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- PDB-3p8c: Structure and Control of the Actin Regulatory WAVE Complex -

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基本情報

登録情報
データベース: PDB / ID: 3p8c
タイトルStructure and Control of the Actin Regulatory WAVE Complex
要素
  • Abl interactor 2
  • Cytoplasmic FMR1-interacting protein 1
  • Nck-associated protein 1
  • Probable protein BRICK1
  • Wiskott-Aldrich syndrome protein family member 1
キーワードPROTEIN BINDING / actin polymerization
機能・相同性
機能・相同性情報


peripheral region of growth cone / negative regulation of synaptic vesicle recycling / SCAR complex / zonula adherens assembly / positive regulation of neurotrophin TRK receptor signaling pathway / actin-based cell projection / lamellipodium morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / modification of synaptic structure ...peripheral region of growth cone / negative regulation of synaptic vesicle recycling / SCAR complex / zonula adherens assembly / positive regulation of neurotrophin TRK receptor signaling pathway / actin-based cell projection / lamellipodium morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / modification of synaptic structure / regulation of actin polymerization or depolymerization / central region of growth cone / modification of postsynaptic actin cytoskeleton / dendrite extension / regulation of translation at postsynapse, modulating synaptic transmission / lens fiber cell morphogenesis / filopodium tip / cytoskeletal anchor activity / regulation of modification of postsynaptic actin cytoskeleton / regulation of actin filament polymerization / regulation of dendritic spine morphogenesis / RNA 7-methylguanosine cap binding / ruffle organization / actin polymerization or depolymerization / cell projection assembly / axon extension / proline-rich region binding / positive regulation of ruffle assembly / positive regulation of dendrite development / regulation of myelination / protein kinase A binding / lamellipodium assembly / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / Rac protein signal transduction / protein kinase A regulatory subunit binding / dendritic growth cone / filamentous actin / lamellipodium membrane / excitatory synapse / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of axon extension / axonal growth cone / positive regulation of lamellipodium assembly / signaling adaptor activity / response to electrical stimulus / translation repressor activity / cellular response to brain-derived neurotrophic factor stimulus / ruffle / cytoskeleton organization / RAC1 GTPase cycle / viral process / actin filament polymerization / mitochondrion organization / neuron projection morphogenesis / receptor-mediated endocytosis / central nervous system development / cell motility / actin filament organization / adherens junction / FCGR3A-mediated phagocytosis / axon guidance / neuron migration / positive regulation of protein-containing complex assembly / cell morphogenesis / terminal bouton / Regulation of actin dynamics for phagocytic cup formation / cognition / small GTPase binding / kinase binding / VEGFA-VEGFR2 Pathway / SH3 domain binding / peptidyl-tyrosine phosphorylation / specific granule lumen / cellular response to insulin stimulus / positive regulation of fibroblast proliferation / actin filament binding / cell migration / actin cytoskeleton / tertiary granule lumen / lamellipodium / regulation of translation / actin binding / regulation of cell shape / fibroblast proliferation / actin cytoskeleton organization / postsynapse / protein-containing complex assembly / secretory granule lumen / in utero embryonic development / mitochondrial outer membrane / dendritic spine / cytoskeleton / neuron projection / focal adhesion / neuronal cell body / apoptotic process
類似検索 - 分子機能
Helix Hairpins - #1620 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #150 / ABL interactor 2 / Cytoplasmic FMR1-interacting / Nck-associated protein 1 / Cytoplasmic Fragile-X interacting family / Nck-associated protein 1 / Protein BRICK1 / Abl interactor 2, SH3 domain / CYRIA/CYRIB, Rac1 binding domain ...Helix Hairpins - #1620 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #150 / ABL interactor 2 / Cytoplasmic FMR1-interacting / Nck-associated protein 1 / Cytoplasmic Fragile-X interacting family / Nck-associated protein 1 / Protein BRICK1 / Abl interactor 2, SH3 domain / CYRIA/CYRIB, Rac1 binding domain / Abl-interactor, homeo-domain homologous domain / SCAR/WAVE family / ABI family / CYRIA/CYRIB Rac1 binding domain / Abl-interactor HHR / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Wiskott Aldrich syndrome homology region 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / WH2 motif / WH2 domain / WH2 domain profile. / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 domain / Helix non-globular / Special / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Abl interactor 2 / Cytoplasmic FMR1-interacting protein 1 / Protein BRICK1 / Actin-binding protein WASF1 / Abl interactor 2 / Nck-associated protein 1
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 / 多重同系置換・異常分散 / 解像度: 2.29 Å
データ登録者Chen, Z. / Borek, D. / Padrick, S.B. / Gomez, T.S. / Metlagel, Z. / Ismail, A.M. / Umetani, J. / Billadeau, D.D. / Otwinowski, Z. / Rosen, M.K.
引用ジャーナル: Nature / 年: 2010
タイトル: Structure and control of the actin regulatory WAVE complex.
著者: Chen, Z. / Borek, D. / Padrick, S.B. / Gomez, T.S. / Metlagel, Z. / Ismail, A.M. / Umetani, J. / Billadeau, D.D. / Otwinowski, Z. / Rosen, M.K.
履歴
登録2010年10月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02010年12月1日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22011年9月21日Group: Database references
改定 1.32017年8月2日Group: Refinement description / Source and taxonomy / カテゴリ: entity_src_gen / software
改定 1.42024年2月21日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: Cytoplasmic FMR1-interacting protein 1
B: Nck-associated protein 1
D: Wiskott-Aldrich syndrome protein family member 1
E: Probable protein BRICK1
F: Abl interactor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)333,84317
ポリマ－333,1055
非ポリマー73912
水17,240957
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 area41520 Å2
ΔGint-296 kcal/mol
Surface area111710 Å2
手法PISA
単位格子
Length a, b, c (Å)97.013, 113.982, 327.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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タンパク質 , 5種, 5分子 ABDEF

