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- PDB-6pol: Crystal structure of the human NELL1 EGF1-3-Robo3 FN1 complex -

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基本情報

登録情報
データベース: PDB / ID: 6pol
タイトルCrystal structure of the human NELL1 EGF1-3-Robo3 FN1 complex
要素
  • Protein kinase C-binding protein NELL1
  • Roundabout homolog 3
キーワードSIGNALING PROTEIN / Axon guidance / Nervous system / Heterodimeric complex / Glycoprotein
機能・相同性
機能・相同性情報


dendrite self-avoidance / ROBO receptors bind AKAP5 / negative regulation of osteoblast proliferation / cell-cell adhesion mediator activity / Regulation of commissural axon pathfinding by SLIT and ROBO / commissural neuron axon guidance / positive regulation of ossification / positive regulation of axon guidance / axon midline choice point recognition / regulation of osteoblast differentiation ...dendrite self-avoidance / ROBO receptors bind AKAP5 / negative regulation of osteoblast proliferation / cell-cell adhesion mediator activity / Regulation of commissural axon pathfinding by SLIT and ROBO / commissural neuron axon guidance / positive regulation of ossification / positive regulation of axon guidance / axon midline choice point recognition / regulation of osteoblast differentiation / homophilic cell adhesion via plasma membrane adhesion molecules / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / axon guidance / protein kinase C binding / negative regulation of protein catabolic process / Regulation of expression of SLITs and ROBOs / neuron migration / chemotaxis / nuclear envelope / nervous system development / heparin binding / regulation of gene expression / cell differentiation / axon / calcium ion binding / perinuclear region of cytoplasm / extracellular space / membrane / plasma membrane / cytoplasm
類似検索 - 分子機能
: / : / Thrombospondin N-terminal -like domains. / EGF domain / EGF domain / : / Laminin G domain / von Willebrand factor (vWF) type C domain / von Willebrand factor type C domain / VWFC domain signature. ...: / : / Thrombospondin N-terminal -like domains. / EGF domain / EGF domain / : / Laminin G domain / von Willebrand factor (vWF) type C domain / von Willebrand factor type C domain / VWFC domain signature. / Laminin G domain / VWFC domain profile. / Laminin G domain / von Willebrand factor (vWF) type C domain / VWFC domain / : / Calcium-binding EGF domain / Immunoglobulin domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
NITRATE ION / Protein kinase C-binding protein NELL1 / Roundabout homolog 3
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: 1.8 Å
データ登録者Wang, J. / Pak, J.S. / Ozkan, E.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS097161 米国
引用ジャーナル: Nat Commun / 年: 2020
タイトル: NELL2-Robo3 complex structure reveals mechanisms of receptor activation for axon guidance.
著者: Pak, J.S. / DeLoughery, Z.J. / Wang, J. / Acharya, N. / Park, Y. / Jaworski, A. / Ozkan, E.
履歴
登録2019年7月4日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年5月6日Provider: repository / タイプ: Initial release
改定 1.12020年7月29日Group: Data collection / Derived calculations / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.22023年10月11日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.32024年10月23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: Roundabout homolog 3
B: Protein kinase C-binding protein NELL1
C: Roundabout homolog 3
D: Protein kinase C-binding protein NELL1
E: Roundabout homolog 3
F: Protein kinase C-binding protein NELL1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)84,49328
ポリマ－82,6576
非ポリマー1,83622
水11,566642
1
A: Roundabout homolog 3
B: Protein kinase C-binding protein NELL1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)28,21610
ポリマ－27,5522
非ポリマー6638
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-2 kcal/mol
Surface area13200 Å2
手法PISA
2
C: Roundabout homolog 3
D: Protein kinase C-binding protein NELL1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)28,0928
ポリマ－27,5522
非ポリマー5396
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-6 kcal/mol
Surface area12990 Å2
手法PISA
3
E: Roundabout homolog 3
F: Protein kinase C-binding protein NELL1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)28,18610
ポリマ－27,5522
非ポリマー6338
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-0 kcal/mol
Surface area12910 Å2
手法PISA
単位格子
Length a, b, c (Å)87.000, 87.000, 211.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
12
22
32

