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- PDB-7rly: Antibody 2F2 in complex with P. vivax CSP peptide DRAAGQPAGDRADGQPA -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 7rly
タイトルAntibody 2F2 in complex with P. vivax CSP peptide DRAAGQPAGDRADGQPA
要素
  • 2F2 Fab heavy chain
  • 2F2 Fab light chain
  • peptide from Circumsporozoite protein variant VK210
キーワードANTIMICROBIAL PROTEIN / antibody / malaria / Plasmodium vivax / circumsporozoite protein
機能・相同性
機能・相同性情報


side of membrane / cell surface / plasma membrane / cytoplasm
類似検索 - 分子機能
Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Circumsporozoite protein
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Plasmodium vivax (マラリア 病原虫)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.67 Å
データ登録者Kucharska, I. / Julien, J.P.
資金援助 カナダ, 4件
組織認可番号国
Other governmentOntario Early Researcher Awards program カナダ
Other governmentCanada Foundation for Innovation カナダ
Other governmentOntario Research Fund カナダ
Other governmentCanada Research Chairs カナダ
引用ジャーナル: Elife / 年: 2022
タイトル: Structural basis of Plasmodium vivax inhibition by antibodies binding to the circumsporozoite protein repeats.
著者: Kucharska, I. / Hossain, L. / Ivanochko, D. / Yang, Q. / Rubinstein, J.L. / Pomes, R. / Julien, J.P.
履歴
登録2021年7月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年1月26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30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
P: peptide from Circumsporozoite protein variant VK210
B: 2F2 Fab light chain
A: 2F2 Fab heavy chain
D: 2F2 Fab light chain
C: 2F2 Fab heavy chain
F: 2F2 Fab light chain
E: 2F2 Fab heavy chain
R: peptide from Circumsporozoite protein variant VK210
Q: peptide from Circumsporozoite protein variant VK210


分子量 (理論値)分子数
合計 (水以外)149,9579
ポリマ－149,9579
非ポリマー00
水2,882160
1
P: peptide from Circumsporozoite protein variant VK210
D: 2F2 Fab light chain
C: 2F2 Fab heavy chain


分子量 (理論値)分子数
合計 (水以外)49,9863
ポリマ－49,9863
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: 2F2 Fab light chain
A: 2F2 Fab heavy chain
Q: peptide from Circumsporozoite protein variant VK210


分子量 (理論値)分子数
合計 (水以外)49,9863
ポリマ－49,9863
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
3
F: 2F2 Fab light chain
E: 2F2 Fab heavy chain
R: peptide from Circumsporozoite protein variant VK210


分子量 (理論値)分子数
合計 (水以外)49,9863
ポリマ－49,9863
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)71.723, 82.287, 82.747
Angle α, β, γ (deg.)95.263, 113.784, 111.471
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
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 3 through 190 or (resid 191...
d_2ens_1(chain "C" and resid 3 through 214)
d_3ens_1(chain "E" and (resid 3 through 190 or (resid 191...
d_1ens_2(chain "B" and (resid 1 through 164 or resid 166 through 213))
d_2ens_2(chain "D" and (resid 1 through 76 or (resid 77...
d_3ens_2(chain "F" and (resid 1 through 164 or resid 166 through 213))
d_1ens_3(chain "P" and resid 2 through 14)
d_2ens_3chain "Q"
d_3ens_3(chain "R" and resid 2 through 14)

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNLYSC1 - 220
d_21ens_1GLNLYSE1 - 220
d_31ens_1GLNLYSG1 - 220
d_11ens_2ASPTHRB1 - 169
d_12ens_2GLNGLUB171 - 218
d_21ens_2ASPTHRD1 - 169
d_22ens_2GLNGLUD171 - 218
d_31ens_2ASPTHRF1 - 169
d_32ens_2GLNGLUF171 - 218
d_11ens_3ASPASPA1 - 13
d_21ens_3ASPASPI1 - 13
d_31ens_3ASPASPH1 - 13