#1: タンパク質 Cytoplasmic FMR1-interacting protein 1 / Specifically Rac1-associated protein 1 / Sra-1 / p140sra-1


分子量: 145363.750 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CYFIP1, KIAA0068
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q7L576
#2: タンパク質 Nck-associated protein 1 / NAP 1 / Membrane-associated protein HEM-2 / p125Nap1


分子量: 128940.727 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NCKAP1, HEM2, KIAA0587, NAP1
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q9Y2A7
#3: タンパク質 Wiskott-Aldrich syndrome protein family member 1 / WASP family protein member 1 / Protein WAVE-1 / Verprolin homology domain-containing protein 1


分子量: 31930.779 Da / 分子数: 1 / Mutation: prolin rich region deletion mutant / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: WASF1, KIAA0269, SCAR1, WAVE1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q92558
#4: タンパク質 Probable protein BRICK1


分子量: 8756.915 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: C3orf10, HSPC300, MDS027 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q8WUW1
#5: タンパク質 Abl interactor 2


分子量: 18112.561 Da / 分子数: 1 / Fragment: N-terminal domain / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: B4DSN1, UniProt: Q9NYB9*PLUS

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非ポリマー , 4種, 969分子

#6: 化合物 ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム


分子量: 122.143 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H12NO3 / コメント: pH緩衝剤*YM
#7: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 7 / 由来タイプ: 合成 / 式: Cl
#8: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C3H8O3
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 957 / 由来タイプ: 天然 / 式: H2O

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 2

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試料調製

結晶マシュー密度: 2.72 Å3/Da / 溶媒含有率: 54.7 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 10 % (w/v) glycerol, 4 % PEG 10,000, 12-20 % PEG 300, 100 mM Tris-HCl, 2 mM TCEP, 2 mM EDTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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データ収集

回折平均測定温度: 150 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 19-ID / 波長: 0.97924 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2009年8月15日
放射モノクロメーター: SAGITALLY FOCUSED 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: 0.97924 Å / 相対比: 1
反射解像度: 2.28→47.98 Å / Num. all: 164128 / Num. obs: 144578 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 2.5 % / Biso Wilson estimate: 33.4 Å2 / Rsym value: 0.065 / Net I/σ(I): 12.4
反射 シェル解像度: 2.28→2.31 Å / 冗長度: 1.6 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1157 / Rsym value: 0.196 / % possible all: 28.3