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERPROPRO(chain 'A' and (resid 553 through 580 or resid 582 through 652))AA553 - 5807 - 34
121THRTHRSERSER(chain 'A' and (resid 553 through 580 or resid 582 through 652))AA582 - 65236 - 106
211SERSERPROPRO(chain 'C' and (resid 553 through 580 or resid 582 through 652))CC553 - 5807 - 34
221THRTHRSERSER(chain 'C' and (resid 553 through 580 or resid 582 through 652))CC582 - 65236 - 106
311SERSERPROPRO(chain 'E' and (resid 553 through 580 or resid 582 through 652))EE553 - 5807 - 34
321THRTHRSERSER(chain 'E' and (resid 553 through 580 or resid 582 through 652))EE582 - 65236 - 106
112ARGARGLYSLYS(chain 'B' and (resid 390 through 419 or resid 421...BB390 - 4194 - 33
122GLYGLYCYSCYS(chain 'B' and (resid 390 through 419 or resid 421...BB421 - 49335 - 107
132ASNASNGLUGLU(chain 'B' and (resid 390 through 419 or resid 421...BB495 - 518109 - 132
212ARGARGLYSLYS(chain 'D' and (resid 390 through 419 or resid 421 through 493 or resid 495 through 518))DD390 - 4194 - 33
222GLYGLYCYSCYS(chain 'D' and (resid 390 through 419 or resid 421 through 493 or resid 495 through 518))DD421 - 49335 - 107
232ASNASNGLUGLU(chain 'D' and (resid 390 through 419 or resid 421 through 493 or resid 495 through 518))DD495 - 518109 - 132
312ARGARGLYSLYS(chain 'F' and (resid 390 through 419 or resid 421 through 493 or resid 495 through 518))FF390 - 4194 - 33
322GLYGLYCYSCYS(chain 'F' and (resid 390 through 419 or resid 421 through 493 or resid 495 through 518))FF421 - 49335 - 107
332ASNASNGLUGLU(chain 'F' and (resid 390 through 419 or resid 421 through 493 or resid 495 through 518))FF495 - 518109 - 132

NCSアンサンブル:
ID
1
2

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要素

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タンパク質 , 2種, 6分子 ACEBDF

#1: タンパク質 Roundabout homolog 3 / Roundabout-like protein 3


分子量: 12254.451 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ROBO3 / 細胞株 (発現宿主): High Five cells / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q96MS0
#2: タンパク質 Protein kinase C-binding protein NELL1 / NEL-like protein 1 / Nel-related protein 1


分子量: 15297.861 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NELL1, NRP1 / 細胞株 (発現宿主): High Five cells / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q92832

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糖 , 1種, 3分子

#4: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


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

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非ポリマー , 4種, 661分子

#3: 化合物
ChemComp-NO3 / NITRATE ION


分子量: 62.005 Da / 分子数: 14 / 由来タイプ: 合成 / 式: NO3
#5: 化合物 ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Ca
#6: 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: 2 / 由来タイプ: 合成 / 式: C3H8O3
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 642 / 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: 2.79 Å3/Da / 溶媒含有率: 55.96 %
結晶化温度: 294 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 20% PEG 3,350, 0.2 M Magnesium nitrate

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データ収集

回折平均測定温度: 120 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 23-ID-D / 波長: 1.0332 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2017年8月3日 / 詳細: Adjustable focus K-B pair Si plus Pt, Rh coatings
放射モノクロメーター: Double Si(111) crystal cryo-cooled
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.0332 Å / 相対比: 1
反射解像度: 1.8→55 Å / Num. obs: 86152 / % possible obs: 99.6 % / 冗長度: 13 % / Biso Wilson estimate: 27.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.238 / Rrim(I) all: 0.246 / Net I/σ(I): 5.75
反射 シェル解像度: 1.8→1.85 Å / 冗長度: 6.2 % / Rmerge(I) obs: 2.053 / Mean I/σ(I) obs: 0.72 / Num. unique obs: 6058 / CC1/2: 0.465 / Rrim(I) all: 2.237 / % possible all: 95.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
XDS20170601データ削減
XSCALE20170615データスケーリング
PHASER2.8.0位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6POG

