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- PDB-6djl: Crystal structure of the Rab11 GEF SH3BP5 bound to nucleotide fre... -

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基本情報

登録情報
データベース: PDB / ID: 6djl
タイトルCrystal structure of the Rab11 GEF SH3BP5 bound to nucleotide free Rab11A
要素
  • Ras-related protein Rab-11A
  • SH3 domain-binding protein 5
キーワードSIGNALING PROTEIN/PROTEIN TRANSPORT / Rab GTPase / Guanine nucleotide exchange factor / membrane trafficking / PROTEIN TRANSPORT / SIGNALING PROTEIN-PROTEIN TRANSPORT complex
機能・相同性
機能・相同性情報


regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / synaptic vesicle endosomal processing / early endosome to recycling endosome transport / regulation of endocytic recycling / establishment of protein localization to organelle / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / establishment of vesicle localization ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / synaptic vesicle endosomal processing / early endosome to recycling endosome transport / regulation of endocytic recycling / establishment of protein localization to organelle / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / establishment of vesicle localization / amyloid-beta clearance by transcytosis / regulation of cilium assembly / regulation of protein transport / presynaptic endosome / exosomal secretion / astral microtubule organization / neurotransmitter receptor transport, endosome to postsynaptic membrane / vesicle-mediated transport in synapse / VxPx cargo-targeting to cilium / protein transmembrane transport / regulation of vesicle-mediated transport / myosin V binding / RAB geranylgeranylation / melanosome transport / multivesicular body assembly / protein localization to cilium / Golgi to plasma membrane protein transport / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / syntaxin binding / dynein light intermediate chain binding / mitotic metaphase chromosome alignment / exocytosis / protein kinase inhibitor activity / cleavage furrow / positive regulation of epithelial cell migration / mitotic spindle assembly / positive regulation of G2/M transition of mitotic cell cycle / transport vesicle / vesicle-mediated transport / phagocytic vesicle / multivesicular body / centriole / Anchoring of the basal body to the plasma membrane / cytoplasmic vesicle membrane / guanyl-nucleotide exchange factor activity / trans-Golgi network membrane / small monomeric GTPase / regulation of cytokinesis / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / regulation of long-term neuronal synaptic plasticity / recycling endosome / SH3 domain binding / Schaffer collateral - CA1 synapse / recycling endosome membrane / neuron projection development / spindle pole / endocytic vesicle membrane / synaptic vesicle membrane / Vasopressin regulates renal water homeostasis via Aquaporins / G protein activity / cytoplasmic vesicle / microtubule binding / vesicle / intracellular signal transduction / nuclear body / Golgi membrane / GTPase activity / centrosome / GTP binding / glutamatergic synapse / Golgi apparatus / signal transduction / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / cytosol / cytoplasm
類似検索 - 分子機能
SH3-binding 5 / SH3 domain-binding protein 5 (SH3BP5) / : / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases ...SH3-binding 5 / SH3 domain-binding protein 5 (SH3BP5) / : / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
SH3 domain-binding protein 5 / Ras-related protein Rab-11A
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 / 単波長異常分散 / 解像度: 3.10001148084 Å
データ登録者Burke, J.E. / Jenkins, M.L. / Boulanger, M.J.
資金援助 カナダ, 1件
組織認可番号国
Natural Sciences and Engineering Research Council (NSERC, Canada)05214 カナダ
引用ジャーナル: Nat Commun / 年: 2018
タイトル: Structural determinants of Rab11 activation by the guanine nucleotide exchange factor SH3BP5.
著者: Jenkins, M.L. / Margaria, J.P. / Stariha, J.T.B. / Hoffmann, R.M. / McPhail, J.A. / Hamelin, D.J. / Boulanger, M.J. / Hirsch, E. / Burke, J.E.
履歴
登録2018年5月25日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年9月26日Provider: repository / タイプ: Initial release
改定 1.12020年1月8日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22024年3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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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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: Ras-related protein Rab-11A
B: SH3 domain-binding protein 5
C: SH3 domain-binding protein 5
D: SH3 domain-binding protein 5
E: SH3 domain-binding protein 5
F: Ras-related protein Rab-11A
G: Ras-related protein Rab-11A
H: Ras-related protein Rab-11A