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解析

ソフトウェア
名称バージョン分類
ADSCQuantumデータ収集
MLPHARE位相決定
REFMAC5.5.0102精密化
HKL-3000データ削減
HKL-3000データスケーリング
精密化構造決定の手法: 多重同系置換・異常分散 / 解像度: 2.29→47.98 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.763 / SU ML: 0.16 / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.239 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.23704 7144 5 %RANDOM
Rwork0.18807 ---
all0.1905 155636 --
obs0.1905 135310 86.94 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 18.077 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0 Å20 Å2
3---0.04 Å2
精密化ステップサイクル: LAST / 解像度: 2.29→47.98 Å
タンパク質核酸リガンド溶媒全体
原子数21789 0 39 957 22785
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02222499
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8791.96530406
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0852721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10524.0191080
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.168154188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.69215159
X-RAY DIFFRACTIONr_chiral_restr0.0630.23416
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02116796
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.387413575
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.122622040
X-RAY DIFFRACTIONr_scbond_it7.10748924
X-RAY DIFFRACTIONr_scangle_it9.2368365
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS精密化 シェル解像度: 2.29→2.349 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.304 192 -
Rwork0.225 3707 -
obs--32.57 %
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)
13.23482.39920.05361.92190.05960.02110.2236-0.51120.21270.2069-0.2177-0.0428-0.08220.065-0.00590.6491-0.07050.00520.658-0.01390.467246.816155.8169255.3159
22.93520.75160.62282.01470.35932.4363-0.076-0.23240.08150.0202-0.04640.23230.0182-0.33440.12240.55060.06620.07170.4850.01310.46572.081445.4123243.4625
36.3037-1.4849-0.32483.5453-1.7052.0679-0.1867-0.76920.45030.6646-0.0384-0.4609-0.41270.33510.22510.55290.0241-0.05560.5252-0.01370.416425.997352.2701249.8193
46.00380.7979-1.84253.07010.75544.6429-0.0926-0.57760.1210.5392-0.04050.73970.0875-0.57710.1330.60120.11560.03880.5556-0.01390.5657-5.86549.7097243.3687
51.21880.17280.20661.46390.20021.2275-0.0816-0.17810.24790.11580.0365-0.0982-0.26380.11460.0450.49770.0082-0.05610.4915-0.01080.446925.704958.7326239.9456
62.935-2.1964-0.98545.7971.81081.26940.05560.27230.2334-0.4376-0.0577-0.2414-0.27690.0720.00220.5715-0.034-0.08590.49330.01830.421923.235866.5813230.5205
76.5641-2.96993.48135.3369-4.05318.906-0.08590.03990.20920.1745-0.1723-0.47-0.0450.44030.25820.439-0.04070.01540.5299-0.03920.480143.647635.4281221.6051
84.0619-1.36981.85881.807-0.84952.56220.02310.30640.2628-0.116-0.15-0.0673-0.07240.13010.12690.4987-0.03340.03220.4672-0.01390.465327.280344.8177221.7031
91.1707-0.41150.92460.7712-0.4712.4782-0.0751-0.21180.11780.2292-0.0096-0.2077-0.09650.26550.08480.50960.0041-0.01160.55950.01020.548642.556236.9769243.2803
100.94960.28731.12744.42431.08121.67660.0276-0.1569-0.07960.74170.1559-0.74840.23620.2796-0.18350.4530.0833-0.18950.95290.09790.325349.949235.4231258.2994