6pog


解像度: 1.8→51.47 Å / SU ML: 0.3037 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 37.4789
Rfactor反射数%反射Selection details
Rfree0.2666 1985 2.31 %Random selection
Rwork0.2298 ---
obs0.2307 85786 99.3 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 45.25 Å2
精密化ステップサイクル: LAST / 解像度: 1.8→51.47 Å
タンパク質核酸リガンド溶媒全体
原子数5105 0 113 642 5860
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00675364
X-RAY DIFFRACTIONf_angle_d0.8597322
X-RAY DIFFRACTIONf_chiral_restr0.0568820
X-RAY DIFFRACTIONf_plane_restr0.0057981
X-RAY DIFFRACTIONf_dihedral_angle_d13.08593238
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.52961350.53715708X-RAY DIFFRACTION95.79
1.85-1.90.5321390.46155901X-RAY DIFFRACTION99.69
1.9-1.950.47421400.39155957X-RAY DIFFRACTION99.79
1.95-2.020.37751450.34925931X-RAY DIFFRACTION99.69
2.02-2.090.34051440.32515950X-RAY DIFFRACTION99.62
2.09-2.170.34661400.30435937X-RAY DIFFRACTION99.53
2.17-2.270.27741410.26785948X-RAY DIFFRACTION99.69
2.27-2.390.28561420.24475947X-RAY DIFFRACTION99.43
2.39-2.540.28351430.22765984X-RAY DIFFRACTION99.46
2.54-2.740.26451390.22745992X-RAY DIFFRACTION99.4
2.74-3.010.2321410.21326024X-RAY DIFFRACTION99.52
3.01-3.450.24041390.19436030X-RAY DIFFRACTION99.28
3.45-4.340.20881450.16766134X-RAY DIFFRACTION99.7
4.34-51.470.20681520.17686358X-RAY DIFFRACTION99.66
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)
18.88676478566-1.748121808770.6037468612549.48027822273-4.100718060198.151580312130.329619409965-0.743602840139-0.03441239909570.497995942285-0.08048149898211.818171964580.572010672701-0.403380443181-0.2593351020260.379288881628-0.002833837399650.06726647588560.30635560308-0.01715897063670.37161742151-16.9355413759-15.981991945963.5195880651
22.404222802-0.522240652798-2.134577281878.27186974174-1.644448983862.444092664530.103950661418-0.218224963536-0.3285134301770.152113024463-0.176723606604-0.7227277242140.1902546195570.6297173501230.07615349009240.283101768703-0.0208060681145-0.04532779934290.32533042090.04390543710920.428532032401-1.95061205235-3.4597444904151.7317914454
35.41541491302-2.865349845723.186726229428.15609595629-1.795627727745.584972677880.140976058675-0.408128682103-0.2124741189680.3876118550990.006230756004640.1468373262080.102699428662-0.221808271665-0.1386221914190.228192156363-0.05478432906970.03774709918480.2642922987780.0195962263660.416606748623-14.5019785283-11.199840561956.7821057143
45.36851443132-4.692308565665.051348619867.448110083-4.066409703114.780440118110.5842609898850.199211312908-0.687334566181-0.271886337253-0.483915295519-0.3244884997760.5396153203570.229910710102-0.08363053758260.328945953234-2.74256039021E-5-0.02650381783970.336579924669-0.01023343778720.528391153399-9.47687195052-15.207375358351.593382615
53.799107517110.64923270528-1.202356755542.79325955349-0.4790541676452.431265114480.135216075207-0.0229179247866-0.2306984943210.012565344974-0.188857782971-0.703499432434-0.1593472581360.08183310250790.0909744149970.286713622142-0.0166688022548-0.02789809245480.259141610631-0.007910405765980.567386745066-9.33673421608-5.5346042993149.9101848802
65.832534245040.4659976022520.2094604638282.002370205381.191952862495.6003636150.546017419442-0.559704615671-0.7595927504750.848424687694-0.3904455151160.705593398020.295627864732-0.257298307411-0.08051452156810.339243037305-0.0419245086264-0.0173056298070.3323697167240.04851110975550.448042900301-19.6372957253-17.294222829159.7530975116
75.10414710307-0.6317743634390.6730515267014.340264618260.8762325803633.448805271490.4458022534010.2084179136990.538117724544-0.0447639226066-0.193809754059-0.121322240955-0.8274031675940.587591204493-0.3346454417150.509389431163-0.02252967073560.0534134389390.390442761-0.0257044903750.0864716650514-6.034692816813.8661577471949.9728664239
