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- PDB-9haf: Dust mite allergen Der f 7 with computationally designed DerF7_b2... -

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基本情報

登録情報
データベース: PDB / ID: 9haf
タイトルDust mite allergen Der f 7 with computationally designed DerF7_b2 binder
要素
  • DerF7_binder2
  • Mite allergen Der f 7
キーワードDE NOVO PROTEIN / dust mite / allergen / der f 7 / computational / de novo / binder
機能・相同性Mite allergen, group-7 / Mite allergen, group-7 superfamily / Group 7 allergen / extracellular region / Mite allergen Der f 7
機能・相同性情報
生物種Dermatophagoides farinae (ダニ)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.99 Å
データ登録者Pacesa, M. / Nickel, L. / Correia, B.E.
資金援助 スイス, 1件
組織認可番号国
Swiss National Science Foundation スイス
引用ジャーナル: bioRxiv / 年: 2025
タイトル: BindCraft: one-shot design of functional protein binders.
著者: Martin Pacesa / Lennart Nickel / Christian Schellhaas / Joseph Schmidt / Ekaterina Pyatova / Lucas Kissling / Patrick Barendse / Jagrity Choudhury / Srajan Kapoor / Ana Alcaraz-Serna / Yehlin ...著者: Martin Pacesa / Lennart Nickel / Christian Schellhaas / Joseph Schmidt / Ekaterina Pyatova / Lucas Kissling / Patrick Barendse / Jagrity Choudhury / Srajan Kapoor / Ana Alcaraz-Serna / Yehlin Cho / Kourosh H Ghamary / Laura Vinué / Brahm J Yachnin / Andrew M Wollacott / Stephen Buckley / Adrie H Westphal / Simon Lindhoud / Sandrine Georgeon / Casper A Goverde / Georgios N Hatzopoulos / Pierre Gönczy / Yannick D Muller / Gerald Schwank / Daan C Swarts / Alex J Vecchio / Bernard L Schneider / Sergey Ovchinnikov / Bruno E Correia
要旨: Protein-protein interactions (PPIs) are at the core of all key biological processes. However, the complexity of the structural features that determine PPIs makes their design challenging. We present ...Protein-protein interactions (PPIs) are at the core of all key biological processes. However, the complexity of the structural features that determine PPIs makes their design challenging. We present BindCraft, an open-source and automated pipeline for protein binder design with experimental success rates of 10-100%. BindCraft leverages the weights of AlphaFold2 to generate binders with nanomolar affinity without the need for high-throughput screening or experimental optimization, even in the absence of known binding sites. We successfully designed binders against a diverse set of challenging targets, including cell-surface receptors, common allergens, designed proteins, and multi-domain nucleases, such as CRISPR-Cas9. We showcase the functional and therapeutic potential of designed binders by reducing IgE binding to birch allergen in patient-derived samples, modulating Cas9 gene editing activity, and reducing the cytotoxicity of a foodborne bacterial enterotoxin. Lastly, we utilize cell surface receptor-specific binders to redirect AAV capsids for targeted gene delivery. This work represents a significant advancement towards a "one design-one binder" approach in computational design, with immense potential in therapeutics, diagnostics, and biotechnology.
履歴
登録2024年11月3日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年12月18日Provider: repository / タイプ: Initial release
改定 1.12024年12月25日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22025年7月16日Group: Database references / カテゴリ: citation / citation_author / Item: _citation.year / _citation_author.identifier_ORCID

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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: Mite allergen Der f 7
B: DerF7_binder2
C: Mite allergen Der f 7
D: DerF7_binder2
E: Mite allergen Der f 7
F: DerF7_binder2


分子量 (理論値)分子数
合計 (水以外)104,6066
ポリマ－104,6066
非ポリマー00
水00
1
A: Mite allergen Der f 7
B: DerF7_binder2


分子量 (理論値)分子数
合計 (水以外)34,8692
ポリマ－34,8692
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Mite allergen Der f 7
D: DerF7_binder2


分子量 (理論値)分子数
合計 (水以外)34,8692
ポリマ－34,8692
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Mite allergen Der f 7
F: DerF7_binder2


