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- PDB-7n9u: CA-targeting nanobody is a tool for studying HIV-1 capsid lattice... -

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データを開く


IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 7n9u
タイトルCA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions
要素
  • Capsid protein
  • Nanobody
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 / hexamer / nanobody / CypA / VIRAL PROTEIN-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / ATP binding / cytoplasm
類似検索 - 分子機能
: / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal ...: / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
類似検索 - ドメイン・相同性
生物種Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
Lama glama (ラマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.19 Å
データ登録者Gerber, E.E. / Digianantonio, K.M. / Tripler, T.N. / Smaga, S.S. / Summers, B.J. / Xiong, Y.
資金援助 米国, 2件
組織認可番号
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50GM082251 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)F32 GM131426 01A1 米国
引用ジャーナル: To Be Published
タイトル: CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions
著者: Gerber, E.E. / Digianantonio, K.M. / Tripler, T.N. / Smaga, S.S. / Summers, B.J. / Xiong, Y.
履歴
登録2021年6月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年6月22日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: Capsid protein
B: Capsid protein
C: Capsid protein
D: Nanobody
E: Nanobody
F: Nanobody


分子量 (理論値)分子数
合計 (水以外)111,7276
ポリマ-111,7276
非ポリマー00
00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Nanobody
E: Nanobody
F: Nanobody

A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Nanobody
E: Nanobody
F: Nanobody


分子量 (理論値)分子数
合計 (水以外)223,45512
ポリマ-223,45512
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
単位格子
Length a, b, c (Å)129.698, 143.570, 228.940
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詳細
d_1ens_1(chain "A" and (resid 1 through 24 or resid 26...
d_2ens_1(chain "B" and (resid 1 through 24 or resid 26...
d_3ens_1(chain "C" and (resid 1 through 24 or resid 26...
d_1ens_2(chain "D" and (resid 1 through 98 or resid 102 through 113))
d_2ens_2(chain "E" and (resid 1 through 98 or resid 102 through 113))
d_3ens_2chain "F"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROVALA1 - 21
d_12ens_1VALGLUA23 - 32
d_13ens_1ILEALAA34 - 62
d_14ens_1GLNHISA64 - 84
d_15ens_1GLNILEA86 - 144
d_16ens_1GLNGLYA146 - 213
d_21ens_1PROVALB1 - 21
d_22ens_1VALGLUB23 - 32
d_23ens_1ILEALAB34 - 62
d_24ens_1GLNHISB64 - 84
d_25ens_1GLNILEB86 - 144
d_26ens_1GLNGLYB146 - 213
d_31ens_1PROVALC1 - 21
d_32ens_1VALGLUC23 - 32
d_33ens_1ILEALAC34 - 62
d_34ens_1GLNHISC64 - 84
d_35ens_1GLNILEC92 - 150
d_36ens_1GLNGLYC152 - 219
d_11ens_2ASPTHRD1 - 101
d_12ens_2TYRSERD103 - 114
d_21ens_2ASPTHRE1 - 101
d_22ens_2TYRSERE103 - 114
d_31ens_2ASPSERF1 - 113

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.493490596433, -0.869677815245, 0.0112928695498), (0.86974930073, 0.493474600917, -0.00435570075657), (-0.00178468797645, 0.0119714627584, 0.999926746801)32.6408997543, -56.1596953057, 0.269093377464
2given(-0.486189226275, -0.873585712051, 0.0216342310726), (0.873853063449, -0.486066201114, 0.0109759571147), (0.00092722919996, 0.0242415311954, 0.9997057009)96.093722914, -56.3987937817, 0.24924312165
3given(-0.34534179829, 0.924744623879, -0.159957566126), (-0.936820104665, -0.329564113922, 0.117284211688), (0.0557416706792, 0.190354604415, 0.980131619084)96.8680313434, 61.9133027878, 3.72364609777
4given(0.639230251226, 0.753784065217, -0.152296647835), (-0.76901538663, 0.626532108023, -0.126778755093), (-0.00014506558391, 0.198159280986, 0.980169821161)26.7690435183, 60.2113723572, 8.06340461641

