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / alkylglycerophosphoethanolamine phosphodiesterase activity / activation of transmembrane receptor protein tyrosine kinase activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / negative regulation of smooth muscle contraction / beta-2 adrenergic receptor binding / Ca2+ pathway / Extra-nuclear estrogen signaling / G alpha (z) signalling events / positive regulation of lipophagy / G alpha (s) signalling events / G alpha (q) signalling events / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / photoreceptor outer segment membrane / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / spectrin binding / Vasopressin regulates renal water homeostasis via Aquaporins / response to psychosocial stress / endosome to lysosome transport / adrenergic receptor signaling pathway / diet induced thermogenesis / positive regulation of protein kinase A signaling / neuronal dense core vesicle / adenylate cyclase binding / smooth muscle contraction / photoreceptor outer segment / D1 dopamine receptor binding / bone resorption / potassium channel regulator activity / positive regulation of bone mineralization / brown fat cell differentiation / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of sodium ion transport / viral release from host cell by cytolysis / cardiac muscle cell apoptotic process / ionotropic glutamate receptor binding / insulin-like growth factor receptor binding / adenylate cyclase activator activity / response to cold / photoreceptor inner segment / peptidoglycan catabolic process / receptor-mediated endocytosis / clathrin-coated endocytic vesicle membrane / positive regulation of protein serine/threonine kinase activity / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to catecholamine stimulus / sensory perception of taste / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to amyloid-beta / cellular response to prostaglandin E stimulus
類似検索 - 分子機能
Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / G-protein alpha subunit, group S ...Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / G-protein alpha subunit, group S / YVTN repeat-like/Quinoprotein amine dehydrogenase / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / Lysozyme / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / Few Secondary Structures / Irregular / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Lysozyme-like domain superfamily / G-protein beta WD-40 repeat / P-loop containing nucleotide triphosphate hydrolases / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Chem-P0G / Endolysin / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Beta-2 adrenergic receptor / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
類似検索 - 構成要素
生物種Bos taurus (ウシ)
Rattus norvegicus (ドブネズミ)
Enterobacteria phage T4 (ファージ)
Homo sapiens (ヒト)
Lama glama (ラマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.2 Å
データ登録者Rasmussen, S.G.F. / DeVree, B.T. / Zou, Y. / Kruse, A.C. / Chung, K.Y. / Kobilka, T.S. / Thian, F.S. / Chae, P.S. / Pardon, E. / Calinski, D. ...Rasmussen, S.G.F. / DeVree, B.T. / Zou, Y. / Kruse, A.C. / Chung, K.Y. / Kobilka, T.S. / Thian, F.S. / Chae, P.S. / Pardon, E. / Calinski, D. / Mathiesen, J.M. / Shah, S.T.A. / Lyons, J.A. / Caffrey, M. / Gellman, S.H. / Steyaert, J. / Skiniotis, G. / Weis, W.I. / Sunahara, R.K. / Kobilka, B.K.
引用ジャーナル: Nature / 年: 2011
タイトル: Crystal structure of the beta2 adrenergic receptor-Gs protein complex
著者: Rasmussen, S.G. / DeVree, B.T. / Zou, Y. / Kruse, A.C. / Chung, K.Y. / Kobilka, T.S. / Thian, F.S. / Chae, P.S. / Pardon, E. / Calinski, D. / Mathiesen, J.M. / Shah, S.T. / Lyons, J.A. / ...著者: Rasmussen, S.G. / DeVree, B.T. / Zou, Y. / Kruse, A.C. / Chung, K.Y. / Kobilka, T.S. / Thian, F.S. / Chae, P.S. / Pardon, E. / Calinski, D. / Mathiesen, J.M. / Shah, S.T. / Lyons, J.A. / Caffrey, M. / Gellman, S.H. / Steyaert, J. / Skiniotis, G. / Weis, W.I. / Sunahara, R.K. / Kobilka, B.K.
履歴
登録2011年6月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02011年7月20日Provider: repository / タイプ: Initial release
改定 1.12012年8月1日Group: Database references
改定 2.02017年6月21日Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Source and taxonomy / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _entity.pdbx_description / _entity.pdbx_mutation / _entity_name_com.name / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_site_gen.auth_seq_id
改定 3.02017年7月12日Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Source and taxonomy / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _entity.pdbx_mutation / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_site_gen.auth_seq_id
改定 3.12019年12月18日Group: Advisory / Database references / Structure summary
カテゴリ: entity / pdbx_poly_seq_scheme ...entity / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_mutation / _pdbx_poly_seq_scheme.pdb_seq_num ..._entity.pdbx_mutation / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.details
改定 3.22023年9月13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: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
R: Endolysin,Beta-2 adrenergic receptor
N: Camelid antibody VHH fragment
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)164,4936
ポリマ－164,1225
非ポリマー3701
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area13280 Å2
ΔGint-61 kcal/mol
Surface area59370 Å2
単位格子
Length a, b, c (Å)119.339, 64.555, 131.240
Angle α, β, γ (deg.)90.00, 91.67, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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Guanine nucleotide-binding protein ... , 3種, 3分子 ABG