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.451314906998, 0.787694746075, -0.419346922879), (-0.634262049215, 0.0474075685993, 0.771663252569), (0.627715307801, 0.614238967704, 0.478209141388)-34.2146554626, -40.6045170818, -5.18300689827
2given(-0.538357510639, -0.618298628402, 0.572606319259), (0.721267090344, 0.013337743632, 0.692528619611), (-0.435826771923, 0.785830077505, 0.438777978212)-9.96383150066, -46.4523002253, 18.2437886952
3given(-0.454587312434, 0.784331640649, -0.422106921112), (-0.638191119994, 0.0437717508196, 0.768632635393), (0.621339254944, 0.618795532714, 0.480655405627)-34.2371418806, -40.784518663, -5.13045069265
4given(-0.529949471035, -0.635427339098, 0.561592071593), (0.714370197446, 0.0223526686944, 0.6994108801), (-0.456977875996, 0.771837065014, 0.442084568743)-10.2563993818, -46.0796340246, 17.8592078193
5given(-0.500257292004, -0.646093854188, 0.576459342346), (0.754456119504, 0.0014491292181, 0.656348888754), (-0.424898347303, 0.763256596175, 0.486724524607)-41.0367974131, 29.7962298764, 18.9406702769
6given(-0.471307032515, 0.757639061446, -0.451500535628), (-0.62983660195, 0.0692292650354, 0.773636325224), (0.617394149588, 0.648991803826, 0.444560572499)2.03428429282, -61.316021517, 68.6543989867

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要素

#1: タンパク質・ペプチド peptide from Circumsporozoite protein variant VK210 / CS


分子量: 1654.698 Da / 分子数: 3 / 由来タイプ: 合成 / 由来: (合成) Plasmodium vivax (マラリア 病原虫) / 参照: UniProt: P08677
#2: 抗体 2F2 Fab light chain


分子量: 24284.227 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 2F2 Fab heavy chain


分子量: 24046.723 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Homo sapiens (ヒト)
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 160 / 由来タイプ: 天然 / 式: H2O
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: 2.66 Å3/Da / 溶媒含有率: 53.79 %
結晶化温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.1M sodium citrate pH 5.0 and PEG 6000

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データ収集

回折平均測定温度: 80 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-B / 波長: 1.033167 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2020年2月26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: 1.033167 Å / 相対比: 1
反射解像度: 2.67→29.61 Å / Num. obs: 43179 / % possible obs: 98.3 % / 冗長度: 3.6 % / Biso Wilson estimate: 46.97 Å2 / CC1/2: 0.987 / Net I/σ(I): 4.7
反射 シェル解像度: 2.67→2.77 Å / 冗長度: 3.5 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4542 / CC1/2: 0.669 / % possible all: 97.8

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
XDSデータ削減
Aimless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: 1xiw