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要素

#1: タンパク質 Capsid protein


分子量: 24639.279 Da / 分子数: 3 / 断片: UNP residues 133-354 / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
遺伝子: gag / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: B6DRA0
#2: 抗体 Nanobody


分子量: 12603.141 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Lama glama (ラマ) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
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: 4.88 Å3/Da / 溶媒含有率: 74.79 %
結晶化温度: 295 K / 手法: マイクロバッチ法
詳細: 0.1 M Bis-Tris propane:HCl, pH 7.0, 1.4 M sodium malonate, pH 7.0

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データ収集

回折平均測定温度: 100 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: 24-ID-C / 波長: 1.0711 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2018年10月29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: 1.0711 Å / 相対比: 1
反射解像度: 3.45→50 Å / Num. obs: 39258 / % possible obs: 96.2 % / 冗長度: 2.8 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.077 / Rrim(I) all: 0.134 / Χ2: 1.049 / Net I/σ(I): 6.6
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.562.80.82219940.5480.57110.87597.3
3.56-3.632.80.76519590.5690.5350.9370.92397.2
3.63-3.692.80.71619690.6180.5040.8790.96397.1
3.69-3.772.70.5619670.7110.3980.690.97896.9
3.77-3.852.80.49519660.7760.3480.6081.00397.2
3.85-3.942.70.4319340.8030.3070.5311.06395.6
3.94-4.042.60.31719100.8880.2310.3941.03194.3
4.04-4.152.50.30218920.8990.2250.3781.09292.7
4.15-4.272.80.25619620.9190.1810.315197.1
4.27-4.412.90.21219650.9480.1460.2581.00496.8
4.41-4.572.90.17519520.9620.1210.2141.10395.7
4.57-4.752.80.16119450.9640.1110.1971.18296
4.75-4.972.80.13419840.9720.0930.1641.16596.5
4.97-5.232.70.13719520.9690.0980.1691.14996.3
5.23-5.552.60.1319070.9740.0940.1621.293.2
5.55-5.9830.11419990.9850.0770.1381.13698.5
5.98-6.5830.0920010.9880.0610.111.08197.9
6.58-7.532.80.06920150.990.0470.0841.08897.4
7.53-9.482.70.05719810.9940.0390.0691.01696
9.48-502.80.0520040.9940.0350.0620.93195.4