分子量 (理論値)分子数
合計 (水以外)222,8958
ポリマ－222,8958
非ポリマー00
水00
1
A: Ras-related protein Rab-11A
C: SH3 domain-binding protein 5


分子量 (理論値)分子数
合計 (水以外)55,7242
ポリマ－55,7242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-12 kcal/mol
Surface area24630 Å2
手法PISA
2
B: SH3 domain-binding protein 5
H: Ras-related protein Rab-11A


分子量 (理論値)分子数
合計 (水以外)55,7242
ポリマ－55,7242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-17 kcal/mol
Surface area24390 Å2
手法PISA
3
D: SH3 domain-binding protein 5
G: Ras-related protein Rab-11A


分子量 (理論値)分子数
合計 (水以外)55,7242
ポリマ－55,7242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-10 kcal/mol
Surface area24220 Å2
手法PISA
4
E: SH3 domain-binding protein 5
F: Ras-related protein Rab-11A


分子量 (理論値)分子数
合計 (水以外)55,7242
ポリマ－55,7242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-12 kcal/mol
Surface area24340 Å2
手法PISA
単位格子
Length a, b, c (Å)114.850, 197.040, 304.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALILEILE(chain 'B' and (resid 41 through 45 or resid 47...BB41 - 4542 - 46
12GLYGLYASNASN(chain 'B' and (resid 41 through 45 or resid 47...BB47 - 5348 - 54
13SERSERARGARG(chain 'B' and (resid 41 through 45 or resid 47...BB55 - 6156 - 62
14GLUGLUVALVAL(chain 'B' and (resid 41 through 45 or resid 47...BB63 - 8864 - 89
15LYSLYSILEILE(chain 'B' and (resid 41 through 45 or resid 47...BB90 - 9191 - 92
16ALAALAVALVAL(chain 'B' and (resid 41 through 45 or resid 47...BB94 - 9595 - 96
17ASPASPTYRTYR(chain 'B' and (resid 41 through 45 or resid 47...BB97 - 10198 - 102
18GLUGLUGLNGLN(chain 'B' and (resid 41 through 45 or resid 47...BB103 - 116104 - 117
19ALAALAGLNGLN(chain 'B' and (resid 41 through 45 or resid 47...BB118 - 123119 - 124
110ALAALAMETMET(chain 'B' and (resid 41 through 45 or resid 47...BB125 - 191126 - 192
111METMETLEULEU(chain 'B' and (resid 41 through 45 or resid 47...BB194 - 201195 - 202
112ARGARGSERSER(chain 'B' and (resid 41 through 45 or resid 47...BB203 - 208204 - 209
113PROPROLYSLYS(chain 'B' and (resid 41 through 45 or resid 47...BB210 - 215211 - 216
114TYRTYRLEULEU(chain 'B' and (resid 41 through 45 or resid 47...BB218 - 222219 - 223
115GLNGLNLEULEU(chain 'B' and (resid 41 through 45 or resid 47...BB224 - 225225 - 226
116LYSLYSLEULEU(chain 'B' and (resid 41 through 45 or resid 47...BB227 - 238228 - 239
117GLYGLYTYRTYR(chain 'B' and (resid 41 through 45 or resid 47...BB241 - 243242 - 244
118METMETGLUGLU(chain 'B' and (resid 41 through 45 or resid 47...BB245 - 251246 - 252
119ILEILEGLUGLU(chain 'B' and (resid 41 through 45 or resid 47...BB253 - 259254 - 260
21VALVALILEILE(chain 'E' and (resid 41 through 45 or resid 47...EE41 - 4542 - 46
22GLYGLYASNASN(chain 'E' and (resid 41 through 45 or resid 47...EE47 - 5348 - 54
23SERSERARGARG(chain 'E' and (resid 41 through 45 or resid 47...EE55 - 6156 - 62
24GLUGLUVALVAL(chain 'E' and (resid 41 through 45 or resid 47...EE63 - 8864 - 89
25LYSLYSILEILE(chain 'E' and (resid 41 through 45 or resid 47...EE90 - 9191 - 92
26ALAALAVALVAL(chain 'E' and (resid 41 through 45 or resid 47...EE94 - 9595 - 96
27ASPASPTYRTYR(chain 'E' and (resid 41 through 45 or resid 47...EE97 - 10198 - 102
28GLUGLUGLNGLN(chain 'E' and (resid 41 through 45 or resid 47...EE103 - 116104 - 117
29ALAALAGLNGLN(chain 'E' and (resid 41 through 45 or resid 47...EE118 - 123119 - 124
210ALAALAMETMET(chain 'E' and (resid 41 through 45 or resid 47...EE125 - 191126 - 192
211METMETLEULEU(chain 'E' and (resid 41 through 45 or resid 47...EE194 - 201195 - 202
212ARGARGSERSER(chain 'E' and (resid 41 through 45 or resid 47...EE203 - 208204 - 209
213PROPROLYSLYS(chain 'E' and (resid 41 through 45 or resid 47...EE210 - 215211 - 216
214TYRTYRLEULEU(chain 'E' and (resid 41 through 45 or resid 47...EE218 - 222219 - 223
215GLNGLNLEULEU(chain 'E' and (resid 41 through 45 or resid 47...EE224 - 225225 - 226
216LYSLYSLEULEU(chain 'E' and (resid 41 through 45 or resid 47...EE227 - 238228 - 239
217GLYGLYTYRTYR(chain 'E' and (resid 41 through 45 or resid 47...EE241 - 243242 - 244
218METMETGLUGLU(chain 'E' and (resid 41 through 45 or resid 47...EE245 - 251246 - 252
219ILEILEGLUGLU(chain 'E' and (resid 41 through 45 or resid 47...EE253 - 259254 - 260