1xiw


解像度: 2.67→29.61 Å / SU ML: 0.3705 / 交差検証法: FREE R-VALUE / σ(F): 1.97 / 位相誤差: 24.2731
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2272 2162 5.01 %
Rwork0.1854 40999 -
obs0.1875 43161 98.32 %
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: 51 Å2
精密化ステップサイクル: LAST / 解像度: 2.67→29.61 Å
タンパク質核酸リガンド溶媒全体
原子数10338 0 0 160 10498
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002310595
X-RAY DIFFRACTIONf_angle_d0.569814406
X-RAY DIFFRACTIONf_chiral_restr0.04371610
X-RAY DIFFRACTIONf_plane_restr0.00461839
X-RAY DIFFRACTIONf_dihedral_angle_d9.6233789
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.554270586479
ens_1d_3CX-RAY DIFFRACTIONTorsion NCS0.497050721507
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.472642567314
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.524799751227
ens_3d_2AX-RAY DIFFRACTIONTorsion NCS1.38233952662
ens_3d_3AX-RAY DIFFRACTIONTorsion NCS1.13712517002
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.730.33591520.27342730X-RAY DIFFRACTION97.63
2.73-2.80.30511330.26412685X-RAY DIFFRACTION97.98
2.8-2.880.31851480.25632752X-RAY DIFFRACTION98.11
2.88-2.960.31921400.24512751X-RAY DIFFRACTION97.9
2.96-3.060.28421420.23392711X-RAY DIFFRACTION98.24
3.06-3.170.28161480.22522731X-RAY DIFFRACTION98.16
3.17-3.290.28231450.21662748X-RAY DIFFRACTION98.33
3.29-3.440.28181430.20042706X-RAY DIFFRACTION98.38
3.44-3.620.23921380.18872729X-RAY DIFFRACTION98.12
3.62-3.850.19851490.1732722X-RAY DIFFRACTION98.29
3.85-4.150.21331400.16752744X-RAY DIFFRACTION97.93
4.15-4.560.18411480.13792741X-RAY DIFFRACTION98.84
4.56-5.220.17691410.14052741X-RAY DIFFRACTION99.14
5.22-6.560.18951510.1792776X-RAY DIFFRACTION99.12
6.56-29.610.18361440.16972732X-RAY DIFFRACTION98.66
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)
14.15163331616-0.805219766420.0754266457214.331100614250.4810155685162.625736720290.00290284039345-0.102022319317-0.877968156853-0.2897237667720.389618144789-0.2477133138120.7072728101260.618857215686-0.4345455494210.3334226009250.105687981305-0.04882208779750.526100344575-0.08183891131890.573839476997-16.6062756702-74.4946650816-28.9742264118
21.51312734011-0.06729891677840.6035891070235.24107943874-3.11000926835.02965630278-0.1899852152760.0386697482164-1.25528006910.9545370459070.458070755525-2.358128235470.07519326000612.33175617527-0.09890052106970.3775860137620.1154640086520.003259343962110.8992596262480.007045130649790.819636239556-6.17907798104-66.148144846-31.0961361595
31.458438400940.92704264605-0.4207881287184.15598922987-1.859441474112.57546937838-0.1593554919640.3229959490550.22896668435-0.616005269176-0.1743406312030.6236436193840.431992316317-0.624562701742-0.08246969733090.463415415611-0.116844681029-0.1214463513490.696032227376-0.009733672532470.569844894243-25.8029978706-15.9955874074-32.3081888384
42.681426513821.03562650501-1.563169572872.0982734002-0.6954253464813.72213640588-0.3108718825530.1275302760420.650802796659-0.7766159771140.5251593716540.2064285181880.0454303860546-0.426744204454-0.01381355103690.60546322562-0.253621688735-0.224820602060.8497529465990.09414582095170.538109913993-19.1202573856-4.67822706927-48.0323467456
58.365883180390.607224741285-1.65291222739.61735721914-1.4722054337.45695785735-0.1156656764390.405517538727-0.420592884562-0.8670513189010.447444396590.2670033076390.0757816515638-0.284106608612-0.2334704999950.382978815614-0.1566207832520.02598420344680.442547011633-0.006501023794660.295855738489-13.0369639574-15.1121287228-31.2696241456
61.76176660511.1338432225-0.7423507375125.86709398597-1.21542612854.7523426439-0.5232903558320.679953406894-0.113736309275-0.9600749750960.3210221882460.4111400990530.488701446621-0.0450352059796-0.01125119161920.70577919207-0.15373505031-0.0377593769370.621905148981-0.1169338043810.401303963083-15.4892794099-18.7516688231-41.5869040467