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.1_4122精密化
DENZOデータ削減
HKL-2000データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB entries 5O2U & 3H47
解像度: 3.19→49.19 Å / SU ML: 0.5147 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 30.1749
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2578 1600 4.88 %
Rwork0.2278 31171 -
obs0.2293 32771 91.41 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 155.18 Å2
精密化ステップサイクル: LAST / 解像度: 3.19→49.19 Å
タンパク質核酸リガンド溶媒全体
原子数7529 0 0 0 7529
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00867776
X-RAY DIFFRACTIONf_angle_d1.599410567
X-RAY DIFFRACTIONf_chiral_restr0.13051186
X-RAY DIFFRACTIONf_plane_restr0.00831382
X-RAY DIFFRACTIONf_dihedral_angle_d5.56131078
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.47970436681
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.90300035639
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.798517021507
ens_2d_3DX-RAY DIFFRACTIONTorsion NCS1.11629184434
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.30.41361350.37642768X-RAY DIFFRACTION90.78
3.3-3.410.41941370.33152884X-RAY DIFFRACTION93.27
3.41-3.550.32771480.30842833X-RAY DIFFRACTION93.19
3.55-3.710.35061470.28972861X-RAY DIFFRACTION92.78
3.71-3.910.27581610.25872815X-RAY DIFFRACTION92.59
3.91-4.150.26381300.222841X-RAY DIFFRACTION91.56
4.15-4.470.23421330.20322833X-RAY DIFFRACTION91.71
4.47-4.920.2131430.18442829X-RAY DIFFRACTION91.39
4.92-5.630.22811500.21212823X-RAY DIFFRACTION90.39
5.63-7.090.2861490.24652831X-RAY DIFFRACTION90.28
7.09-49.190.21811670.18922853X-RAY DIFFRACTION87.89
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.95495649417-2.3605269165-1.280628393114.55526848972-1.666184928854.75697807920.177429147171-0.329043156294-0.1866039417450.378375878037-0.3282736382520.4884231691040.4282160801420.1999748762320.2099701669520.919092551868-0.1068228037970.1587524977980.853418879255-0.09081302483450.67284787064343.2341372905-6.2967626378126.2562653712
21.16492136919-0.367543477630.5011317609445.464460737490.1944190654891.93349656230.163281393671-0.208411019737-0.191874684022-0.723885693133-0.4417424230610.7920238776610.584581844311-0.3984124212210.3871651469040.9101452858850.1250587102990.008632053749120.946136768711-0.1701151650420.86789099587435.0476627191-3.9275991683123.497185768
34.89157452653-1.59829139418-4.239321010468.814375129870.2727669083583.741967276380.583582887210.3258178340320.2215239733220.029741700487-0.4420342972570.255184323089-0.817428097769-0.115297499212-0.08683542762231.180563527990.1764815677280.1855581136731.14918262512-0.2291070189840.91483423094432.91725499221.660842266242.607580987
44.656334642240.303439568594-0.1493858628783.12690550141-1.83559981974.233933277130.164721016480.379102715954-0.214490571766-0.0682013234906-0.1981349498980.0731262800666-0.0357576151630.38711141930.1750892609250.8123316564320.1466018119940.09226667965821.009375181560.1027697849850.54349066974960.0118715367-24.320096205523.4219210157
52.947202184-0.545208469406-1.698147347853.684191641160.4577540107667.44733515712-0.05595307318181.87794153225-0.6373023661960.0602083231187-0.6736921709250.4768483224670.361827330543-0.1691437558650.1504426461750.6505715285690.08361878925310.05452405079571.5499045288-0.05825383720750.66597631248256.3873967313-26.542822933418.4442402328
64.24397337162-1.074835308411.044237403882.33911293373-2.043160362971.9000707429-0.100651113409-1.96491335187-0.3727798793313.067378746240.1820792107071.31387184235-0.8970633117580.455134656426-0.2956078853322.02032952477-0.2950370800710.6676042231871.682902592060.08205494841141.3774348595137.8531490936-18.877789663648.2112312841
79.1269967722-0.651890498178-0.497337174146.193546033050.428709051380.1665314383511.21959864220.317563307410.32322176241-1.33355666427-0.661874514750.5659608881270.141110909403-0.341864118026-0.06623726742561.27851808045-0.2757463709810.1656946639261.29735284055-0.01970961133631.0592723596837.453354164-22.895177602636.4956363341