113.31731.50012.25293.13912.44015.2616-0.062-0.33180.34030.2441-0.0541-0.2701-0.35380.23980.11610.50720.0287-0.0280.53420.04280.461641.881842.9778245.6066
120.6646-0.3718-0.50660.63530.771.35090.01980.00620.0342-0.0183-0.0074-0.0346-0.07670.0206-0.01240.419-0.0017-0.0120.41360.0190.434518.23233.328210.4389
130.34140.10350.33570.58381.14242.7168-0.06550.04030.071-0.03060.0084-0.0449-0.11980.15050.05710.45040.00580.02190.46030.02960.473619.750318.8724196.463
140.11390.0732-0.31820.33650.02032.1708-0.03110.02880.00670.00970.00980.06530.0183-0.15480.02130.46220.01060.02630.4532-0.00940.473516.145610.1941176.2515
1532.4065-5.4632-35.19055.84457.402938.73451.03871.4793-0.3831-0.0521-1.37290.3963-1.1272-1.74660.33420.15410.09040.0791.2314-0.34910.53913.016818.6834168.9379
160.44770.50330.36432.86251.78073.6798-0.0115-0.03740.08970.0298-0.1060.3926-0.2384-0.36330.11760.44060.01330.02010.49250.01650.499720.109918.414176.1732
170.4978-0.0427-0.22050.4233-0.36772.0423-0.04730.1221-0.0188-0.0644-0.01040.18720.0016-0.52650.05770.4927-0.02070.00920.5752-0.03840.52497.011-0.5446142.5086
180.6684-0.03520.40830.9609-0.3731.84060.08620.0049-0.17410.0703-0.0654-0.19620.32260.2515-0.02080.51250.00210.05480.4356-0.01410.455831.535-5.8186171.8597
190.8184-0.26320.03730.69560.45221.291-0.00640.09590.0357-0.1192-0.02510.0617-0.0339-0.11770.03150.4009-0.0127-0.00150.4507-0.00790.425213.65180.8359139.8172
201.97783.80434.435911.016110.840212.41680.2773-0.0455-0.43830.637-0.0005-0.0711.073-0.3326-0.27680.5304-0.07810.06420.58060.01190.584617.2326-25.7441136.7234
219.67420.787-0.6478.8236-2.63482.9182-0.00760.8035-1.0559-0.75070.07510.03040.5465-0.1312-0.06740.54870.0671-0.00430.5045-0.0050.498547.3266-39.7244110.2064
224.30080.022-0.85531.37670.06452.08260.1732-0.28330.57930.15210.0709-0.5129-0.2580.7615-0.24410.49260.00370.04460.6561-0.06390.548470.786-16.4851120.3789
234.7014-0.19492.25841.30920.37533.37470.08770.1975-0.0203-0.07190.0884-0.76470.03590.9844-0.17610.44360.11780.1130.6689-0.08770.632477.9874-23.9562116.6649
241.94720.31290.29050.82220.20040.7222-0.00780.1551-0.1656-0.10670.0286-0.06990.09430.0948-0.02080.49230.00870.02930.4468-0.00620.423648.7492-28.2539107.5174
255.9737-1.84173.59464.2201-1.23535.78750.11730.2439-0.23320.03780.0239-0.57190.4690.8306-0.14130.43750.0510.09040.5821-0.06830.497274.8546-25.6326111.7079
261.1003-0.1558-0.04580.77190.20590.71940.03840.1624-0.0115-0.1297-0.031-0.0437-0.0293-0.0086-0.00730.4778-0.00570.00570.43310.00550.412239.5909-15.5789107.7619
277.8113.530812.179723.707521.200319.0355-0.22290.3051-0.3979-0.97660.8613-0.8548-0.61180.5665-0.63841.3935-0.3570.40450.7611-0.08380.491150.4916-9.87789.7673
281.1030.1748-0.35570.8492-0.13540.67530.020.06170.0807-0.03640.00980.0026-0.0525-0.0395-0.02980.4391-0.0032-0.0040.4301-0.01080.419933.9182-8.5702119.3767
291.09630.24310.08331.60580.48781.3112-0.00640.042-0.0245-0.0009-0.00230.09540.0955-0.06690.00870.46580.03630.01120.51810.01620.456630.5214-19.9117125.5859
302.1657-0.1909-0.35681.8991-0.07572.8228-0.05010.0876-0.38450.0185-0.00960.0820.4812-0.12070.05970.5092-0.03420.0090.4128-0.00080.524631.1063-39.9198117.1737
