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- PDB-4n78: The WAVE Regulatory Complex Links Diverse Receptors to the Actin ... -

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基本情報

登録情報
データベース: PDB / ID: 4n78
タイトルThe WAVE Regulatory Complex Links Diverse Receptors to the Actin Cytoskeleton
要素
  • Abl interactor 2
  • Cytoplasmic FMR1-interacting protein 1
  • Nck-associated protein 1
  • Protein BRICK1
  • WIRS
  • Wiskott-Aldrich syndrome protein family member 1
キーワードPROTEIN BINDING / actin dynamics
機能・相同性
機能・相同性情報


actin-based cell projection / peripheral region of growth cone / SCAR complex / negative regulation of synaptic vesicle recycling / zonula adherens assembly / positive regulation of neurotrophin TRK receptor signaling pathway / lamellipodium morphogenesis / cell projection morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding ...actin-based cell projection / peripheral region of growth cone / SCAR complex / negative regulation of synaptic vesicle recycling / zonula adherens assembly / positive regulation of neurotrophin TRK receptor signaling pathway / lamellipodium morphogenesis / cell projection morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / 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 / regulation of actin filament polymerization / cytoskeletal anchor activity / regulation of modification of postsynaptic actin cytoskeleton / regulation of dendritic spine morphogenesis / RNA 7-methylguanosine cap binding / ruffle organization / actin polymerization or depolymerization / cell projection assembly / proline-rich region binding / positive regulation of ruffle assembly / axon extension / cortical actin cytoskeleton organization / lamellipodium assembly / positive regulation of dendrite development / regulation of myelination / positive regulation of actin filament polymerization / protein kinase A binding / protein kinase A regulatory subunit binding / Rac protein signal transduction / filamentous actin / dendritic growth cone / lamellipodium membrane / excitatory synapse / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / positive regulation of axon extension / axonal growth cone / response to electrical stimulus / mitophagy / positive regulation of lamellipodium assembly / ruffle / translation repressor activity / cellular response to brain-derived neurotrophic factor stimulus / signaling adaptor activity / actin filament polymerization / cytoskeleton organization / RAC1 GTPase cycle / receptor-mediated endocytosis / axon guidance / neuron projection morphogenesis / central nervous system development / actin filament organization / filopodium / adherens junction / mitochondrion organization / FCGR3A-mediated phagocytosis / cell motility / positive regulation of protein-containing complex assembly / terminal bouton / cell morphogenesis / peptidyl-tyrosine phosphorylation / small GTPase binding / SH3 domain binding / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / kinase binding / cognition / cellular response to insulin stimulus / specific granule lumen / positive regulation of fibroblast proliferation / neuron migration / actin filament binding / tertiary granule lumen / cell migration / regulation of translation / lamellipodium / actin cytoskeleton / regulation of cell shape / actin binding / actin cytoskeleton organization / protein-containing complex assembly / fibroblast proliferation / secretory granule lumen / dendritic spine / in utero embryonic development / mitochondrial outer membrane / cytoskeleton / postsynapse / neuron projection / focal adhesion / neuronal cell body
類似検索 - 分子機能
Helix Hairpins - #1620 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #150 / 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 ...Helix Hairpins - #1620 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #150 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Wiskott Aldrich syndrome homology region 2 / 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 / Variant SH3 domain / Helix Hairpins / SH3 domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / 分子置換 / 解像度: 2.43 Å
データ登録者Chen, Z.C.
引用ジャーナル: Cell(Cambridge,Mass.) / 年: 2014
タイトル: The WAVE Regulatory Complex Links Diverse Receptors to the Actin Cytoskeleton.
著者: Chen, B. / Brinkmann, K. / Chen, Z. / Pak, C.W. / Liao, Y. / Shi, S. / Henry, L. / Grishin, N.V. / Bogdan, S. / Rosen, M.K.
履歴
登録2013年10月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年2月5日Provider: repository / タイプ: Initial release
改定 1.12024年2月28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: Protein BRICK1
F: Abl interactor 2
P: WIRS
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)403,90126
ポリマ－402,2856
非ポリマー1,61520
水13,439746
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 area44400 Å2
ΔGint-268 kcal/mol
Surface area111240 Å2
手法PISA
単位格子
Length a, b, c (Å)97.492, 114.750, 323.605
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: 61728.980 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: WASF1, KIAA0269, SCAR1, WAVE1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q92558
#4: タンパク質 Protein BRICK1 / BRK1