85.10915174033-2.93395563842-3.91827557694.569643763853.088204791113.243429002390.117300138798-1.9672419266-1.204711128831.44153909587-0.3809345857542.97253715646-0.605203362231-2.12508023637-0.3085212900721.70566811571-0.166370503251.041907992782.41756008914-0.3042557463742.5583363147725.0590137382-18.666760846848.7489542578
96.28269647022-1.95714535462-0.7169214253147.72218095320.03950514009044.878248748710.435964818551-0.08056400024340.5064466609350.47704380521-0.325758424691.805872547060.786935430321-0.0878298482896-0.3756413489572.10129371203-0.2537886953310.6948974237561.780781651010.07225543690052.3107563900325.5708942307-10.45338546743.4981881696
103.047022101271.05533299472-0.2276845912661.99574060857-0.5568996570542.86762525272-0.3725097949420.0686901700642-0.4205799309040.2391797687890.0194905985706-0.26165293722-0.1443481240710.06868818132310.2059447644020.857390897632-0.0579229025807-0.03033135147590.9290776760170.1511084455730.64144312033781.2774821099-19.654733088425.4353263838
118.212097652771.78624655087-1.185008980773.76936375368-1.324882892032.56962235611-0.16675335936-0.525804355037-0.826242909820.458219352537-0.1840476043920.01187115763440.5634085700490.1352697864270.4482194236371.18641261288-0.04714535340730.1475291191380.9419490090860.3291438697271.0327211820162.1948456495-38.914479225343.0058810144
125.426515976682.18208715934-0.9342857466615.268009835390.5324533021662.887950300350.000740268352079-0.477142046133-0.549219498973-0.09575884324890.070025026772-0.4987250197880.447527056946-0.4715341378570.0643898072041.52191193812-0.2513682714040.5116706904071.185295060750.3876255231261.2584335731337.3153675335-50.576122257650.6680975807
133.137849911133.09867801497-1.365492734774.401957456420.0269212265051.9290449939-1.200392464330.0130780010226-1.568658017520.1603073376320.43646346361-1.439189812481.13326932712-0.06586171685710.1474049400481.706690573050.04205883614130.6308972185151.19323795950.2682161134741.7764648083648.694645497-54.500666451446.9395157009
145.073520087911.67379520219-0.6066089775274.072733554780.5950791797663.57797961002-0.5365566694371.88326062060.140977542274-0.09102203915841.08123119607-0.1426897519180.400114185081-1.376826704860.1493290503011.63549390082-0.2977240443170.3113621509011.522444548390.05524529467071.0550910467840.0379274733-49.868850009140.7489310851
152.292709163132.152211097080.9184150929293.601799627580.2030662363543.187020006910.0537773768029-0.735171983584-0.8650782510870.0201819455942-0.837597981650.4871132964360.700925207808-0.0268885692246-0.8839839727361.89902086376-0.199802202910.6163829235090.7504379185550.3024342758441.2947312107144.9000323467-54.122427123849.6860014854
163.131591737282.81296637196-0.08249123607894.931250141011.287077786340.785876038242-0.1575453838080.480341522345-1.39467161076-1.227153017950.717985253406-0.8059984293310.713527273006-0.4620346920830.566451258792.51549513774-0.7552890431480.357634963960.7825693840650.3255802000932.4019541744737.8386247401-68.141972467248.1291492496
174.96215361077-2.47012197154-1.319357022541.92300722843-0.0312829373791.04507949744-0.0812598333184-0.3433033672080.5637627620110.4942284250370.1208634891840.30079971945-1.6122894385-1.619120663060.3867602330843.159427301770.3561242338311.521125960142.29769853794-1.0391489762.8453746661930.635157161747.145794642253.5183771049
186.81662212801-2.561837297125.602612079479.1932657171-4.970385234455.60355602403-0.0356225939417-0.751604134891-0.0547779374490.2969263503910.4661911357331.29127390959-0.4117287535520.0129891926639-0.7391417385792.796379311041.002877904090.9039217096473.418135757410.3677674013813.1208469399816.190101863156.898950161337.2563473382
190.3809861758220.7207177984430.2824334744261.895040326770.4742654660590.200445029929-0.6291781997930.2059062776510.6390798096510.6803784040360.05972472638481.00561022189-1.40651128229-1.29625453302-0.3952354470672.745503359850.7749928353450.3790537943031.8858609627-0.08909730779751.9488414261327.645283036152.684162223542.3040742268