#1: タンパク質 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase-stimulating G alpha protein


分子量: 44370.168 Da / 分子数: 1 / 変異: G72S / 由来タイプ: 組換発現 / 由来: (組換発現) Bos taurus (ウシ) / 遺伝子: GNAS, GNAS1
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P04896
#2: タンパク質 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


分子量: 38744.371 Da / 分子数: 1 / 変異: M1Q / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Gnb1
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P54311
#3: タンパク質 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


分子量: 7563.750 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Bos taurus (ウシ) / 遺伝子: GNG2
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P63212

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タンパク質 / 抗体 / 非ポリマー , 3種, 3分子 RN

#4: タンパク質 Endolysin,Beta-2 adrenergic receptor / Lysis protein / Lysozyme / Muramidase / Beta-2 adrenoreceptor / Beta-2 adrenoceptor


分子量: 58303.109 Da / 分子数: 1 / 変異: C54T,C97A,M96T,M98T,N187E / 由来タイプ: 組換発現
由来: (組換発現) Enterobacteria phage T4 (ファージ), (組換発現) Homo sapiens (ヒト)
遺伝子: ADRB2, ADRB2R, B2AR
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P00720, UniProt: P07550, lysozyme
#5: 抗体 Camelid antibody VHH fragment


分子量: 15140.742 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Lama glama (ラマ) / 発現宿主: Escherichia coli (大腸菌)
#6: 化合物 ChemComp-P0G / 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one


分子量: 370.442 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C21H26N2O4

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詳細

構成要素の詳細CHAIN R IS A FUSION PROTEIN WITH T4 LYSOZYME FUSED TO THE N TERMINUS OF THE BETA2 ADRENERGIC RECEPTOR
配列の詳細SEQUENCE OF CHAIN A CORRESPONDS TO ISOFORM P04896-2

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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: 20

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試料調製

結晶マシュー密度: 3.08 Å3/Da / 溶媒含有率: 60.05 %
結晶化温度: 293 K / 手法: 脂質キュービック相法 / pH: 6.5
詳細: 350-450 mM potassium nitrate, 100 mM MES, 1 mM TCEP, 10 mM phosphonoformate, 0.01 mM BI167107, 18-22% PEG400. Crystals were grown in a 10:1 (w:w) MAG 7.7:cholesterol lipid mix. , pH 6.5, ...詳細: 350-450 mM potassium nitrate, 100 mM MES, 1 mM TCEP, 10 mM phosphonoformate, 0.01 mM BI167107, 18-22% PEG400. Crystals were grown in a 10:1 (w:w) MAG 7.7:cholesterol lipid mix. , pH 6.5, Lipidic cubic phase, temperature 293K