86.74757264006-5.053523733862.075770370924.01879066013-0.9339643604642.286761208590.07788033782690.15772928844-0.625083321764-0.3307061819440.0145978952971-0.909440693084-0.04847625631330.596982014163-0.07971065254320.3239225557990.05274786150020.03655231706810.485135283431-0.03935624240810.5976079316062.34198959367-42.939009614436.8373243088
98.08671008121-4.14346263744-4.908549005257.953350275032.012523984153.119399135210.1223751466960.5165804525280.0158891271653-0.237837103044-0.2950276872450.440820089574-0.0853769813046-0.2661694892930.1629363834640.2682756365060.00992921474987-0.01494040555580.251981489587-0.003577698698550.621070906693-5.3503824267-39.032252332242.7285471544
103.15423522124-3.75596124405-0.2761241280087.966470257411.36991698170.4354238570850.0950409324392-0.0145777191546-0.3020575938260.0644343348293-0.1546387903090.05520166004410.113011447179-0.0612749528390.0519263372560.280320939164-0.01474640655660.02752058048150.2811895131270.02817551366710.495811552997-22.7234835191-27.146637574149.2746918976
111.180268390540.923252502270.7301180172036.45220428796-0.2362220333021.540026000440.09764586023280.1258286419620.946132799419-0.0405189116618-0.02226393945840.6781850082-0.346313449866-0.1723880053050.03246831324370.2973404882430.03525950613170.02606963640590.2825437778290.006810342534890.663997122732-30.3410882242-5.6641108824549.8843186835
126.445542794183.539931858-0.934440170827.706144285670.7348135605152.851693120.333773672885-0.2097567235961.546568659540.399074972896-0.08600299710960.817760884683-0.674570953247-0.0788026439045-0.2237516702840.436643950453-0.005632733088560.07770201840230.278162803196-0.03222438221540.733628147115-21.66715534087.1022808873355.1208667986
132.304451914321.796442121890.4057674035071.426594526640.4706345502440.9685345393260.0323292110248-0.7596603248520.6275791686350.258939826129-0.2054572585130.166741374002-0.4533788347850.2673869139050.1902322252610.706576973907-0.108196492660.0626647361790.613362920667-0.3521213570811.24499010372-15.977032225313.996035978460.4511445647
146.41760685607-0.568116301739-0.9753904415174.07946901819-0.1783666719719.627547554790.720840271490.5857010242880.311001042894-1.28688758334-0.4413490844241.33180901008-0.314626091261-0.683457519047-0.2820436381020.247854241855-0.0146838595689-0.08935739234430.343927338974-0.0598776617450.498296576475-17.1829421313-1.733196107796.93310356635
154.30549998608-1.491711760651.871277126925.6127475565-3.32296092622.218364783530.147091347565-0.01133788403390.2100733273550.132696600543-0.277209491854-0.655616957169-0.001356493526260.6263101377030.1177906897960.2671146126370.016301096808-0.03372586578760.402793148999-0.03892701683880.546953487094-1.95563901756-14.055841257518.727015264
164.157242929232.44396447943-2.36654801215.018799459940.3326907568872.187702402310.01244568232990.4290979350590.0305737056007-0.1541888543220.006653633848540.084941490614-0.17877626882-0.1712527262030.001639783719470.237645005710.0432806283457-0.07005654969430.3205777860830.05432785044710.31992360002-14.5025941288-6.3547308867313.6564013195
179.902045243646.10521648118-6.631573808753.76097007184-4.088047764614.439077109170.67205745778-0.5826612191430.2914355500010.38358083289-0.597114789906-0.165832912599-0.4783609606540.629060451513-0.04657010211520.3402309443340.00131589521256-0.05553473156450.356919565993-0.01241722156560.534566236711-9.49325666291-2.2963330733918.8111497589
180.404768779236-0.01412880123660.04055142366090.6979835891630.07605812113970.1330806720040.0278932906161-0.213377053683-0.05067993782590.1637527926140.0998941811845-0.03153892971010.127428258739-0.003090025292520.03829672356910.3264553531880.00687059363617-0.1962786264990.3390604030280.249414482785-0.298217971262-9.36454944959-11.967192920420.5579659162