71.366824221410.749413830331-0.4345402065486.41103477576-1.233584433741.91742428963-0.0687519711160.3000695682350.197775064117-0.839775601498-0.01035372480410.7293543704720.117404483638-0.0151415427561-0.09917917489980.396944813712-0.106357941672-0.06696803617690.6065004407710.03698583724010.364405873332-18.9538894364-13.2324948817-34.3945981807
80.8858111083090.195740514739-1.141624554962.63933793013-1.807451178192.399326061870.1504222378650.2018410403540.2353242733980.0398747976393-0.2120416786850.4335935760890.124114471331-0.4296625279280.02376605215550.281235047034-0.129516803047-0.04718362722070.5770727716470.03335007465950.312826124649-23.2378817326-27.1430083528-18.6592880662
92.699568684061.742190805481.816521132976.205314300862.828625164112.79000898452-0.0447638532273-0.7536887664340.1112457082051.03695931772-0.143617478874-0.7180633466780.09659491390481.04717377319-0.2051479097260.55004021683-0.19805266159-0.08033597900830.767416881412-0.07395802542380.407564632644-8.69867111627-20.96657943977.960950591
101.488069903940.580715704124-0.476694703143.264769199850.5708830107963.99175709023-0.0951748137163-0.227099645703-0.005363142414020.198371884708-0.1659514618060.137396569358-0.2794139447290.0577713040510.1934916931550.40545529219-0.04788747314180.01025913022190.437719563082-0.03088959215160.37779105848-20.6936873724-23.6269033373-1.08095553522
113.564385185080.366649671119-2.994729319472.13118067043-0.7944890610957.23038237691-0.295309091090.125475332223-0.6250132570320.652524562786-0.3409927488580.529970928938-0.741509735488-0.7817213090280.4095737396760.5269571101260.02972720979540.09705496806230.477139198422-0.1202512939470.57736311078-23.2311571564-17.95336065885.69900518461
122.060908577090.8067523570990.9601508280292.926481437241.061714003396.020333520560.056865308768-0.312282883663-0.2378814383550.246667411823-0.07464816342820.05505837049250.196201269931-0.3160134818120.0297656876450.357198652771-0.03962091782350.101253135610.4510114464680.02941853677490.384788295634-18.5743721171-24.72731030763.35150049101
133.325717296450.711372479654-0.9892704404222.275606949080.1193787118313.2748049235-0.2581303027420.3602301910380.256606393305-0.264541216980.234479497324-0.001112743526450.0741097281793-0.03872638667350.05473581671660.297907484057-0.09007990259190.02495140552270.3986293459250.01296517428020.303788592696-4.42357752222-0.254232237002-28.9263992036
141.15002105929-0.474849048273-0.2630325657867.88892357991-0.532349445072.292221313010.0921213021637-0.21413683496-0.2823744583020.319326461879-0.0904329720483-0.6215130593820.2636322947950.1684152834820.0137297535650.210739821917-0.0212687876601-0.01834719601460.421527696899-0.03258580522720.459526287562-4.26319315029-18.70032782-2.74503647811
153.33566613494-2.015932304610.1648812827133.21169974094-1.777692028812.348243719720.2944278318020.08635039077310.0147765171916-0.563298650547-0.448913763799-0.3504209625160.1435624641330.4746303392160.1942959215840.377690402734-0.01852566428320.08777586471530.490227317775-0.00887443405750.292226465949-17.2066604722-55.213827504-45.2855765627
163.24669158003-2.06920599595-0.125943391986.908875024080.3283171389293.77927583241-0.2041397814490.4626015414110.0337648611065-0.04216488989490.02791287993340.4258923990080.128433081967-0.02030419210460.1269232028520.326794274187-0.06414779165660.1067858155630.524534570720.04460880324650.308340540547-26.6304209106-58.894290409-44.131158182
171.27717796802-0.9809982460760.4495228217191.88627933055-0.05714003672811.61257955535-0.151028872779-0.1697136524790.1973053135730.174164306119-0.0390888876966-0.112530922741-0.228698535417-0.1908687229370.207111872230.268718899979-0.08559520876290.07966125549090.499462926309-0.006038171708530.337321869221-36.7985337204-36.4803283087-32.462369913
181.67722172254-0.8649555823760.6787777301073.86515675811.602255939333.67433524721-0.298094075907-0.3570871804470.2630107010180.2331240185260.2054016600370.170002550837-0.223793288934-0.4435930992760.08558403415330.3551383480120.0224660252220.07829581797140.596995321229-0.07772276310050.395742905047-46.4100009622-27.6625532007-30.3918574346