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データ収集

回折
ID平均測定温度 (K)Crystal-ID
1781
2781
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-B / 波長: 1.033 Å
検出器
タイプID検出器日付詳細
MARMOSAIC 300 mm CCD1CCD2011年4月15日Mirrors
MARMOSAIC 300 mm CCD2CCD2011年4月24日Mirrors
放射
IDモノクロメータープロトコル単色(M)・ラウエ(L)散乱光タイプWavelength-ID
1Si(111) double crystalSINGLE WAVELENGTHMx-ray1
2Si(111) double crystalSINGLE WAVELENGTHMx-ray1
放射波長波長: 1.033 Å / 相対比: 1
反射解像度: 3.2→50 Å / Num. obs: 31685 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / 冗長度: 6.5 % / Rmerge(I) obs: 0.156
反射 シェル解像度: 3.2→3.26 Å / 冗長度: 5 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.81 / Num. unique all: 943 / % possible all: 53.9

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解析

ソフトウェア
名称バージョン分類
Blu-Iceデータ収集
PHASER位相決定
PHENIX(phenix.refine: 1.7_650)精密化
HKL-2000データ削減
HKL-2000データスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB entries 3P0G, 1AZT, 1GP2, 2RH1

3p0g

1azt

1gp2

2rh1


解像度: 3.2→40.675 Å / SU ML: 0.39 / σ(F): 1.35 / 位相誤差: 29.18 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2772 1557 5.01 %
Rwork0.2255 --
obs0.2282 31073 92.82 %
溶媒の処理減衰半径: 0.04 Å / VDWプローブ半径: 0.4 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 52.862 Å2 / ksol: 0.32 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1--7.0864 Å2-0 Å21.9451 Å2
2--2.9389 Å2-0 Å2
3---1.7946 Å2
精密化ステップサイクル: LAST / 解像度: 3.2→40.675 Å
タンパク質核酸リガンド溶媒全体
原子数10247 0 27 0 10274
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00310478
X-RAY DIFFRACTIONf_angle_d0.70914209
X-RAY DIFFRACTIONf_dihedral_angle_d12.3853748
X-RAY DIFFRACTIONf_chiral_restr0.0511617
X-RAY DIFFRACTIONf_plane_restr0.0031818
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.30330.36421000.30981768X-RAY DIFFRACTION62
3.3033-3.42130.4071160.31562263X-RAY DIFFRACTION79
3.4213-3.55820.34541220.30272565X-RAY DIFFRACTION89
3.5582-3.720.35031300.28442727X-RAY DIFFRACTION95
3.72-3.9160.26661370.2232829X-RAY DIFFRACTION98
3.916-4.16110.24571530.192855X-RAY DIFFRACTION99
4.1611-4.4820.20041700.16182846X-RAY DIFFRACTION100
4.482-4.93240.22651770.16632867X-RAY DIFFRACTION100
4.9324-5.64450.25621280.20762933X-RAY DIFFRACTION100
5.6445-7.10530.31491440.25252916X-RAY DIFFRACTION99
7.1053-40.67850.28561800.22972947X-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)
10.04460.0208-0.00730.04520.03650.0267-0.03450.0356-0.01480.00780.0006-0.0596-0.0322-0.03160.00020.8753-0.33730.12931.17970.06010.409430.234819.3723-0.4144
20.08570.0213-0.02760.03120.01660.0121-0.07830.19290.0555-0.1361-0.14560.00430.01690.0829-0.00861.1377-0.1857-0.03531.6856-0.04660.499330.00249.05321.83
30.0597-0.02950.02890.05530.01210.0091-0.05870.21690.12440.1301-0.22120.03460.1090.0035-0.02580.95960.038-0.12911.2084-0.10770.113721.21570.71756.6139
40.2507-0.18870.10270.3236-0.0760.0646-0.26220.1443-0.043-0.95370.0299-0.15860.0329-0.1479-0.40280.3358-0.3428-0.50611.1527-0.1582-0.27916.03431.27751.5531
50.0271-0.0365-0.0290.07860.0196-0.0010.03380.45370.1213-0.41650.1146-0.16170.3791-0.02850.00451.1555-0.2514-0.04011.59180.09290.751717.177113.28552.6988