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: BRK1, 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: 55806.977 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: ABI2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: J3KNB2, UniProt: Q9NYB9*PLUS

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タンパク質・ペプチド , 1種, 1分子 P

#6: タンパク質・ペプチド WIRS


分子量: 1687.894 Da / 分子数: 1 / 由来タイプ: 合成

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非ポリマー , 3種, 766分子

#7: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 4 / 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: 16 / 由来タイプ: 合成 / 式: C3H8O3
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 746 / 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: 1

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試料調製

結晶マシュー密度: 2.25 Å3/Da / 溶媒含有率: 45.33 %
結晶化温度: 277 K / 手法: 蒸発脱水法 / pH: 8.5
詳細: 10% glycerol, 4% PEG 10,000, 12-20% PEG 300, 100 mM Tris-HCl, 2mM EDTA, 2 mM TCEP, pH 8.5, EVAPORATION, temperature 277K

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データ収集

回折平均測定温度: 173 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: 0.9796 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2010年1月12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: 0.9796 Å / 相対比: 1
反射解像度: 2.43→20 Å / Num. all: 263711 / Num. obs: 262551 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
反射 シェル解像度: 2.43→2.48 Å / % possible all: 99

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解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
PHASER位相決定
PHENIX(phenix.refine: 1.7.1_743)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 / 解像度: 2.43→19.977 Å / SU ML: 0.69 / σ(F): 1.34 / 位相誤差: 24 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2089 3512 1.34 %
Rwork0.1891 --
obs0.1894 262551 99.56 %
all-263711 -
溶媒の処理減衰半径: 0.95 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 45.526 Å2 / ksol: 0.323 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1-16.7148 Å20 Å2-0 Å2
2--0.0943 Å20 Å2
3----16.8091 Å2
精密化ステップサイクル: LAST / 解像度: 2.43→19.977 Å
タンパク質核酸リガンド溶媒全体
原子数21908 0 100 746 22754
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00222517
X-RAY DIFFRACTIONf_angle_d0.46330397
X-RAY DIFFRACTIONf_dihedral_angle_d10.9828527
X-RAY DIFFRACTIONf_chiral_restr0.0363417
X-RAY DIFFRACTIONf_plane_restr0.0023871
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.46320.37821350.30969742X-RAY DIFFRACTION94
2.4632-2.49840.29421400.286310217X-RAY DIFFRACTION98
2.4984-2.53560.29181410.275210245X-RAY DIFFRACTION99
2.5356-2.57510.31430.263210414X-RAY DIFFRACTION100
2.5751-2.61720.30421400.259510389X-RAY DIFFRACTION100
2.6172-2.66230.30021390.247710441X-RAY DIFFRACTION100
2.6623-2.71060.29031410.248310415X-RAY DIFFRACTION100
2.7106-2.76260.30811380.245310339X-RAY DIFFRACTION100
2.7626-2.81880.25171420.233510381X-RAY DIFFRACTION100
2.8188-2.87990.23361430.225810477X-RAY DIFFRACTION100
2.8799-2.94670.29871430.220110432X-RAY DIFFRACTION100
2.9467-3.02020.28281410.227610401X-RAY DIFFRACTION100
3.0202-3.10150.25961410.218810304X-RAY DIFFRACTION100