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要素

#1: タンパク質
Ras-related protein Rab-11A / Rab-11 / YL8


分子量: 24691.818 Da / 分子数: 4 / 変異: Q70L / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RAB11A, RAB11 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P62491
#2: タンパク質
SH3 domain-binding protein 5 / SH3BP-5 / SH3 domain-binding protein that preferentially associates with BTK


分子量: 31032.000 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SH3BP5, SAB / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: O60239

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.87 Å3/Da / 溶媒含有率: 73.7 %
結晶化温度: 289 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 / 詳細: 23% PEG-3350, 200 mM NaCl, 100 mM Bis Tris pH-6.5

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: CLSI / ビームライン: 08ID-1 / 波長: 0.97949 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2017年12月17日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97949 Å / 相対比: 1
反射解像度: 3.1→50 Å / Num. obs: 62902 / % possible obs: 99.74 % / 冗長度: 4.9 % / Biso Wilson estimate: 114.717887746 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1363 / Rpim(I) all: 0.06845 / Rrim(I) all: 0.1531 / Net I/σ(I): 8.26
反射 シェル解像度: 3.1→3.21 Å / 冗長度: 5.1 % / Rmerge(I) obs: 2.189 / Mean I/σ(I) obs: 0.75 / Num. unique obs: 6236 / CC1/2: 0.281 / Rpim(I) all: 1.072 / % possible all: 99.79