60.0998-0.016-0.09020.1775-0.1020.12630.11590.04320.0981-0.15570.04810.21380.2364-0.22610.05090.2822-0.2096-0.00420.3873-0.22020.082732.0134-9.852635.8037
70.1162-0.0149-0.02620.1106-0.00080.1048-0.08210.36540.15310.02160.08670.2189-0.1203-0.3335-0.02010.7877-0.1036-0.00120.76750.3310.714824.2068-30.332533.1899
80.6381-0.0355-0.08870.25550.02240.4513-0.3510.162-0.2835-0.05340.2430.38310.4395-0.3217-0.32560.1788-0.2098-0.08530.2470.04290.29538.51655.904846.2569
90.1967-0.32820.32490.5881-0.55580.55990.1898-0.1343-0.12810.17170.19520.2415-0.0795-0.17220.47560.35070.00160.04680.3936-0.25160.297739.114623.275676.4978
100.1465-0.0478-0.07780.2093-0.17540.16690.0899-0.0277-0.0068-0.0746-0.08890.08930.0940.2411-0.01540.3929-0.0507-0.02830.4331-0.16790.511447.95754.487239.6695
110.1799-0.03010.00030.0565-0.05330.0681-0.00790.0919-0.31660.07160.1298-0.21480.47390.09690.02710.42070.214-0.0939-0.6103-0.17260.374239.4588-8.379151.2956
12-0.0028-0.02360.00930.0995-0.01710.0525-0.0918-0.14020.03360.2285-0.06060.02370.4260.31370.00110.35740.2319-0.0537-0.09830.02920.259442.99873.36962.8324
130.44590.6093-0.2621.0895-0.40460.15610.18850.11510.3163-0.22730.26790.38520.08160.2650.55130.20510.03420.05440.2317-0.09150.112946.999617.060551.0398
140.3012-0.04370.25820.1657-0.11920.22740.22370.005-0.1844-0.14880.0154-0.0578-0.0723-0.03310.19820.2598-0.07390.02440.3163-0.02720.22645.682811.168338.0581
150.00860.0113-0.00520.0087-0.00610.0001-0.0298-0.0419-0.03650.07750.08530.26020.0294-0.05820.00010.70090.09190.07220.5493-0.00780.829636.321712.86276.9112
160.05770.0507-0.03420.1215-0.0940.101-0.20090.3106-0.15-0.0542-0.0226-0.1690.1105-0.03-0.21140.12290.0330.00570.4545-0.28380.367261.247113.661148.0792
170.0143-0.03010.00370.1258-0.00640.00260.121-0.27210.07630.30450.11880.0089-0.1638-0.1909-0.02570.29440.10430.13040.6771-0.10770.650220.921729.921770.9194
180.1084-0.026-0.00170.0859-0.01140.01970.0346-0.05530.06940.0627-0.0380.06860.00140.02660.02140.22750.13880.17930.07290.06880.422421.168625.563561.6441
190.03310.0043-0.0254-0.0023-0.0060.02260.06150.0129-0.0229-0.1648-0.048-0.05220.0112-0.00740.02140.31410.14920.01280.29210.13480.298317.37830.062151.4832
200.0077-0.00650.02110.0208-0.00910.04970.0566-0.0450.04320.12980.1410.0373-0.1025-0.12730.1297-0.00590.19950.03190.20720.14580.572114.592431.610763.1253
210.34860.08370.04150.1117-0.01080.0049-0.30430.2206-0.1695-0.21230.08690.0006-0.0418-0.0324-0.01350.2994-0.04940.01480.19630.01260.265523.702121.9156.5549
220.0492-0.00370.00430.00560.00840.0127-0.0466-0.02990.0056-0.0505-0.04480.04290.0592-0.0287-0.04440.2547-0.03610.02870.0985-0.05960.373125.607417.266163.4849
230.051-0.0064-0.02680.0497-0.03190.0754-0.0335-0.01230.002-0.0165-0.03670.01490.04630.01-0.10090.07420.06610.03630.35980.41010.16612.837827.140476.5361
240.02550.0080.0128-0.0017-0.00840.0218-0.0875-0.1045-0.04080.0181-0.02710.1146-0.0659-0.05790.01340.85230.0847-0.12971.32050.20841.173429.024542.6953-37.4182