3.1015-3.19240.25881420.21210453X-RAY DIFFRACTION100
3.1924-3.29510.22151390.20910341X-RAY DIFFRACTION100
3.2951-3.41230.23081410.201110452X-RAY DIFFRACTION100
3.4123-3.54820.22581400.199410363X-RAY DIFFRACTION100
3.5482-3.70870.22491410.190610449X-RAY DIFFRACTION100
3.7087-3.90280.21081370.170210385X-RAY DIFFRACTION100
3.9028-4.14530.16911400.154810364X-RAY DIFFRACTION100
4.1453-4.46210.18751450.144510439X-RAY DIFFRACTION100
4.4621-4.90510.11971430.140110411X-RAY DIFFRACTION100
4.9051-5.60120.15071420.162310368X-RAY DIFFRACTION100
5.6012-7.00590.2051360.20610430X-RAY DIFFRACTION100
7.0059-19.97760.14811390.147710387X-RAY DIFFRACTION100
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)
1-0.04130.1251-0.0102-0.0379-0.0372-0.03130.0395-0.22020.4331-0.04950.01030.41590.07570.202800.5168-0.0306-0.05570.50450.04650.394545.643956.0738253.0081
20.33020.439-0.4879-0.34890.34560.3078-0.16340.1129-0.09520.44180.1629-0.10460.1269-0.1464-00.22710.05170.08410.32820.05360.18680.778345.4532240.807
30.11530.0127-0.28240.19320.16660.2777-0.3575-0.14370.16520.09170.1312-0.038-0.1285-0.0757-00.32930.0809-0.04470.27140.01880.282517.677652.9928243.9399
40.0462-0.04920.03180.01620.04760.1144-0.1523-0.00360.38680.25020.06570.1832-0.305-0.163200.4160.1730.04850.4763-0.02290.4068-6.686251.7564244.0854
50.2101-0.14380.06490.0998-0.1430.2333-0.2371-0.0236-0.02490.01770.13280.0169-0.15150.0521-00.37820.0205-0.11950.2318-0.01280.296525.701461.1756236.3616
6-0.0071-0.005-0.04630.0044-0.0081-0.03680.0130.2424-0.22520.05010.4042-0.088-0.3414-0.2295-00.70560.0853-0.0250.48870.10340.255430.691554.8363214.6862
70.1078-0.09230.0233-0.04-0.01410.0248-0.31880.0016-0.21040.2020.32580.24540.01830.5409-00.11930.1086-0.10840.2885-0.11730.25745.200633.0612221.7771
80.0451-0.2661-0.5167-0.06150.05750.48880.04830.08750.09550.03270.0116-0.1032-0.1007-0.024800.29080.0027-0.03940.20340.01360.308727.080645.4627220.0639
9-0.0455-0.0233-0.07620.3939-0.16130.1830.02770.0143-0.03980.10140.0133-0.11590.0284-0.0313-00.28760.0187-0.09780.2579-0.010.28141.362938.1077240.052
100.02230.00570.01660.0253-0.00840.0121-0.5792-0.25520.03310.1358-0.4187-0.25010.27-0.0339-00.93840.0394-0.59191.0946-0.04510.978858.888934.4288261.2691
110.1726-0.00610.02380.2801-0.14130.32710.11350.16430.06690.1246-0.0993-0.0820.0005-0.024400.42950.0122-0.07670.30660.02540.369941.410941.706246.228
12-0.0876-0.2481-0.23480.39640.22420.1482-0.00040.0631-0.02050.0492-0.01-0.0297-0.0256-0.0593-00.2074-0.0206-0.01740.2445-0.020.241217.959933.6725208.2219
13-0.146-0.08950.05270.3340.34620.11070.02080.052-0.0540.0179-0.085-0.0529-0.08360.0078-00.2496-0.0348-0.00060.2821-0.02890.309819.989318.5458193.5673
14-0.03050.2144-0.03030.16460.36410.32350.0810.0081-0.00870.0284-0.1383-0.04260.1173-0.1457-00.24790.00790.00350.2478-0.05210.244415.46379.8279173.4137
150.14520.01720.19480.05280.2160.1180.0622-0.0005-0.0175-0.0233-0.1999-0.0049-0.0606-0.1049-00.3739-0.0255-0.00050.3337-0.04540.374917.601319.1466173.7394
160.2485-0.2142-0.12180.83530.16250.0795-0.0293-0.02190.0171-0.1035-0.240.1327-0.1196-0.3947-00.19380.0598-0.02310.3975-0.08530.25825.76951.0402142.4106