190.5625000839960.3617583268120.4323789318598.304075102212.875971233182.700968617340.154204746213-0.0391836329860.03509687759960.00616048437982-0.2035895790970.06188543614870.1164763124430.09809167237180.01807973457250.205031785469-0.02478590417430.01869675643230.4793442268450.03784079037740.356360180217-23.5645242816-58.5263207148-20.5534013125
201.176311099140.2415195352060.09974485722133.381750036220.1172162967091.438669807930.0730859333093-0.213693566148-0.06586525161070.036102764728-0.109238912905-0.3015673043220.09143073355610.3171566566120.0173638930510.249537363609-0.02877571882720.05688122805760.4865050149840.009643701081870.34665986348-18.7426308173-60.9061374449-22.715390074
213.826765717080.05988129745951.090102130910.7130280872380.816945409731.248491563130.283438020203-0.158954110367-0.09184018386360.06983732084340.13576471020.1751616381670.345970700996-1.020751518270.4727004820180.334651946346-0.1244548007580.1152762744490.9020968284820.1572145018440.394418945092-44.1663180071-39.3847996576-20.0147807017
223.690466863560.3877847030090.6002933706240.933523669351-0.1315509667580.5213555960020.0480703966462-0.298881855055-0.1987838086020.09506495567170.2459054015610.3372885042760.0986785732468-1.17741112372-0.08959684027640.302970468844-0.1707896082390.1029915593170.9713249097750.1697079925440.466113997147-46.7467101516-42.1646984732-21.1017040471
235.82787940258-0.689540950973-1.832595242591.619600139740.2597526380012.838577274690.06590337163760.09554922340570.474713846628-0.004715956408820.343621625402-0.1039370041950.07774998514240.1080691375440.02747333133550.3067930006820.03132010209740.08127374980320.4828055606420.04105519212790.525712200754-4.51235107852-87.3772006493.01281065416
244.58738978911-0.9516528208870.6765060908023.0853111580.3810564327523.06693667874-0.131938817002-0.0429494523644-0.469764946411-0.510890216053-0.207628935392-0.2959638886110.1109608098660.1327747252980.08185830934680.13144400234-0.01255864549430.08225707465780.37823298422-0.04753864375330.271838558219-16.5301252605-84.0989986019-0.139901429276
255.71774091513-1.061042792640.07471482032684.454092661730.05282664416283.29952847904-0.01567096688710.810024121981-0.514627623617-0.9384868408650.2371316362110.03530827563950.143329760881-0.0433073463590.1791494654670.307163804550.01029873962820.04715176379840.358199564373-0.1166275778780.379798150199-13.3609738635-86.5985532108-7.92148300029
268.507736767993.83624475649-1.672388883143.644855780320.1614104770352.01346043663-0.2265298944040.720038421198-0.360531828879-0.3358387807520.218303896303-0.4156977300690.02352251608320.538960717712-0.1251010836280.215386984929-0.007466517653970.04083141163090.507121178896-0.03312086521710.504106385059-3.86816693649-84.331235055-5.4872061152
276.085272453661.68992816942-0.899699648161.030468308980.1205683388210.3714163911010.22501357699-0.834370484811-0.3090969591980.5177502938530.0849835061475-0.125955757710.1899428049070.09602240993450.2653502652970.265308245738-0.01858602496380.1430576966190.5471506484860.1314465807820.523844994328-16.5749894563-83.65788035136.13446217175
288.998581864363.45272128174-0.1252181092171.77115939078-0.4903741848720.412998246933-0.1299558911040.05434215142210.220328651127-0.138466548150.1379367183690.09551077081050.07619224919940.0704511266983-0.2285985520890.25932905295-0.01253515537080.09564753226930.429750745241-0.1014927968130.4149883375518.74548313567-76.3003654531-0.69360824063
293.50232232021-0.2260689453060.3363619297057.135584438233.899881917653.182488473730.0467421320982-0.4641890555780.5118465589980.1419906655160.216097963242-0.253036466503-0.2518162757860.094192306463-0.1671591806780.266712303052-0.008734992263470.1042160889160.477538679893-0.1140595874710.42272696665513.9322244415-56.41628967488.68750766456
303.499051151251.159357020691.317287779055.307452608283.265193924534.42433027126-0.15635025105-1.095221605180.557116245750.724748020683-0.0905997476763-0.459506067070.4258562099810.0435502706525-0.1822698557430.3771715643960.0238183217362-0.1112787688890.807697049412-0.06185919369040.53834349522116.5009473433-59.066539696217.0926466526