250.0109-0.00510.00740.0017-0.00280-0.0764-0.05530.0183-0.02290.00230.0209-0.09650.00840.00010.7432-0.0880.0350.99870.31631.269332.710349.4511-45.5974
26-0.00060.003-0.00390.0068-0.0080.011-0.08240.01210.0313-0.0547-0.06310.036-0.0332-0.0182-0.00720.8350.05150.071.10970.25381.363724.595947.7641-52.5553
270.00970.0263-0.00650.0835-0.01550.0078-0.09030.01730.0007-0.0833-0.105-0.21930.0975-0.01430.02870.55240.06810.00091.11440.33570.337232.337634.004-46.3973
280.00150.0016-0.00110.0046-0.00790.0053-0.01020.0598-0.04190.04860.00840.03530.12120.04080.00020.50450.0101-0.04480.74460.10430.648146.476825.4891-39.9481
290.00670.0078-0.00270.0021-0.0055-0.0022-0.0742-0.0186-0.0179-0.0382-0.01990.0660.1326-0.0268-0.00020.42380.0450.14121.23660.13531.036638.992231.8979-35.7321
300.0566-0.00570.06230.0054-0.01150.07880.0753-0.05040.0435-0.04260.0368-0.025-0.04020.11910.10920.4246-0.16260.10130.6890.37990.450150.02431.3857-34.199
31-0.00310.00020.00170.0291-0.05370.0915-0.0046-0.0872-0.0647-0.0362-0.0203-0.02720.13730.0126-0.01810.6272-0.0063-0.35171.06270.41870.263248.071726.487-24.8843
320.01520.0018-0.00270.00680.00530.01860.13790.01050.0511-0.0550.09990.0538-0.1281-0.1280.02280.6986-0.18030.22511.52250.0840.895339.22335.0259-26.0115
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'R' and (resseq 30:60)
2X-RAY DIFFRACTION2chain 'R' and (resseq 61:102)
3X-RAY DIFFRACTION3chain 'R' and (resseq 103:146)
4X-RAY DIFFRACTION4chain 'R' and (resseq 147:264)
5X-RAY DIFFRACTION5chain 'R' and (resseq 265:366)
6X-RAY DIFFRACTION6chain 'A' and (resseq 9:88)
7X-RAY DIFFRACTION7chain 'A' and (resseq 89:186)
8X-RAY DIFFRACTION8chain 'A' and (resseq 187:394)
9X-RAY DIFFRACTION9chain 'B' and (resseq 1:24)
10X-RAY DIFFRACTION10chain 'B' and (resseq 25:94)
11X-RAY DIFFRACTION11chain 'B' and (resseq 95:161)
12X-RAY DIFFRACTION12chain 'B' and (resseq 162:222)
13X-RAY DIFFRACTION13chain 'B' and (resseq 223:289)
14X-RAY DIFFRACTION14chain 'B' and (resseq 290:340)
15X-RAY DIFFRACTION15chain 'G' and (resseq 5:23)
16X-RAY DIFFRACTION16chain 'G' and (resseq 24:62)
17X-RAY DIFFRACTION17chain 'N' and (resseq 1:17)
18X-RAY DIFFRACTION18chain 'N' and (resseq 18:51)
19X-RAY DIFFRACTION19chain 'N' and (resseq 52:60)
20X-RAY DIFFRACTION20chain 'N' and (resseq 61:91)
21X-RAY DIFFRACTION21chain 'N' and (resseq 92:108)
22X-RAY DIFFRACTION22chain 'N' and (resseq 109:121)
23X-RAY DIFFRACTION23chain 'N' and (resseq 122:128)
24X-RAY DIFFRACTION24chain 'L' and (resseq 1002:1024)
25X-RAY DIFFRACTION25chain 'L' and (resseq 1025:1039)
26X-RAY DIFFRACTION26chain 'L' and (resseq 1040:1059)
27X-RAY DIFFRACTION27chain 'L' and (resseq 1060:1080)
28X-RAY DIFFRACTION28chain 'L' and (resseq 1081:1092)
29X-RAY DIFFRACTION29chain 'L' and (resseq 1093:1106)
30X-RAY DIFFRACTION30chain 'L' and (resseq 1107:1122)
31X-RAY DIFFRACTION31chain 'L' and (resseq 1123:1134)
32X-RAY DIFFRACTION32chain 'L' and (resseq 1135:1160)

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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