170.04280.0377-0.0997-0.0083-0.27180.0762-0.1098-0.0235-0.0107-0.08120.0346-0.09420.1323-0.0628-00.29190.03090.03230.3026-0.03650.330531.3509-2.1738168.0379
180.0554-0.0053-0.01390.2661-0.1386-0.0392-0.04930.00390.09930.0222-0.1602-0.1510.6557-0.175500.45250.13240.00980.25140.05880.379239.6947-11.6657178.2632
190.14810.1135-0.28910.37140.55330.46660.00530.0161-0.0207-0.0526-0.0733-0.0388-0.0578-0.157800.2710.04810.00780.3142-0.03190.296314.05340.5154138.2062
20-0.0012-0.02610.02760.0135-0.0050.0019-0.07450.0636-0.18480.10670.23740.1742-0.0754-0.11500.7263-0.21970.09160.6611-0.12890.457214.8608-32.1373129.4916
210.1015-0.1130.07390.06-0.01390.0459-0.01370.033-0.0590.03640.0282-0.09960.16360.140700.28780.06940.10320.3199-0.05250.377665.7965-22.2384114.7955
220.1638-0.22-0.1334-0.40540.54980.1194-0.199-0.07820.011-0.10790.18030.0980.27720.047900.26070.08840.11490.2951-0.05620.294459.2076-28.0335110.6435
230.12410.14630.00030.0872-0.110.0544-0.11340.4393-0.0251-0.0610.1649-0.0138-0.06220.3727-00.27570.07070.09260.4803-0.09710.345372.9806-23.7659110.0139
240.2618-0.2729-0.26750.21120.39110.39940.02720.07740.0302-0.0732-0.0219-0.0122-0.0643-0.103500.3194-0.00770.05830.29740.00530.264339.6673-16.0845106.0872
250.3014-0.0246-0.06820.11110.0309-0.0138-0.06290.13440.0962-0.0617-0.00040.0444-0.0703-0.23100.2673-0.02190.03410.26380.00020.31634.1961-7.9841113.3587
260.24390.2778-0.23760.54330.07910.5695-0.05230.00920.01220.04120.0006-0.0350.1112-0.068700.27170.00330.05150.2274-0.01960.252332.2205-28.7004120.097
270.0309-0.144-0.2545-0.0867-0.00820.40240.0049-0.08470.0135-0.08920.0198-0.0034-0.01140.115500.28790.01360.02920.2933-0.03620.330345.8007-6.9472136.5488
28-0.00010.0080.05180.0452-0.06780.04590.0364-0.0126-0.2011-0.43320.177-0.2036-0.5536-0.0195-00.40320.03130.0420.2809-0.02830.202827.709928.9381166.6542
29-0.3103-0.009-0.1007-0.14610.02850.55360.0077-0.02740.0032-0.04560.02920.0193-0.01620.050100.30240.0150.01970.3204-0.02890.30838.41093.0386154.8491
300.10380.06330.1260.2102-0.03510.46570.02260.0683-0.07930.0354-0.0110.1216-0.0830.232900.0758-0.02110.02530.158-0.03720.154548.106415.8494178.4307
310.1218-0.2235-0.08330.4188-0.01850.1545-0.0818-0.0245-0.0026-0.02990.0638-0.21050.09720.1719-00.17140.044-0.07230.3924-0.02350.334661.207518.0791202.555
320.15940.0063-0.01380.19530.0390.04340.025-0.09420.05770.191-0.0259-0.00170.09290.0167-00.3029-0.006-0.02570.21740.01020.242939.0573-0.3301191.1585
330.22740.0404-0.13810.0719-0.0240.20740.0215-0.05150.0614-0.00220.0131-0.02240.14310.145200.38770.0065-0.09290.46-0.00030.416157.278314.3773202.6841
340.3372-0.2678-0.0750.05430.45490.491-0.0576-0.0597-0.01330.09360.07340.0804-0.04390.160600.3002-0.0113-0.01240.3057-0.02730.31146.748822.6878206.5823
35-0.00120.01730.00780.0009-0.0073-0.001-0.0894-0.001-0.082-0.0679-0.08950.00270.0169-0.0468-01.52790.0108-0.41351.4006-0.02291.242532.400431.7312261.2885
36-0.00270.0103-0.00480.0044-0.0040.00690.1636-0.02690.19930.19680.0305-0.0738-0.0318-0.127300.904-0.0036-0.08550.6742-0.0970.535231.429820.8986260.9308