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解析

ソフトウェア
名称バージョン分類
XDSデータ削減
XSCALEデータスケーリング
PHENIX精密化
PDB_EXTRACT3.24データ抽出
CRANK2位相決定
精密化構造決定の手法: 単波長異常分散 / 解像度: 3.10001148084→49.6123632974 Å / SU ML: 0.662234327786 / 交差検証法: FREE R-VALUE / σ(F): 1.3308053611 / 位相誤差: 33.0337293174
Rfactor反射数%反射
Rfree0.277638805607 3145 5.00246544402 %
Rwork0.235203699975 --
obs0.237315729513 62869 99.7762259959 %
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: 132.438293234 Å2
精密化ステップサイクル: LAST / 解像度: 3.10001148084→49.6123632974 Å
タンパク質核酸リガンド溶媒全体
原子数12888 0 0 0 12888
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0028749846856113048
X-RAY DIFFRACTIONf_angle_d0.54650580873517531
X-RAY DIFFRACTIONf_chiral_restr0.03770223259361974
X-RAY DIFFRACTIONf_plane_restr0.002689525877582261
X-RAY DIFFRACTIONf_dihedral_angle_d13.75410301788113
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.14840.4737216965471410.4474762573332667X-RAY DIFFRACTION99.7513321492
3.1484-3.20010.4472302394921420.4361674260522698X-RAY DIFFRACTION99.8242530756
3.2001-3.25520.4245613605371420.3907484676962693X-RAY DIFFRACTION99.823943662
3.2552-3.31440.4181194349031400.3768608040692660X-RAY DIFFRACTION99.8929718159
3.3144-3.37810.3870437328781430.3416584275452703X-RAY DIFFRACTION99.9297752809
3.3781-3.44710.3418116734351410.3181589028042680X-RAY DIFFRACTION99.7172145634
3.4471-3.5220.3559047189551420.3038369324212710X-RAY DIFFRACTION99.8599439776
3.522-3.60390.3822506730311420.3130439622312682X-RAY DIFFRACTION99.5768688293
3.6039-3.6940.329263738541420.3004131717832695X-RAY DIFFRACTION99.9647639183
3.694-3.79390.3418611254741410.2926943790492686X-RAY DIFFRACTION99.8234463277
3.7939-3.90550.3442885073471420.2731662699382700X-RAY DIFFRACTION99.8594518623
3.9055-4.03150.3067793686211430.2578219515582713X-RAY DIFFRACTION99.9649982499
4.0315-4.17550.265244447511420.2387619385612691X-RAY DIFFRACTION99.8590059922
4.1755-4.34260.3110921999111420.226751263722710X-RAY DIFFRACTION99.9299229152
4.3426-4.54010.257944964121440.2177372419212734X-RAY DIFFRACTION99.9652657173
4.5401-4.77920.2112754235681430.1970788446912715X-RAY DIFFRACTION99.8602375961
4.7792-5.07840.2422030865531420.1987976600382698X-RAY DIFFRACTION99.5792426367
5.0784-5.47010.2778014923411440.2312076637952746X-RAY DIFFRACTION99.7928176796
5.4701-6.01970.3422022005881450.2673811104132740X-RAY DIFFRACTION99.8615437868
6.0197-6.88880.303827386631440.2392429147612739X-RAY DIFFRACTION99.6887966805
6.8888-8.67160.232988258791470.1913034899632792X-RAY DIFFRACTION99.6271186441
8.6716-49.61870.2029334530351510.1714070241012872X-RAY DIFFRACTION98.9849377865
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)
15.31030354459-2.05549080858-3.614050141446.26713701717-1.446669555027.573822849430.3037769129740.5319324316461.637493589550.534856856477-0.659412377186-0.03153557910190.942543976157-1.034270906330.2726797658471.50222482549-0.271221087664-0.01585222129210.836362144908-0.103978935680.945896674763-34.5602004509-38.664528572192.7861451718
21.72133414723-0.2116994044610.3730068825271.06571440032-0.2798815891690.997972233975-0.393942269505-0.5637903264580.4220275891910.541814002588-0.5045864231720.7971112299690.2892267187161.099353175640.5033796507282.33888491319-0.501460953014-0.5304902285332.65366380507-0.06754128302360.729378564018-39.6192731773-44.7880850249111.120297785
36.283356441532.842792991142.015100223153.438046384031.696162775964.622199235050.495060203194-0.2923383334630.2744298442662.360967790920.0923486805858-1.436214222-0.5470955625150.795020921138-0.6011102081422.212514583970.00315301122323-0.3661627000721.25944783526-0.07583638293361.22826324321-28.1058364583-41.6243639762105.677657528
42.58468298224-0.1284291070440.3892567235570.167297563581-0.4130488482123.83366689482-0.0271371205977-1.055809316930.08638738740371.41108048408-0.4751338571230.887982872411.96880865123-0.3492614866140.3054038127451.71727340171-0.5606978599090.4379074000581.35722635075-0.1339868478141.2009508712-39.3273641853-37.6445054689102.818880179