3110.51865.1878-1.88088.58-6.53927.9134-0.0580.1957-0.7054-0.2561-0.0222-0.22510.56540.20680.08020.49690.01860.00640.4424-0.01950.441937.9107-23.372127.5591
320.5209-0.5021-0.75841.23061.47452.32190.0615-0.01610.0663-0.13280.0464-0.1365-0.13020.0584-0.10780.4163-0.02530.01770.44590.01440.44143.8081-2.1528142.8676
332.94613.7754-3.62924.856-4.66074.48360.13060.03550.34280.17790.19590.4251-0.2203-0.1096-0.32650.80910.152-0.38841.0434-0.00371.015423.938533.1594166.9092
340.2997-0.0544-0.13431.07150.51231.146-0.0044-0.00560.0320.04050.0276-0.0015-0.03650.0378-0.02320.4168-0.0180.0340.45060.01620.417939.10942.0912152.4579
351.94961.38181.98183.41062.95533.71820.00430.056-0.14380.04010.00610.05120.18120.0113-0.01050.4589-0.00310.04870.48930.01620.436937.42783.4389164.4582
361.25460.2802-0.00561.9350.29031.5960.00360.01470.0380.00320.0234-0.1253-0.01530.1617-0.0270.43480.00620.00920.50040.01980.414748.505814.9139180.5021
372.01040.63861.75711.21611.0952.55590.0166-0.24940.10960.25390.024-0.31150.1020.264-0.04060.47250.033-0.00390.57840.01380.436557.715915.9758202.3668
388.10991.49670.54674.87610.91495.7541-0.0142-0.756-0.15730.8387-0.0893-0.50710.04980.22170.10350.6493-0.00470.02430.4152-0.00610.494638.1793-4.2977194.2186
391.20780.90450.5591.53431.57821.94440.1091-0.1202-0.23810.24580.078-0.32630.40190.3392-0.18710.49120.0396-0.0170.55660.03940.439855.04611.7128202.9591
401.7864-0.8581-0.03581.14380.40462.4402-0.0312-0.09190.00560.13380.041-0.06080.02460.1796-0.00970.4401-0.01430.0010.5060.01570.446346.726221.9271208.4993
410.27270.84590.4463.20111.53910.7722-0.063-0.15080.13050.1337-0.11580.23990.0111-0.1520.17870.98950.29490.20820.74930.17960.490929.573129.7919261.6386
423.75313.57274.46034.51862.93666.8499-0.1583-0.14120.1626-0.0495-0.09120.1201-0.385-0.1810.24960.5380.01680.04280.51160.06510.393726.766719.3025253.314
434.0285-1.62315.44913.96625.081823.3685-0.04960.14210.1557-0.1873-0.2701-0.0063-0.5151-0.21260.31970.48650.01510.02860.48480.05190.611121.898512.8403239.0589
448.26343.44486.25737.84613.800414.2426-0.1548-0.03070.46870.043-0.1330.3524-0.4473-0.61770.28780.51110.020.05950.45170.0120.423418.54157.0035226.3968
453.5261-0.17972.02897.32663.63268.8317-0.0043-0.3741-0.27760.4468-0.20870.23360.4435-0.45510.21310.5702-0.01750.09170.49320.05520.436215.2378-2.5204214.4242
467.858513.80311.884931.9097-7.906816.89330.2769-0.49910.74290.4722-0.48831.30690.2164-0.73150.21130.7415-0.00050.21480.59120.12920.515913.608-9.8188205.2128
474.8817-0.23453.75415.93221.451614.13990.23890.1747-0.7206-0.0350.15750.16530.7061-0.3584-0.39640.9159-0.10490.12940.34080.01890.403315.1362-15.726192.0195
486.6374-8.7655.7409239.41691.6625.3489-1.0788-5.2312-1.6047-9.21132.1969.9822-1.2474-4.6536-1.11721.76761.3284-0.00335.07080.70710.90258.106-12.1192182.232
493.2762-3.59773.20111.60637.579623.35690.36380.2452-0.6827-0.7214-0.98831.28970.8083-1.16190.62460.6113-0.4101-0.0140.6819-0.09890.58941.0099-1.2126184.6205
500.08650.59870.53928.3678.43339.2244-0.14740.01730.0201-0.1535-0.34630.5507-0.1378-0.48630.49370.5003-0.01960.0460.5211-0.01280.43638.955914.4988206.1358
516.5308-3.5621-3.14086.85962.95399.2779-0.374-0.2415-0.34750.36030.12720.06780.70830.33240.24680.5327-0.02820.06190.51450.06410.50887.778422.2674231.0358