370.0169-0.02570.01120.0027-0.02940.0098-0.4185-0.09640.01250.0122-0.2065-0.4999-0.2209-0.353800.3916-0.1567-0.13290.7903-1.0314-0.418224.099913.2068242.6941
380.00230.03240.01090.0062-0.03070.0186-0.1826-0.20220.3764-0.20240.22820.2270.0469-0.392-00.5497-0.27980.05140.9703-0.25990.722918.46525.1838223.3337
390.0088-0.0028-0.01480.01650.00090.0078-0.1728-0.31160.2665-0.0102-0.16550.25360.0652-0.1376-00.6514-0.21320.03590.394-0.01640.405215.3301-5.5601209.2524
400.0187-0.00780.0024-0.0047-0.00480.0050.2597-0.2252-0.1322-0.17580.03660.01920.1328-0.1217-00.7609-0.20310.03770.4926-0.05330.376415.0091-15.6498192.0057
410.0009-0.00220.0019-0.00140.0031-0.0151-0.07650.0413-0.0006-0.0641-0.10330.0889-0.0676-0.1547-01.27430.0215-0.06010.94550.11371.51073.3409-5.6222181.1846
420.01270.0061-0.01020.0169-0.0070.00320.2151-0.1089-0.15630.0003-0.02430.2773-0.1574-0.072-00.4879-0.04780.04840.5219-0.06670.39167.38786.4336194.7578
43-0.00670.00570.0115-0.0050.00740.00810.01940.20020.0028-0.03620.08230.21620.0037-0.1862-00.4719-0.0158-0.05610.658-0.16730.48819.119218.9565208.6816
440.01020.00460.01120.01520.03210.0167-0.43240.1336-0.43330.26730.1198-0.06610.15010.0042-00.5952-0.0310.06190.3680.0630.38329.203720.5981225.5763
450.0058-0.0025-0.01130.005-0.00370.0117-0.1221-0.11970.1610.0426-0.02360.19-0.014-0.0109-00.6883-0.0080.16750.5775-0.04570.48483.12129.4456233.9794
460.00490.0185-0.00070.00630.00330.001-0.22010.0915-0.1322-0.1153-0.12950.01980.0327-0.0949-00.4483-0.14540.12740.7142-0.02230.6185-14.156234.8568226.4794
470.0258-0.0459-0.0041-0.0277-0.02170.00830.0570.135-0.1401-0.0371-0.15140.23910.0643-0.185800.40130.042-0.03310.5734-0.0310.4607-1.656634.7185216.644
480.00190.008-0.00330.0083-0.0030.00760.08730.04530.06880.0692-0.01590.1351-0.11160.0854-00.70660.30760.04351.06330.16230.47491.633637.9569200.3934
490.0046-0.00040.00030.0021-0.0047-0.0008-0.0078-0.00820.02720.06230.01220.03610.00990.066301.29010.1840.03491.65340.07641.25741.631741.2314190.2299
500.1069-0.06310.1259-0.01930.0655-0.0843-0.374-0.0710.3552-0.15720.0327-0.01590.4651-0.269700.86720.2069-0.1810.7807-0.18960.7961-0.50997.434168.7486
510.0017-0.0034-0.00460.0002-0.00470.00130.057-0.06250.0999-0.00970.02680.1706-0.0126-0.074601.0089-0.06820.09361.34030.05970.8483-1.62795.5375174.7661
520-0.00060.00090.0062-0.00480.00130.0412-0.0213-0.13560.09340.0404-0.05470.0297-0.024-0.00011.5823-0.3110.03051.89230.27361.4302-2.398312.8891183.3288
530.00640.0027-0.00430.00210.00430.00060.015-0.01250.0113-0.02110.038-0.04440.01810.006400.38340.05330.03190.60510.00450.56211.674224.5053203.2764
54-0.011-0.0045-0.00230.00270.00840.00610.1542-0.02720.3071-0.072-0.19840.06890.1474-0.2351-00.39120.1969-0.03410.60220.01480.4636.826631.0013194.3738
550.0082-0.0024-0.0007-0.00110.0025-0.0005-0.0052-0.05790.05640.07640.0304-0.0730.01580.0401-00.83270.1737-0.34830.6603-0.09020.608443.454626.7947263.3893
560.0198-0.0129-0.00010.02420.0336-0.0099-0.00010.1024-0.08510.3406-0.083-0.0901-0.0166-0.1095-00.465-0.0218-0.03960.3679-0.04740.425338.040620.6485248.8674