52.720045391770.927141293893-1.968172006561.208131083140.5174048439098.000404436210.1823453097290.2327999023440.3016656113220.55408704713-0.1353407111630.364319231659-0.844250754202-1.805604822560.0460180467841.66671586731-0.4028798978710.5616639502791.56051549879-0.5039198635571.61816490611-52.2289715662-39.7583805141104.22298179
62.803598389490.760585451702-2.426388675763.389199304261.011506437163.739419850430.151923946475-0.152412952551-0.007465548617991.20645994506-0.3209632393573.6293889271.48571754878-0.2888632366120.4450653733051.98145355452-0.6060206919980.7748242274951.70109396746-0.2909561014552.59404633353-53.2811250682-54.3093686879108.114173395
73.08730874454-0.281702343385-0.5720568371252.02372504547-0.6612964937463.331215410290.4452196301420.519514038722-0.944918674020.726479767671-0.7738661141853.126407044950.0939548294595-1.99422658046-0.102586679691.59918085792-1.147836011670.6987880088520.89153093849-0.396058088262.25891055567-45.5634170798-53.0933290609103.255370293
83.4582656997-2.236667645750.7328580358463.95597711042-1.123017785215.710931893470.8631554945740.0519637089939-0.9647944761670.468236380567-0.671513715450.09009077285691.40652281351-0.0796738058638-0.1852722180131.36627185129-0.468508371081-0.000163888944761.12005101899-0.02353176425811.76342039029-42.4345387282-45.75554852587.8777008763
93.884890327-0.910030334703-5.039956785051.475755938511.476635146587.272938415210.05308531056691.76239864077-0.949627992057-1.02160326511-0.622906318940.354557124316-0.707240563612-1.968251686130.6827017453350.998193146457-0.1309560426-0.03938021023751.07029841943-0.2355074865871.20896163846-23.1578967194-14.949464644949.4401174263
107.33024403947-4.245281532860.6799045457181.9971493748-0.642576253338-0.0137579939446-0.282153341785-0.633372417386-0.195311978660.2494550522790.3208890871790.0962805071750.0868538541315-0.121911985471-0.005171272919960.9235105512740.1115507203160.1380178878910.858821196561-0.1069047052421.05580029797-5.90206917011-32.777686221788.6812381717
114.017789324240.632120596803-4.479283327880.195624948316-0.3519281918475.91475368832-0.551369944754-0.297333131484-0.466392854727-0.350024981948-0.02017864705470.3351757672840.8208124752870.5467160621730.4729725841661.081974923070.005646345647530.1659572009750.8934869079250.02000743245851.12390899579-17.755879596-17.009115897455.8251517321
120.7640734198980.270621577832-0.9483827503181.692002467641.027679786835.94492647436-0.2199390669210.1499354666970.349744456779-0.357406456458-0.3434387233880.545487691517-0.681619557627-1.290498037380.3028846134860.812626772023-0.0168348336459-0.03874029895880.781602860196-0.2095714664111.09275917563-31.5809410226-33.202661905576.7828509314
134.1704953735.293160407282.258213018744.114581749690.9209981041311.30944508213-0.09635164540440.125324899363-0.833865470133-0.2143105198330.0392929695131-1.059660691380.3406806379910.3621751731450.1637056066750.973133192260.008097601451960.09188149833221.00994091688-0.07030992296841.461204267976.13851904204-12.493063476555.9707582355
141.22537094749-0.506358045851-2.551937057221.268232023981.967105097277.63995394944-0.0800501068893-0.3384054958270.0161537666130.116054655761-0.1777160199110.376286876308-0.6600361182471.185226771790.2213581951731.00089665395-0.235043752882-0.008322569733650.910744520281-0.08724817676240.89304077523-23.7094943005-29.907716888579.0130330822
150.559437589546-0.60786801999-0.4887314273545.87947614189-4.317727923666.71187783615-0.640113692011-0.02715822332230.121075529986-0.32708044499-0.301852866418-1.574540499250.472572183120.3308354110510.9103641150730.784093153943-0.00647198399265-0.01647186446530.728750898825-0.02431445846861.0909907120525.4813294739-33.249708777481.5565763434