202.388394148910.152679112015-0.2499468982852.890073918670.134613618340.7640593327970.34327537282-0.8133986733030.7591080701230.101205971791-0.0883695549662-0.0800299544926-1.625131764990.0872655972226-0.5731012896171.859330080970.2575672384091.594280297111.33403432173-1.069376763431.9551754470631.862540525742.163438896346.03208126
211.0763899308-0.1640225230411.690561871985.04193882453-2.570100044173.691858271970.388810585704-0.9647389400591.731837632560.002873032591550.8586473843630.376638320139-1.2333015717-0.980124659598-0.4087636735412.025089290180.9499120541750.8216273079161.00681187311-0.1007982591321.6204813192320.575481863438.75001023741.3085295526
221.032084344960.6730277944181.021143385436.0842475337-1.520357623942.042326426290.7256977594110.07140280939070.701810580881-0.304405977682-0.0141181916668-0.396583716967-1.115222916950.763132222147-0.01672948683952.147580020640.3361570758130.8996063029761.41197609620.1249936071791.6808361344730.449345663545.693500889236.4107775081
233.18340809888-1.231709593823.308821119728.41179537156-0.4744813045063.51542828803-0.027876565995-1.32351786714-0.3032747159990.5931901396150.526392619252.04200376496-0.362569693514-0.668547257378-0.881089266292.594730913640.7831263349060.2390437199753.232727791010.6955921890591.9762990013314.722128496448.580791627833.2730860354
240.7444715653131.5605422915-1.287402479024.64277861736-0.96400446274.329704013611.01529797596-0.2824258163842.062242085670.8835189707050.443186939761.05216908748-2.20123979566-0.686514989094-0.2237610041372.446271379740.5998396098571.050568315191.50244188782-0.3863274426831.8923621981727.751384466640.346306571749.2343247233
250.1013142211850.455565237480.02906973684392.170509580410.1551238796450.0144398871257-1.53077624745-0.914531457402-0.9253876050030.70975689211.19696939790.140615569656-0.191636291266-0.0751673555442-0.8039551862862.563321059480.6121575883680.6487034854452.81530529224-0.3463807955072.1294921907614.475758724451.998699330142.8331860457
264.91840129894-4.970191008430.2334029095427.68628348943-1.410161081861.716687841280.159490271803-1.39284536976-0.809115669943-0.747123468464-0.1325027597281.47237798997-0.0567379890053-1.05752104049-0.4480377937482.368257148820.343048682430.8468153688892.72641186684-0.6699310163933.59204796017.67030714485-7.0132354406455.4327084915
270.0325471721351-0.03139169900350.1164229691180.0446772799183-0.1408163303220.3399713329730.532540390788-0.955622461341-0.491789292725-2.180211593940.744060195339-0.01283196073170.905710572839-1.23227332339-0.5741285209212.457024430240.4965648368030.1092508513973.538898582370.4919935474032.36179960722-3.06390949881-9.672696025741.9625983892
280.439740727345-0.493011040998-0.355780371111.017375762820.527582085840.318511558809-0.280397146883-0.2791375592630.5359353533170.121743120718-0.0976119468056-0.0982596125232-0.805674865026-0.9915792379120.03633735000831.92427364011-0.1127707781131.06516410111.94415706608-1.216277218385.9459760157915.7435519078-0.81329479766851.1964237566
292.56138756543-0.4575191336732.114091271190.0825121022207-0.3817212212411.72884487678-0.2237586222060.1455976381260.3879012271230.139170529715-0.9087835650011.095282283580.54141225237-3.01713019144-1.003423081861.9282857701-0.3745922088841.202619804632.6230425154-0.4480956552572.790717760289.57651218133-17.342306306143.1784213154
302.31616003968-1.777316915180.4507558075112.17209968992-1.256343217352.956849108971.60022614308-0.35480844359-0.3462166021590.234383472429-0.6072736609311.69711588644-0.6994457968310.639808863253-0.279905826551.94451394478-0.0277026203653-0.5616443660651.528916862060.3046962239733.9763918991312.2858446146-10.969484138634.1109819633
315.05230342397-0.07182958848423.033278415381.24791694743-0.04504089076251.8561032960.380522882842-0.6603599969580.674179709612-0.30206749154-0.1444329906560.3110763750210.0938019104148-0.5714296191290.08879436631691.54955654807-0.05429806724141.027763225823.08729179757-0.6375344292894.473176342267.68397335642-1.2029382085141.7466460993