315.148021218860.2281090517510.5150818535227.379990780855.100705390184.175245020330.0952582925057-0.1557434523330.427760724628-0.220601619344-0.276458078647-0.129498031039-0.117714469443-0.475298165080.2140298676320.1935252775610.0610529948060.04251677813990.5161991103230.01485179143590.4652726913765.47020672554-69.254428938-1.36274978009
323.250163126670.1896798761220.4413401371624.772550565792.578696269263.836182995430.101721739733-0.6299325483150.7479302273350.4022674815640.321527309563-0.866066352069-0.01463731445970.173949968154-0.4950081483770.274706494155-0.03726043884960.03625175263970.629859842845-0.20221582610.66494329708820.2060800674-54.32934885411.7582130619
334.624748702290.9399624291184.74550484872.143110732771.54453807236.741860681-0.1033572575960.3076035603860.3783005480670.1157871917240.2497568759630.331003437486-0.5231528380460.734334613321-0.1540166814070.2248164248420.002694983127220.09009690606050.379044123038-0.01484328169350.362053060204-21.3280817748-60.663576959410.7001570253
341.69679266414-1.379102122160.1853364094873.268713721910.01250345030914.63057287273-0.06814027139780.1098508740140.00487062696960.1601995521190.04827090210030.160715764376-0.06639491316060.1229541847550.01011348281140.173483509801-0.06745620001810.1151041692950.3964716382150.009077812818820.352556180841-25.7133319588-72.90603638125.26319916502
353.28905788922-0.8355302046580.7268311585371.633631339340.3624426380631.43965430692-0.244180814019-0.325236216453-0.2064557429630.297594010791-0.0787516981510.04063136172820.245881058518-0.02976493490170.04294581746170.245864758009-0.05335740462190.1745245921760.5561193029180.03592666699710.430441686302-28.2739061319-72.230331052814.8191306693
365.10650297423-0.5693099490224.560258730492.77212684664-0.7478684360214.21011627527-0.000458351065181-0.3930039420850.1165185071520.154801082612-0.121591986891-0.147383316121-0.0662571657807-0.0185424196210.2871623966040.221074022009-0.03815874186170.05209590077570.5691859518130.01096916956920.430656828772-25.025490292-64.982037454713.4481734405
372.572664271790.6382155130311.010488212481.58836910859-0.04104625937050.620133620211-0.04973836745910.100509723417-0.125287006451-0.08786854176230.132209439883-0.0663602656444-0.0446408384220.0279082949302-0.2036851923320.212474000733-0.04109364672640.05295961208620.434975735769-0.05688974079440.309987872406-20.7098548061-72.79359160740.562912496686
382.427034784251.759499258860.4790927378551.485246723820.2506913302570.6944576816580.2997475041680.2010633925450.1605301674540.269899761009-0.230423775782-0.130725035581-0.389240808862-0.4790574838650.002902561391170.2856213458680.002880552988130.07116158574760.466622548428-0.04610435973850.362165088933-3.11164810173-50.270563021314.7416432589
393.404422834550.303386070117-0.9819484260651.732885017970.5527947995772.863414156220.192075474829-0.02709668283350.294033644283-0.375999357303-0.259753956756-0.765230588766-0.4766515458040.847945099534-0.355524950270.3196892233220.02590882229940.2112334305910.6062079048610.1051894579220.52628363684810.6229630768-51.7893216492.51936859767
403.73202272083-0.182433920919-2.256661760981.71142792097-0.2980554494245.366432551350.06429870459590.2422170131710.0945721802327-0.254856892963-0.295260037549-0.258261592654-0.2300120437710.04025315887580.1816991486350.2733845425070.0005921182772020.0689603512450.456895273338-0.009498059661510.3738587404650.611893543569-53.85859391072.93507471687
416.81253462361-1.24239876278-2.912544831184.061617647150.06823381318548.142297219610.5045045897830.8935442139891.35836735954-0.186512804787-0.109064709539-0.32599232961-0.746586626315-0.283567331271-0.2262089175230.482678511790.1104487858390.1257781728210.322600435088-0.01806835754180.5266785129320.884979685043-44.24419801872.57161297375