165.23399570458-6.17593463897-0.1357304518757.09621922343-1.780407109151.212361054850.01300650531690.1732880365870.756223631901-0.5364941148380.12286183212-0.9511776444510.2277129712030.152304095444-0.05915544631720.988826560147-0.1423103316590.06514158315520.876904431794-0.1864684577120.914175349618-2.83498059776-26.1414294202106.808727914
177.218264492121.596595650511.494277867017.622144275942.064298339336.144053238970.6162993820150.89440045088-1.153719623150.537171700592-0.190584049463-1.531601288731.17736240150.375705607025-0.3874301545041.136342611160.157199037528-0.08983088250661.025748952180.04069969052061.17000986909-14.053503253611.919477801199.193566668
181.82750760824-2.922486308750.05126307436413.2588222364-0.8321110459571.941132960460.249536678950.0416753246475-0.473233884592-1.14987902855-0.324831377031.381034428830.235852510324-0.02746966521270.112458784721.20443642033-0.0741825177844-0.01708798462940.934374926974-0.02371230576311.14282705462-10.6065302806-25.254642251107.566307017
190.9980726940570.144646713347-1.59251333732.80392620409-2.135180063044.94489508625-0.0001465291544980.157449885570.228026162023-0.3822448401840.0145382685224-0.1837407939270.138318883799-0.291656728704-0.05109152050140.76404966548-0.00425856672517-0.02045503567380.760648465186-0.02239438841390.80321633855117.7297067063-29.548874004180.3076406942
205.593707778393.44809768094-6.423052726755.03239407732-6.267421565789.456684064530.29459755346-1.11945825381-0.3044485835670.64078311224-0.6971290249760.0316754468925-0.3216165768011.036068522520.4066495035310.951698386158-0.144748516276-0.06698458843350.948050871670.009568401646590.77621784899416.3256116292-26.0373804043113.009029123
216.316847198914.126310182381.750872486940.8526290175330.313128800367-0.130750152463-0.1686550262150.605205252152-0.28741835953-0.2513565177830.242680915024-0.1734111499180.09820013743810.176353424538-0.1287711554440.950325059587-0.1914815433610.06299125686670.950728885088-0.2072971199121.21732864111-1.07725485877-29.850997607669.680189893
221.91537957471.48985537268-2.417189953811.89707420586-2.618859535945.52778951378-0.513703489170.209454017435-0.249568092292-0.03846104042770.238271670665-0.2457766536830.746678321273-1.013374276190.3581065960560.95011642055-0.06565170563480.1561067970061.01938647231-0.05442587823680.7964200260519.32317885251-26.1260565217109.283515508
231.746600161641.037518811620.8375248707645.90720574134-0.7514649986811.430798579630.471612275193-1.569724959810.362889576389-1.153399687560.1557978211631.18525979256-0.5226011962370.49361836694-0.4192601776270.977397752911-0.04051420272580.2373353898371.95951916387-0.07665102829120.9084677991217.31755148196-25.4720777754136.642693163
242.730191276352.52937846116-0.2128114266544.49027018967-0.4216065171344.722646975040.0108427731883-1.745534395750.0807327464096-0.220043655269-0.455679422611-0.450524636876-0.3085938294380.7846287643920.3066647062471.161688133420.01877353285150.2852843586591.660742731350.005316538887230.8286134340654.95932046482-31.5241286477134.675697587
255.09247622688-1.827391088512.791066129725.14642098562-0.7547207526836.015107643160.152994714588-1.30423811124-2.60041451635-0.068516769756-1.44043374420.9980573300341.121007652222.205749938410.7128683567631.004900443470.2520434815870.1456519672962.79011896461-0.03575619722831.0488344827314.6007774415-36.277707402148.861437953
263.32479455158-0.0677481870287-0.148450620741.77901004154-1.86072000191.98152284612-0.408086622451-1.959502734150.337387662893-0.123479515241-0.1048583480730.120479929928-0.8734999194482.48339439491-0.1238821876460.929636458971-0.0862087160241-0.01398088660512.279226536730.1045312951160.66099517076813.5711411258-28.1615345697150.831731425