322.13389264956-2.559124846420.5224960561733.25668229434-0.6645334288320.2857079896540.956918837112-0.6801354849790.3915715335550.1095799455490.5085042239140.05242590637110.705279656349-0.38020931016-0.7935884090583.012771917680.2642325221790.34708904023.29170778451-0.8751592622983.056487763082.9222320142-6.8264763836239.8031799058
330.0872067304231-0.0873099636682-0.1380289400490.08950889346950.1413487307670.2164152418510.415906328233-2.017076389970.5142143259621.32684155580.2944768662650.86020086399-1.39312060964-0.931124641255-0.9317264956281.66524229599-0.207666881060.3685715856373.12139950535-0.2678232318493.19008323948-2.11237633734-19.239592613735.1363118657
340.746620653728-0.788870244026-0.5671756355271.498368728180.01613809461670.933707664311-0.04020319088830.135055792149-0.212513923960.08015445853540.544587440440.510224371049-0.143571410182-1.53218033816-0.09212077509851.7497036877-0.3488041528721.604135069673.88049723381-0.4146958323085.774973729986.79846094006-14.505817307447.4777999145
351.12503408546-1.89053161745-0.2491028920655.21361695974-2.83141724835.25088471117-0.191362104791-1.06748804971-0.06489684134030.70008993220.3642701419050.785648934961-0.814547383716-2.25617617248-0.3332877018341.32501942308-0.1238531307250.7375269883763.02763814043-0.8076955985773.2879845309514.3355134055-11.256827703953.952718102
360.116134471550.05653715918460.0485985715190.3079558524680.1021193644880.03613574823650.573072291914-2.154703132080.4936827782990.2000722740260.453093310677-0.508324395553-0.315938489657-0.264295194182-0.5083788849611.76275060429-0.5995728745580.01496800653843.99762793009-1.637472867195.44082971069-5.52789168518-17.73096162842.4753155606
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 83 )AA1 - 831 - 80
22chain 'A' and (resid 84 through 160 )AA84 - 16081 - 151
33chain 'A' and (resid 161 through 223 )AA161 - 223152 - 214
44chain 'B' and (resid 1 through 110 )BB1 - 1101 - 101
55chain 'B' and (resid 111 through 144 )BB111 - 144102 - 135
66chain 'B' and (resid 145 through 167 )BB145 - 167136 - 158
77chain 'B' and (resid 168 through 187 )BB168 - 187159 - 178
88chain 'B' and (resid 188 through 205 )BB188 - 205179 - 196
99chain 'B' and (resid 206 through 223 )BB206 - 223197 - 214
1010chain 'C' and (resid 1 through 167 )CC1 - 1671 - 164
1111chain 'C' and (resid 168 through 222 )CC168 - 222165 - 219
1212chain 'D' and (resid 1 through 32 )DD1 - 321 - 32
1313chain 'D' and (resid 33 through 52 )DD33 - 5233 - 52
1414chain 'D' and (resid 53 through 82A)DD53 - 8253 - 83
1515chain 'D' and (resid 82B through 106 )DD82 - 10684 - 107
1616chain 'D' and (resid 107 through 115 )DD107 - 115108 - 116
1717chain 'E' and (resid 1 through 7 )EE1 - 71 - 7
1818chain 'E' and (resid 8 through 16 )EE8 - 168 - 16
1919chain 'E' and (resid 17 through 24 )EE17 - 2417 - 24
2020chain 'E' and (resid 25 through 39 )EE25 - 3925 - 39
2121chain 'E' and (resid 40 through 52 )EE40 - 5240 - 52
2222chain 'E' and (resid 53 through 82A)EE53 - 8253 - 83
2323chain 'E' and (resid 82B through 87 )EE82 - 8784 - 90
2424chain 'E' and (resid 88 through 103 )EE88 - 10391 - 104
2525chain 'E' and (resid 104 through 115 )EE104 - 115105 - 116
2626chain 'F' and (resid 1 through 7 )FF1 - 71 - 7
2727chain 'F' and (resid 8 through 24 )FF8 - 248 - 24
2828chain 'F' and (resid 25 through 32 )FF25 - 3225 - 32
2929chain 'F' and (resid 33 through 52 )FF33 - 5233 - 52
3030chain 'F' and (resid 53 through 66 )FF53 - 6653 - 66
3131chain 'F' and (resid 67 through 76 )FF67 - 7667 - 76
3232chain 'F' and (resid 77 through 82A)FF77 - 8277 - 83
3333chain 'F' and (resid 82B through 87 )FF82 - 8784 - 90
3434chain 'F' and (resid 88 through 94 )FF88 - 9491 - 97
3535chain 'F' and (resid 95 through 106 )FF95 - 10698 - 106
3636chain 'F' and (resid 107 through 113 )FF107 - 113107 - 113

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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