426.01417638601-0.998342709088-1.909403706723.80678913804-3.253123618194.603264629560.01748478646330.1870909104120.3202744234880.6407340670370.2218076340671.23089237962-0.806647554752-0.304988399316-0.3976625594420.301170390341-0.01530467576450.02849469434080.448190046266-0.04738993534650.55186803587-31.9933680507-80.0947140395-0.705433850101
430.957187912134-0.373067861343-0.1827027385380.9364525540760.3585691599350.367308456894-0.113873872394-0.200687037770.1499932096070.06333800306730.03644320018260.1480046140010.144712021670.2747735458-0.3746593066250.822342040929-0.2613354923050.5313786944551.144649742070.04841615981450.955891154092-31.5926895875-88.15924215758.4194888157
442.845500692794.16619600738-1.054737377448.51711936151-4.099725015289.49176475908-0.7962048083160.336482628007-0.189051208128-1.404290119240.0847869435644-0.6177554074940.9484705476091.013175065340.8433257135110.80694792465-0.1388230361670.1260590187590.605998265560.02893619914610.4065537613-1.13803400829-1.97966821597-45.0132429186
452.48371029486-0.9646288193511.387925764712.936685252852.387178451184.119162831510.7844019563160.128208851711.40948924939-0.680264590738-0.688087976879-0.94018015474-1.750466792790.492755639439-0.05163375401571.01066633422-0.1905811848320.01208038310070.6173311628680.1042692309490.610484194433-12.09990923724.49205093359-43.7173544454
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 'P' and (resid 2 through 7 )PA2 - 71 - 6
22chain 'P' and (resid 8 through 16 )PA8 - 167 - 15
33chain 'B' and (resid 1 through 25 )BB1 - 251 - 25
44chain 'B' and (resid 26 through 32 )BB26 - 3226 - 37
55chain 'B' and (resid 33 through 48 )BB33 - 4838 - 53
66chain 'B' and (resid 49 through 69 )BB49 - 6954 - 74
77chain 'B' and (resid 70 through 101 )BB70 - 10175 - 106
88chain 'B' and (resid 102 through 113 )BB102 - 113107 - 118
99chain 'B' and (resid 114 through 128 )BB114 - 128119 - 133
1010chain 'B' and (resid 129 through 150 )BB129 - 150134 - 155
1111chain 'B' and (resid 151 through 163 )BB151 - 163156 - 168
1212chain 'B' and (resid 164 through 213 )BB164 - 213169 - 218
1313chain 'A' and (resid 3 through 111 )AC3 - 1111 - 117
1414chain 'A' and (resid 112 through 215 )AC112 - 215118 - 221
1515chain 'D' and (resid 1 through 32 )DD1 - 321 - 37
1616chain 'D' and (resid 33 through 83 )DD33 - 8338 - 88
1717chain 'D' and (resid 84 through 163 )DD84 - 16389 - 168
1818chain 'D' and (resid 164 through 213 )DD164 - 213169 - 218
1919chain 'C' and (resid 3 through 44 )CE3 - 441 - 42
2020chain 'C' and (resid 45 through 111 )CE45 - 11143 - 117
2121chain 'C' and (resid 112 through 157 )CE112 - 157118 - 163
2222chain 'C' and (resid 158 through 215 )CE158 - 215164 - 221
2323chain 'F' and (resid 1 through 25 )FF1 - 251 - 25
2424chain 'F' and (resid 26 through 48 )FF26 - 4826 - 53
2525chain 'F' and (resid 49 through 69 )FF49 - 6954 - 74
2626chain 'F' and (resid 70 through 83 )FF70 - 8375 - 88
2727chain 'F' and (resid 84 through 101 )FF84 - 10189 - 106
2828chain 'F' and (resid 102 through 113 )FF102 - 113107 - 118
2929chain 'F' and (resid 114 through 150 )FF114 - 150119 - 155
3030chain 'F' and (resid 151 through 163 )FF151 - 163156 - 168
3131chain 'F' and (resid 164 through 174 )FF164 - 174169 - 179
3232chain 'F' and (resid 175 through 213 )FF175 - 213180 - 218
3333chain 'E' and (resid 3 through 24 )EG3 - 241 - 22
3434chain 'E' and (resid 25 through 59 )EG25 - 5923 - 58
3535chain 'E' and (resid 60 through 72 )EG60 - 7259 - 71
3636chain 'E' and (resid 73 through 87 )EG73 - 8772 - 89
3737chain 'E' and (resid 88 through 111 )EG88 - 11190 - 117
3838chain 'E' and (resid 112 through 124 )EG112 - 124118 - 130
3939chain 'E' and (resid 125 through 145 )EG125 - 145131 - 151
4040chain 'E' and (resid 146 through 203 )EG146 - 203152 - 209
4141chain 'E' and (resid 204 through 214 )EG204 - 214210 - 220
4242chain 'R' and (resid 2 through 10 )RH2 - 101 - 9
4343chain 'R' and (resid 11 through 17 )RH11 - 1710 - 16
4444chain 'Q' and (resid 2 through 7 )QI2 - 71 - 6
4545chain 'Q' and (resid 8 through 14 )QI8 - 147 - 13

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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