272.390764729470.0336107809941-1.69375079044.21933948659-2.059813794823.87649586826-0.154798381314-1.639525397060.143082030882-0.209310809671-2.12312927005-0.6694384331930.559634855138-0.316059369361.448847591941.17444354112-0.0209127817378-0.1481677687953.13292749505-0.3402627639741.4776984659924.7456527409-28.4207325447152.80297318
283.34374471438-0.762070794343-2.097875642612.00463931295-0.2406242491725.065225865430.440410361845-1.307406409730.775244581021-0.3059894225350.192381074558-0.67311314831-0.9070791928291.6607992569-0.5319427061281.08507190044-0.334639708660.119421885391.84140019222-0.2523924851171.1484471665318.8877138314-22.3970042421137.639083405
293.56594815261-0.3246393384541.542148203848.12736799113-1.654878280018.85522733555-0.413052099282-0.9155386767210.0897038485718-0.4120340380620.293071773264-1.557086768110.9668959416120.5745337527160.1406737328621.08926443734-0.0309194329990.4083918075960.724063034832-0.1653218463421.3266956710929.7397673616-32.665583363264.6543593196
301.01764714049-1.289326265421.700485316881.83947639793-2.330083485793.042101643620.3180566255171.547500539081.061827990870.3633320955240.21359226145-1.35169665329-0.2402198681021.826162125780.08000007058062.934628070520.6265544198470.1628577303692.59629483560.3428282580061.199787045435.3121770995-32.049144011846.1413823974
313.170426677-2.9394861805-0.1856010113937.9394195682.072929177810.830491753651.575436778780.1800013154180.117733279054-0.754647037538-1.67141400354-0.06695555450681.89644219201-1.03831117994-0.2070984834062.55339626709-0.204638985078-0.1131276994781.160418297280.06170024526991.0890998817822.9873729319-32.337700839551.8758720143
321.95635184775-0.2995984637750.9365082206438.50101995032-1.686751614091.813146767440.9721864049060.423884178364-0.7705440178451.15681694647-0.2682222749811.58667826692-1.38517722437-0.348667357269-0.3296937549691.827409751750.08574577331560.4675067967451.14554106119-0.2083193448841.2600276518527.6884066887-28.935898378155.4194207969
333.154787377744.67178854888-0.3942490592046.32668955602-0.9242825249735.63261732074-1.138328856880.580167610547-0.881602216381-1.00485052285-0.341321724188-4.096589712962.393563819171.133692458411.144450271431.402051160150.1656450379780.665906123721.236009920490.09917361945421.5225371280532.9928916967-26.504711469457.3255339032
341.017089422340.17401657264-0.034534629231.56227431347-1.997399834012.7233371280.02570013784180.9953652240430.697886831657-1.14243680021-0.228637053922-1.435281336870.0548351976661.818624504640.1536504423291.41915776818-0.1014094839530.6741851697511.877949684010.02832231789562.4701044204544.8704893251-28.20649456852.975044312
352.835880623990.4462713022740.6350802718030.878262655754-1.563839261693.39297517730.3624441954860.00036438941659-2.56589259344-1.587152045850.0678680136047-2.78787196419-0.5642381720911.80865405662-0.03626726668591.624106545980.132444202460.9738949670971.63382700156-0.325304277761.7968158384745.5325825895-39.583741665652.0209759645
369.279697740061.28399675347-1.567697055247.32711000470.5162897166975.013877557790.9892247072-0.745246925743-0.738840034787-1.38191455537-0.665570296638-2.394105611071.598079998660.109477157449-0.1028387214491.644374324930.2571795198510.4729563592421.12219872361-0.01662977294862.1138517623736.7975878275-40.99380373866.5738666469
373.68485868034-0.7418702438760.6283751575345.68517006585-1.263113398562.79107772448-0.1656181610980.2264231038150.271627452119-0.567020686786-0.616211797094-1.29964515556-0.265221151521-0.3068734309210.8325238279271.71553442136-0.2686386645590.04198937286141.32281455113-0.07166956978561.15023694956-7.51650935268-7.4108752783827.3164025088
385.94463257492-0.565915360983-3.323273105844.18402046552.721340609129.09549277120.1687176661320.166564493478-0.488096760762-1.24503572166-0.5240938568740.530688843701-1.69471630446-0.8462157838980.2638633234911.61782409569-0.136838000195-0.1364065375921.189923044950.08940801975850.867669106672-12.8844464819-5.2648907601334.4994978277