57-0.01720.0258-0.0264-0.0011-0.02760.0281-0.3622-0.1574-0.0622-0.1327-0.22360.2525-0.1368-0.0923-00.61250.0896-0.1280.4027-0.0630.46929.005212.9773226.172
58-0.0004-0.00040.0128-0.00510.00890.004-0.3234-0.14630.0074-0.069-0.01430.13870.0064-0.067800.3403-0.0811-0.03990.3371-0.02080.324621.01524.7932207.8812
590.0012-0.0030.00180.0293-0.0067-0.0186-0.2319-0.1847-0.2704-0.2683-0.3072-0.0205-0.1627-0.3336-00.464-0.09690.02270.3506-0.08250.432511.8047-2.7767194.2186
600.00230.00090.00070.01110.00010.00090.1856-0.0219-0.1305-0.0899-0.0599-0.08150.068-0.084101.1596-0.4051-0.41380.1167-0.18120.280224.2549-10.3776219.9587
610.00130.01150.0011-0.00230.0010.00480.2495-0.0113-0.0780.03760.10130.1630.1163-0.1687-00.9508-0.6849-0.2910.6535-0.3482-0.059822.2699-6.6236227.1601
62-0.00090.03130.0022-0.00670.01660.0032-0.571-0.14730.0060.1550.02720.00320.0548-0.249-00.2593-2.0974-0.54470.4841-1.3251-0.158920.25332.9293239.6128
630.045-0.0514-0.0329-0.00310.00380.0295-0.11810.3038-0.18030.3143-0.33350.0773-0.0244-0.156500.7659-0.18090.12441.1778-0.1210.380125.853410.9082260.1938
640.0072-0.0114-0.0063-0.0031-0.00390.0061-0.1125-0.0625-0.08590.1420.1418-0.04450.22430.038900.611-0.1045-0.04250.6577-0.06150.539933.9759.6743257.3505
650.0404-0.07210.0050.00620.02270.00450.07020.01490.16650.2592-0.27320.15030.2922-0.177900.6336-0.15710.01380.38-0.01640.237730.93844.1086236.4917
660.02430.0061-0.0010.00610.01720.01250.00160.06630.17680.1774-0.2151-0.00370.26840.1645-00.5777-0.05620.06040.286-0.00450.333726.9951-3.0247213.4456
670.0084-0.021-0.01350.0049-0.0530.0373-0.08520.12490.00810.015-0.1102-0.1170.08460.1366-00.4205-0.0763-0.00790.33820.01540.382922.4493-7.9669190.6185
680.01420.02120.02330.01370.00170.0124-0.0474-0.1328-0.34740.0352-0.0539-0.0230.3255-0.2072-00.5141-0.00190.03720.2806-0.03230.322120.1928-12.0716169.1486
690.01210.04750.03710.05020.05110.0255-0.03310.17870.05560.0448-0.47290.2530.30540.1637-00.64750.16030.06510.5236-0.05670.396445.7899-18.3926152.1991
70-0.00180.00640.0053-0.00640.02040.0018-0.1107-0.2667-0.37470.19260.1475-0.2835-0.0913-0.031500.59590.18960.07230.4710.00730.65862.3924-31.4955130.1721
710.07350.11110.09870.0196-0.0039-0.04840.24851.5571-1.2692-0.47910.0075-0.20840.87531.4362-0-0.98821.53380.9814-0.4598-0.8732-0.338550.0041-44.5415116.4606
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:68)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 69:144)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 145:185)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 186:223)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 224:334)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 335:350)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 351:382)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 383:439)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 440:521)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 522:546)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 547:617)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 618:738)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 739:806)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 