523.8698-2.0785-1.03832.43462.36222.9067-0.440.6626-0.26570.1141-0.24520.6391-0.0028-0.35260.68520.4628-0.0983-0.04750.84390.03420.533-13.368634.9192227.8537
531.5957-1.4552-4.16091.77223.044912.4501-0.00720.1957-0.24080.0974-0.03040.41740.1657-0.75650.03760.45410.00730.00570.5440.01730.5366-1.414234.5975220.2983
543.13581.183-0.7569.3106-8.97620.31040.18220.94060.5977-0.9185-0.20530.2262-0.3721-0.39870.02310.49930.1318-0.08660.71770.12060.42212.430438.473198.6456
550.7835-4.20980.335622.7067-1.81190.1486-0.23390.00010.10031.16280.2251-0.4057-0.07190.02090.00880.64090.0479-0.16541.0740.15310.30782.920745.4407182.6988
561.0072-0.46850.88190.2472-0.47030.89920.50320.1397-0.2127-0.0708-0.17320.15650.08950.3077-0.331.4698-0.1450.09880.855-0.42740.42310.39558.5019167.7376
578.4608-12.7813-9.839720.957816.288812.7835-0.09690.7935-0.1019-0.1496-0.96541.26280.1233-1.14111.06230.7911-0.9571-0.13341.82160.32030.8603-0.37543.881173.9898
583.571714.4202-0.947194.668213.51538.77410.09740.27990.52760.7262-0.72182.92030.3449-1.3430.62440.25-0.06840.26931.1529-0.57760.8332-0.884210.8916181.1717
598.14876.33956.957516.38369.13167.15120.16860.7381-0.4352-0.4161-0.09790.53850.01010.3841-0.07070.6287-0.30090.16420.6292-0.32410.53-2.528917.9381194.6764
603.7067-3.0839-5.385110.1837-2.797816.25890.44120.91560.6566-1.2814-0.4497-0.67740.0917-1.0680.00850.45230.02-0.06710.86520.26140.7196.99330.5942196.69
618.5244-7.01075.02395.7783-4.13032.9625-0.61290.27181.46790.5854-0.2452-1.1454-0.3160.16630.85821.41960.13260.01741.0570.02110.69242.334125.7331263.2652
6226.409511.9546-2.03347.44713.29088.97710.491-1.1277-0.66380.7383-0.2883-0.51510.92150.5102-0.20260.57660.1137-0.05310.61750.07780.518440.099423.2667257.2617
639.2766-7.9353-4.96769.71869.990413.9170.2343-0.11440.3508-0.06460.3244-0.51750.12550.4745-0.55870.50950.0107-0.00240.53390.08170.479737.823420.2845251.696
6418.6329-2.04698.49540.6147-3.038815.2948-0.2303-0.18681.16330.0503-0.0983-0.1094-0.13490.63670.32860.51170.0497-0.02370.5227-0.00210.632636.111518.0887244.8744
655.32683.72695.18357.2652-3.529419.1197-0.2228-0.07990.5975-0.0984-0.1405-0.4174-0.60860.67020.36330.48660.00860.0950.5463-0.13671.012932.337716.2447236.9822
666.22842.38782.765.15676.302414.1636-0.04670.12380.692-0.08710.02920.1448-0.7878-0.34240.01750.54550.01270.02630.49190.06170.424728.467112.4388227.3215
6710.13653.7215-1.83066.28171.848628.8429-0.32-0.0623-0.21810.1279-0.1028-0.52330.54550.77480.42280.52250.00590.03610.44120.05340.457925.06729.0158219.1122
683.23931.65942.0015.7520.854913.5829-0.02460.13870.1291-0.33980.008-0.44030.37540.41930.01670.51030.01660.05550.45070.04030.441922.3725.6142210.493
690.51610.640.84568.9518-1.30635.9494-0.0393-0.06250.0137-0.3068-0.0749-0.2610.27090.14860.11430.4901-0.00480.05490.46050.04110.430317.26981.5057202.6529
7015.53154.963910.841830.64475.925513.9016-0.2687-0.97770.26970.748-0.04340.72040.5009-0.78860.31210.5135-0.00170.04620.44940.01430.437913.0412-2.3346196.2901
7155.0951-29.2-10.359619.58463.46032.9756-2.09413.28660.91271.52742.1775-0.31180.2268-2.5634-0.08340.34560.2550.023.89720.0490.77135.4646-4.7659191.7762