197.38988417337-4.127823156122.861744796972.41884345152-2.350027208996.125156383930.5337360806350.297408528551-0.615103792415-0.446865846674-0.2849461018150.4473867190550.4496461181160.145325418475-0.2250001825980.164546210428-0.05139246219680.0203011394690.2248765178770.01320363259030.45891874833-12.8350874886-11.205555576615.4525258121
205.827402220786.686977191713.175562660768.459656877942.715942775447.150259498210.113411243366-0.5449981183840.1837738990350.156085602373-0.3036911200760.3063518109120.0718357370476-0.1026687958740.1820963750220.2840164890580.02445630940020.001058937108070.251973339414-0.02346491385420.597538881972-3.3133739788422.568759293629.2247861417
213.303357549862.818465849010.1177741668132.60716224520.4727237805640.6655425610070.0008150380818970.09366446242670.165654451245-0.0489086313547-0.009882587137630.136498784048-0.0559912579316-0.08662672016490.02107466041650.2732106119920.0185928412725-0.05586598264890.276470675223-0.0007142936808820.460110465591-24.20699955225.617931024721.1469541538
228.17075853889-3.76591442043-0.163266793856.6233167410.8548442517333.213912608120.02922266177740.174027604264-1.71511047747-0.205687348456-0.0004350251709241.170294074640.5586838275-0.108215210141-0.04932453822460.341512909979-0.0153147147739-0.06752303141620.283586079827-0.03490699853280.676858098209-23.8900164428-23.459662906916.3596599721
235.00305441006-4.39341034644-5.280130459274.949539806373.362187608657.05956600421-0.3922899200620.950180145787-1.90974865558-0.3003613955850.3717860111480.1083355337270.3610937528850.6423539010070.04276549004880.6673786358280.0841191886801-0.08359989051050.443502057824-0.1957760364060.863035941899-16.4629975359-31.293889381110.4647009074
247.074615962970.681138340393-1.800014107771.49543919629-3.480952799998.66526596793-0.26713406450.506031154179-1.06296646292-0.9035264383710.222010835939-0.1628375990070.624724409078-0.4968626126340.02762813595910.3456449719490.0402085072014-0.03902025460140.255519087546-0.02588951614920.56807786740310.6005787146-30.19318597527.40554564635
255.64781984946-0.6490373158022.597635872932.97220856725-0.8852737172026.93322445384-0.0578525028157-0.3514465575520.478321572297-0.02364467771040.1175730010010.407043297051-0.53177456397-0.473216104247-0.03258070403840.3134384625680.0384132985069-0.03373237352170.29790859937-0.0123935482930.61844783774313.1331974654-12.194557914218.7390462495
267.46117362817-0.0114904347322.160822748793.00544386544-1.377523314044.232461627130.1510848743860.15874171822-0.195570304371-0.4988551401120.02920066682240.2647521011270.156161467696-0.0839200223434-0.1684111038750.3385813827340.0282676934769-0.05835517037430.175886380103-0.03938281703260.42967239235212.6633159917-27.058212332613.2215519677
275.97402292467-5.444176751017.488794074184.95603223517-6.820063745069.38141139146-0.313534289711-0.6216891482670.291219673451-0.03787659007580.308633085050.489515616483-0.292386113092-0.708788701551-0.01517106636990.370489378040.0236830505354-0.02319720170980.335042312584-0.03764872366990.609957582016.73946143108-24.583774644518.8657769741
283.319888284411.67000801650.8599434515375.325916458592.972314467243.56472274676-0.0899273761959-0.2362270809190.405967138474-0.0803853843902-0.06789551482950.423179110972-0.0998777698219-0.1450439503130.1758556580980.2774720785740.0198818573335-0.03814315553250.226856965710.005427222237890.5004475968815.0213041525-19.62443880420.6113726729
292.339342027262.26873275791-1.846470893412.20270693654-1.829612540076.04350502791-0.3384268337360.409608700405-1.18091141555-0.7103572833920.4801662039080.07884918667160.772480826687-0.337762039695-0.1440038745630.392588930064-0.0192777861617-0.08026765459060.243925563538-0.007460722656660.6195475500510.0063079342-34.445238896110.7540441671