392.85865594195-3.20143137912-2.560488408046.187303147562.801852925742.46726884920.184337917735-1.2507307876-0.275574569878-0.9337800280160.712851183758-0.127436573122-0.1745443447212.24200391463-1.343500747561.98845813321-0.441248651897-0.3647713322181.87304040994-0.07649024397051.26502995421-11.8125676734-18.66751821819.8208598616
402.96873972038-2.42639542006-0.06897590938861.992526547840.4454305994272.42748764810.4526254586511.02739608169-0.960798110911-0.8542476154840.04597029530720.9403761231540.1518865598480.252310542152-0.2115883200252.31781651065-0.528121510147-0.5010370811632.03465255702-0.1199567824621.19811630773-19.3010886965-8.2752156233714.970830805
410.417779384393-0.176362633733-0.375542670637.217277155122.360278093551.008813816550.666834095471-0.937123004918-0.735921470169-0.250181555152-0.0832454699002-2.24757364494-0.260069229737-2.346298137-0.3775921551562.070164500920.0164168751178-0.2998443072132.073907121260.6667193268111.49007413645-10.49044005416.361697618887.2410354664
421.280656138620.0957747165139-0.0009169096706081.50286085265-1.226009926390.66586610528-0.5406918083540.4733915115840.166920203791-0.9629523130790.3128588513450.820580990508-0.00380486191944-1.059577698680.1120181810521.56103614526-0.00944658866399-0.4358397654611.97088910054-0.04414596785241.31948034462-22.90632100370.099246444018624.9074559074
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 39 )
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 95 )
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 123 )
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 145 )
7X-RAY DIFFRACTION7chain 'A' and (resid 146 through 158 )
8X-RAY DIFFRACTION8chain 'A' and (resid 159 through 183 )
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 91 )
10X-RAY DIFFRACTION10chain 'B' and (resid 92 through 201 )
11X-RAY DIFFRACTION11chain 'B' and (resid 202 through 261 )
12X-RAY DIFFRACTION12chain 'C' and (resid 41 through 91 )
13X-RAY DIFFRACTION13chain 'C' and (resid 92 through 201 )
14X-RAY DIFFRACTION14chain 'C' and (resid 202 through 264 )
15X-RAY DIFFRACTION15chain 'D' and (resid 41 through 91 )
16X-RAY DIFFRACTION16chain 'D' and (resid 92 through 137 )
17X-RAY DIFFRACTION17chain 'D' and (resid 138 through 161 )
18X-RAY DIFFRACTION18chain 'D' and (resid 162 through 201 )
19X-RAY DIFFRACTION19chain 'D' and (resid 202 through 264 )
20X-RAY DIFFRACTION20chain 'E' and (resid 39 through 93 )
21X-RAY DIFFRACTION21chain 'E' and (resid 94 through 201 )
22X-RAY DIFFRACTION22chain 'E' and (resid 202 through 264 )
23X-RAY DIFFRACTION23chain 'F' and (resid 6 through 33 )
24X-RAY DIFFRACTION24chain 'F' and (resid 34 through 85 )
25X-RAY DIFFRACTION25chain 'F' and (resid 86 through 112 )
26X-RAY DIFFRACTION26chain 'F' and (resid 113 through 135 )
27X-RAY DIFFRACTION27chain 'F' and (resid 136 through 145 )
28X-RAY DIFFRACTION28chain 'F' and (resid 146 through 182 )
29X-RAY DIFFRACTION29chain 'G' and (resid 6 through 18 )
30X-RAY DIFFRACTION30chain 'G' and (resid 19 through 28 )
31X-RAY DIFFRACTION31chain 'G' and (resid 29 through 38 )
32X-RAY DIFFRACTION32chain 'G' and (resid 39 through 55 )
33X-RAY DIFFRACTION33chain 'G' and (resid 56 through 76 )
34X-RAY DIFFRACTION34chain 'G' and (resid 77 through 112 )
35X-RAY DIFFRACTION35chain 'G' and (resid 113 through 158 )
36X-RAY DIFFRACTION36chain 'G' and (resid 159 through 182 )
37X-RAY DIFFRACTION37chain 'H' and (resid 6 through 46 )
38X-RAY DIFFRACTION38chain 'H' and (resid 47 through 66 )
39X-RAY DIFFRACTION39chain 'H' and (resid 67 through 85 )
40X-RAY DIFFRACTION40chain 'H' and (resid 86 through 124 )
41X-RAY DIFFRACTION41chain 'H' and (resid 125 through 135 )
42X-RAY DIFFRACTION42chain 'H' and (resid 136 through 182 )

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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

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