728.1267-7.3094-0.116120.836910.987811.79780.06130.4554-0.9610.9812-0.12170.29871.14950.01840.06040.6691-0.03810.10790.44570.07980.390921.8578-8.8415223.6817
7310.08312.28760.88917.68422.888212.04710.31320.393-0.73890.0851-0.3243-0.14481.0885-0.11810.01120.5823-0.01640.07230.4710.05180.396518.9518-3.1246231.6617
746.76610.0318-4.673115.42255.954812.6464-0.08890.2241-0.0389-0.1164-0.20870.96220.5585-0.95610.29760.5478-0.01720.04420.55240.06450.423717.71185.199241.4053
7510.3825-3.0428-5.672523.544111.6529.6722-0.17590.0225-0.23530.1915-0.29651.62370.7719-1.37090.47250.5242-0.0310.08910.48710.02580.450219.08849.0086250.1217
765.45462.80494.0362.07224.51313.0839-0.1450.07670.10580.0458-0.16850.10060.3569-0.1610.31350.5589-0.00480.05020.58780.03040.408422.174214.5118259.12
775.9535-4.862-1.26237.4097.00510.859-1.0402-0.36411.11210.9250.6796-0.61080.05720.8310.36050.7304-0.0571-0.13010.79880.12460.462926.430115.9251266.8419
781.2628-5.85183.255435.8143-1.726528.96530.06540.05610.06530.7618-0.0212-0.41651.76960.6636-0.04420.54140.0563-0.00420.99210.37470.504631.016311.2809262.2433
792.1225-0.5693-2.98430.16831.218519.2094-0.0767-0.0844-0.29670.06670.0290.09930.605-0.00410.04770.60870.0363-0.01640.54590.09640.4930.61069.4582251.9482
800.6670.27792.10973.22935.278313.14780.1735-0.0488-0.07550.0051-0.0078-0.21960.5485-0.0434-0.16570.56290.04040.04760.45260.05570.482528.65562.822235.4375
8119.2377-4.83252.56665.56863.311623.7297-0.1101-0.5827-0.37460.24740.2085-0.34590.26370.9611-0.09840.584-0.00370.05430.48110.03890.383527.7527-0.4089222.14
822.41561.3935-3.00072.9013-0.23344.9112-0.09730.1029-0.06090.12490.0401-0.3420.3597-0.23740.05730.59490.03240.10870.4923-0.01490.473625.171-3.2296214.4994
8315.3346-0.5299.264414.72736.815227.3589-0.2192-0.33050.10170.529-0.207-0.57640.42720.98640.42620.61570.03260.06390.4660.03870.431226.2291-5.4642206.5815
841.60010.63340.62182.8133.4399.7522-0.0487-0.02450.04390.09950.0658-0.15740.01820.2741-0.01710.5176-0.00160.05130.41930.03410.425121.2755-8.5451190.3865
852.20250.482-0.41860.2059-1.083110.7476-0.20680.0898-0.1285-0.07170.04420.01440.7202-0.53360.16260.5714-0.04840.10880.4537-0.0420.541317.6742-11.1449172.5213
8642.5453-2.7207-15.95650.30640.47238.28650.02090.2359-0.99950.0521-0.05230.1344-0.1652-0.03420.03140.65960.01010.040.4978-0.06140.506633.0139-14.6012160.8974
874.8937-3.0174-0.27041.9255-0.30693.7681-0.0898-0.26290.09250.03580.1148-0.09550.3680.4433-0.0250.53430.03110.01920.55030.02770.493749.5491-20.5766151.0636
8810.1187.37386.50215.91296.605510.76390.2269-0.2761-1.19510.6620.12-0.78751.73320.8305-0.34690.67320.3034-0.05260.58230.02260.450860.6082-30.4034137.8004
8913.38063.1832-1.47183.45746.571319.32710.10830.1186-0.14280.51290.0974-0.15581.2854-0.8929-0.20580.60240.0177-0.00830.82450.09020.573963.5447-33.719124.8978
9012.61052.7673-3.51052.7370.41744.5116-0.0198-0.2296-0.50380.2170.001-0.04380.56530.12270.01880.56360.0736-0.03080.41070.02050.502451.1723-41.9695118.966
9138.21-1.4206-10.64614.8632-8.966921.18991.17141.6269-3.1464-0.2628-0.86790.71830.09531.1094-0.30350.58130.11580.00620.2571-0.09621.098144.5395-48.6599115.7307