301.800383962430.8567505457450.8939046217044.826290455474.956560913155.07890484404-0.131682756558-0.3163290296510.94767805613-0.617228463280.492649615772-0.826506447575-1.129011169330.688954869417-0.3693928019290.492860606167-0.0696182116685-0.02556603096150.354747424235-0.04553549312890.53717353293521.5518381278-12.817773760619.6115052817
318.02618082945-5.51978978443-6.089778979955.725416044934.759165948744.78192371406-0.364713379927-0.455242636426-0.4215202833620.4177460107220.1573737637010.1684087507050.1657704956150.1236659016680.2989018890230.3708019546870.0532020065511-0.008140646938910.382229238941-0.00281380400210.648422081389-18.0097425391-32.879351387931.4469600755
323.07788119257-1.2890784851-0.4842308250250.961823744748-0.1638377635070.354697610419-0.0690416664249-0.0780283912492-0.0949840027149-0.07525402940790.07791419058340.3026664577710.03628204946670.025635761643-0.003384431738070.3286569788420.014041715051-0.03721843909070.29975048436-0.03120552978810.59162346527-0.594596675403-39.800408512421.8360937652
334.009829552863.08206337741-0.2864617448128.92301347984-2.287657348012.48081804145-0.01277804714180.009768528917210.1023732363840.0311491494268-0.0260555860917-1.34491421813-0.1012894491840.2402466258040.05510701587830.2808801950490.02130852244050.006528562808940.317557787132-0.05102902462520.42343450373529.1587988506-29.99007343517.6993876884
347.264341181324.352995150864.80411132962.859999913282.216422938034.919553302650.4798334466180.3161121275860.719764189915-1.09220887765-0.92564929994-1.0498526521-0.6402462355710.01431113698670.4634774329170.579169214109-0.02895345500620.1767799439420.5618517436690.113139624460.9175561679835.2384877382-16.084532195110.5050387172
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 552 through 562 )
2X-RAY DIFFRACTION2chain 'A' and (resid 563 through 575 )
3X-RAY DIFFRACTION3chain 'A' and (resid 576 through 602 )
4X-RAY DIFFRACTION4chain 'A' and (resid 603 through 612 )
5X-RAY DIFFRACTION5chain 'A' and (resid 613 through 632 )
6X-RAY DIFFRACTION6chain 'A' and (resid 633 through 642 )
7X-RAY DIFFRACTION7chain 'A' and (resid 643 through 653 )
8X-RAY DIFFRACTION8chain 'B' and (resid 390 through 397 )
9X-RAY DIFFRACTION9chain 'B' and (resid 398 through 418 )
10X-RAY DIFFRACTION10chain 'B' and (resid 419 through 462 )
11X-RAY DIFFRACTION11chain 'B' and (resid 463 through 482 )
12X-RAY DIFFRACTION12chain 'B' and (resid 483 through 510 )
13X-RAY DIFFRACTION13chain 'B' and (resid 511 through 518 )
14X-RAY DIFFRACTION14chain 'C' and (resid 552 through 562 )
15X-RAY DIFFRACTION15chain 'C' and (resid 563 through 575 )
16X-RAY DIFFRACTION16chain 'C' and (resid 576 through 602 )
17X-RAY DIFFRACTION17chain 'C' and (resid 603 through 612 )
18X-RAY DIFFRACTION18chain 'C' and (resid 613 through 632 )
19X-RAY DIFFRACTION19chain 'C' and (resid 633 through 652 )
20X-RAY DIFFRACTION20chain 'D' and (resid 390 through 418 )
21X-RAY DIFFRACTION21chain 'D' and (resid 419 through 475 )
22X-RAY DIFFRACTION22chain 'D' and (resid 476 through 510 )
23X-RAY DIFFRACTION23chain 'D' and (resid 511 through 518 )
24X-RAY DIFFRACTION24chain 'E' and (resid 553 through 562 )
25X-RAY DIFFRACTION25chain 'E' and (resid 563 through 575 )
26X-RAY DIFFRACTION26chain 'E' and (resid 576 through 602 )
27X-RAY DIFFRACTION27chain 'E' and (resid 603 through 612 )
28X-RAY DIFFRACTION28chain 'E' and (resid 613 through 632 )
29X-RAY DIFFRACTION29chain 'E' and (resid 633 through 642 )
30X-RAY DIFFRACTION30chain 'E' and (resid 643 through 652 )
31X-RAY DIFFRACTION31chain 'F' and (resid 390 through 409 )
32X-RAY DIFFRACTION32chain 'F' and (resid 410 through 462 )
33X-RAY DIFFRACTION33chain 'F' and (resid 463 through 510 )
34X-RAY DIFFRACTION34chain 'F' and (resid 511 through 518 )

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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