807:873)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 874:920)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 921:998)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 999:1036)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 1037:1098)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 1099:1227)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 1237:1250)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 7:66)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 67:143)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 144:186)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 187:314)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 315:368)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 369:534)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 535:624)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 625:660)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 661:768)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 769:850)
31X-RAY DIFFRACTION31(CHAIN B AND RESID 851:917)
32X-RAY DIFFRACTION32(CHAIN B AND RESID 918:968)
33X-RAY DIFFRACTION33(CHAIN B AND RESID 969:1017)
34X-RAY DIFFRACTION34(CHAIN B AND RESID 1018:1121)
35X-RAY DIFFRACTION35(CHAIN D AND RESID 15:22)
36X-RAY DIFFRACTION36(CHAIN D AND RESID 23:33)
37X-RAY DIFFRACTION37(CHAIN D AND RESID 34:49)
38X-RAY DIFFRACTION38(CHAIN D AND RESID 50:62)
39X-RAY DIFFRACTION39(CHAIN D AND RESID 63:73)
40X-RAY DIFFRACTION40(CHAIN D AND RESID 74:87)
41X-RAY DIFFRACTION41(CHAIN D AND RESID 88:98)
42X-RAY DIFFRACTION42(CHAIN D AND RESID 99:106)
43X-RAY DIFFRACTION43(CHAIN D AND RESID 107:111)
44X-RAY DIFFRACTION44(CHAIN D AND RESID 112:125)
45X-RAY DIFFRACTION45(CHAIN D AND RESID 126:132)
46X-RAY DIFFRACTION46(CHAIN D AND RESID 133:144)
47X-RAY DIFFRACTION47(CHAIN D AND RESID 145:162)
48X-RAY DIFFRACTION48(CHAIN D AND RESID 163:169)
49X-RAY DIFFRACTION49(CHAIN D AND RESID 170:176)
50X-RAY DIFFRACTION50(CHAIN D AND RESID 177:501)
51X-RAY DIFFRACTION51(CHAIN D AND RESID 502:511)
52X-RAY DIFFRACTION52(CHAIN D AND RESID 512:516)
53X-RAY DIFFRACTION53(CHAIN D AND RESID 527:532)
54X-RAY DIFFRACTION54(CHAIN D AND RESID 533:543)
55X-RAY DIFFRACTION55(CHAIN E AND RESID 6:13)
56X-RAY DIFFRACTION56(CHAIN E AND RESID 14:29)
57X-RAY DIFFRACTION57(CHAIN E AND RESID 30:46)
58X-RAY DIFFRACTION58(CHAIN E AND RESID 47:58)
59X-RAY DIFFRACTION59(CHAIN E AND RESID 59:72)
60X-RAY DIFFRACTION60(CHAIN F AND RESID 0:5)
61X-RAY DIFFRACTION61(CHAIN F AND RESID 6:12)
62X-RAY DIFFRACTION62(CHAIN F AND RESID 13:26)
63X-RAY DIFFRACTION63(CHAIN F AND RESID 27:44)
64X-RAY DIFFRACTION64(CHAIN F AND RESID 45:53)
65X-RAY DIFFRACTION65(CHAIN F AND RESID 54:73)
66X-RAY DIFFRACTION66(CHAIN F AND RESID 74:86)
67X-RAY DIFFRACTION67(CHAIN F AND RESID 87:104)
68X-RAY DIFFRACTION68(CHAIN F AND RESID 105:116)
69X-RAY DIFFRACTION69(CHAIN F AND RESID 117:130)
70X-RAY DIFFRACTION70(CHAIN F AND RESID 131:139)
71X-RAY DIFFRACTION71(CHAIN F AND RESID 140:155)

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万見について

-
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