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 68
2X-RAY DIFFRACTION2A69 - 147
3X-RAY DIFFRACTION3A148 - 171
4X-RAY DIFFRACTION4A172 - 216
5X-RAY DIFFRACTION5A217 - 313
6X-RAY DIFFRACTION6A314 - 346
7X-RAY DIFFRACTION7A347 - 381
8X-RAY DIFFRACTION8A382 - 442
9X-RAY DIFFRACTION9A443 - 521
10X-RAY DIFFRACTION10A522 - 571
11X-RAY DIFFRACTION11A578 - 617
12X-RAY DIFFRACTION12A618 - 738
13X-RAY DIFFRACTION13A739 - 799
14X-RAY DIFFRACTION14A800 - 873
15X-RAY DIFFRACTION15A874 - 878
16X-RAY DIFFRACTION16A879 - 921
17X-RAY DIFFRACTION17A922 - 981
18X-RAY DIFFRACTION18A982 - 1094
19X-RAY DIFFRACTION19A1095 - 1222
20X-RAY DIFFRACTION20A1223 - 1247
21X-RAY DIFFRACTION21B7 - 21
22X-RAY DIFFRACTION22B22 - 61
23X-RAY DIFFRACTION23B62 - 103
24X-RAY DIFFRACTION24B104 - 150
25X-RAY DIFFRACTION25B151 - 186
26X-RAY DIFFRACTION26B187 - 313
27X-RAY DIFFRACTION27B314 - 320
28X-RAY DIFFRACTION28B321 - 389
29X-RAY DIFFRACTION29B390 - 449
30X-RAY DIFFRACTION30B450 - 528
31X-RAY DIFFRACTION31B529 - 538
32X-RAY DIFFRACTION32B539 - 638
33X-RAY DIFFRACTION33B639 - 661
34X-RAY DIFFRACTION34B662 - 731
35X-RAY DIFFRACTION35B732 - 769
36X-RAY DIFFRACTION36B770 - 853
37X-RAY DIFFRACTION37B854 - 929
38X-RAY DIFFRACTION38B930 - 960
39X-RAY DIFFRACTION39B961 - 1017
40X-RAY DIFFRACTION40B1018 - 1121
41X-RAY DIFFRACTION41D21 - 27
42X-RAY DIFFRACTION42D28 - 39
43X-RAY DIFFRACTION43D40 - 49
44X-RAY DIFFRACTION44D50 - 59
45X-RAY DIFFRACTION45D60 - 70
46X-RAY DIFFRACTION46D71 - 75
47X-RAY DIFFRACTION47D76 - 86
48X-RAY DIFFRACTION48D87 - 91
49X-RAY DIFFRACTION49D92 - 100
50X-RAY DIFFRACTION50D101 - 113
51X-RAY DIFFRACTION51D114 - 131
52X-RAY DIFFRACTION52D132 - 145
53X-RAY DIFFRACTION53D146 - 160
54X-RAY DIFFRACTION54D161 - 176
55X-RAY DIFFRACTION55D177 - 183
56X-RAY DIFFRACTION56D184 - 221
57X-RAY DIFFRACTION57D222 - 228
58X-RAY DIFFRACTION58D229 - 234
59X-RAY DIFFRACTION59D235 - 250
60X-RAY DIFFRACTION60D251 - 264
61X-RAY DIFFRACTION61E10 - 13
62X-RAY DIFFRACTION62E14 - 18
63X-RAY DIFFRACTION63E19 - 22
64X-RAY DIFFRACTION64E23 - 28
65X-RAY DIFFRACTION65E29 - 34
66X-RAY DIFFRACTION66E35 - 42
67X-RAY DIFFRACTION67E43 - 47
68X-RAY DIFFRACTION68E48 - 54
69X-RAY DIFFRACTION69E55 - 61
70X-RAY DIFFRACTION70E62 - 66
71X-RAY DIFFRACTION71E67 - 73
72X-RAY DIFFRACTION72F0 - 8
73X-RAY DIFFRACTION73F9 - 16
74X-RAY DIFFRACTION74F17 - 24
75X-RAY DIFFRACTION75F25 - 29
76X-RAY DIFFRACTION76F30 - 37
77X-RAY DIFFRACTION77F38 - 44
78X-RAY DIFFRACTION78F45 - 49
79X-RAY DIFFRACTION79F50 - 58
80X-RAY DIFFRACTION80F59 - 72
81X-RAY DIFFRACTION81F73 - 77
82X-RAY DIFFRACTION82F78 - 83
83X-RAY DIFFRACTION83F84 - 89
84X-RAY DIFFRACTION84F90 - 104
85X-RAY DIFFRACTION85F105 - 114
86X-RAY DIFFRACTION86F115 - 120
87X-RAY DIFFRACTION87F121 - 130
88X-RAY DIFFRACTION88F131 - 135
89X-RAY DIFFRACTION89F136 - 139
90X-RAY DIFFRACTION90F140 - 149
91X-RAY DIFFRACTION91F150 - 155

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万見について

-
お知らせ

-
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

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.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

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