分子量 (理論値)分子数
合計 (水以外)34,8692
ポリマ－34,8692
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)118.810, 95.880, 87.310
Angle α, β, γ (deg.)90.000, 100.497, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-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 7 through 26 or resid 28...
d_2ens_1(chain "C" and (resid 7 through 26 or resid 28...
d_3ens_1(chain "E" and (resid 7 through 26 or resid 28...
d_1ens_2(chain "B" and (resid 4 through 15 or resid 17...
d_2ens_2(chain "D" and (resid 4 through 15 or resid 17...
d_3ens_2(chain "F" and (resid 4 through 15 or resid 17...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1LYSLYSSERSERAA7 - 2615 - 34
d_12ens_1THRTHRMETMETAA28 - 5636 - 64
d_13ens_1ASNASNLYSLYSAA58 - 7666 - 84
d_14ens_1VALVALVALVALAA8290
d_15ens_1ALAALAMETMETAA84 - 9792 - 105
d_16ens_1TYRTYRGLUGLUAA99 - 128107 - 136
d_17ens_1THRTHRARGARGAA136 - 143144 - 151
d_18ens_1PHEPHEGLUGLUAA145 - 194153 - 202
d_21ens_1LYSLYSSERSERCC7 - 2615 - 34
d_22ens_1THRTHRMETMETCC28 - 5636 - 64
d_23ens_1ASNASNLYSLYSCC58 - 7666 - 84
d_24ens_1VALVALVALVALCC8290
d_25ens_1ALAALAMETMETCC84 - 9792 - 105
d_26ens_1TYRTYRGLUGLUCC99 - 128107 - 136
d_27ens_1THRTHRARGARGCC136 - 143144 - 151
d_28ens_1PHEPHEGLUGLUCC145 - 194153 - 202
d_31ens_1LYSLYSSERSEREE7 - 2615 - 34
d_32ens_1THRTHRMETMETEE28 - 5636 - 64
d_33ens_1ASNASNVALVALEE58 - 8266 - 90
d_34ens_1ALAALAMETMETEE84 - 9792 - 105
d_35ens_1TYRTYRGLUGLUEE99 - 128107 - 136
d_36ens_1THRTHRARGARGEE136 - 143144 - 151
d_37ens_1PHEPHEGLUGLUEE145 - 194153 - 202
d_11ens_2GLUGLULEULEUBB4 - 1512 - 23
d_12ens_2LYSLYSARGARGBB17 - 1925 - 27
d_13ens_2ARGARGVALVALBB21 - 3129 - 39
d_14ens_2GLUGLULYSLYSBB33 - 5141 - 59
d_15ens_2VALVALGLUGLUBB57 - 7765 - 85
d_21ens_2GLUGLULEULEUDD4 - 1512 - 23
d_22ens_2LYSLYSARGARGDD17 - 1925 - 27
d_23ens_2ARGARGVALVALDD21 - 3129 - 39
d_24ens_2GLUGLUGLUGLUDD33 - 7741 - 85
d_31ens_2GLUGLULEULEUFF4 - 1512 - 23
d_32ens_2LYSLYSARGARGFF17 - 1925 - 27
d_33ens_2ARGARGVALVALFF21 - 3129 - 39
d_34ens_2GLUGLULYSLYSFF33 - 5141 - 59
d_35ens_2VALVALGLUGLUFF57 - 7765 - 85

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.500458203182, 0.825940089235, 0.259546827881), (0.820154496997, -0.548306650566, 0.163420983967), (0.277287193941, 0.13108312607, -0.951803039571)2.01618348048, 18.586852407, 18.8531354344
2given(-0.461006534103, 0.835025559554, -0.300341955787), (-0.848090500176, -0.514199142572, -0.127834835982), (-0.26118093159, 0.195784464833, 0.945226409017)46.2799602476, 29.938699486, 38.016796272
3given(0.436867287329, 0.857421162306, 0.27198515344), (0.847091616472, -0.493869299933, 0.196287818997), (0.302626447233, 0.144644616263, -0.942069619732)3.92085430653, 17.8499941674, 18.1958570328
4given(-0.444320248724, 0.851799123564, -0.277520755386), (-0.852339865167, -0.497324011758, -0.161819595772), (-0.275855525268, 0.164642280185, 0.946993478729)45.7173187874, 29.7570386419, 38.532433534

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要素

#1: タンパク質 Mite allergen Der f 7 / Allergen Der f VII


分子量: 22889.014 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Dermatophagoides farinae (ダニ) / 遺伝子: DERF7 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q26456
#2: タンパク質 DerF7_binder2


分子量: 11979.742 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli (大腸菌)
Has protein modificationN

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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: 2.34 Å3/Da / 溶媒含有率: 47.37 %
結晶化温度: 289.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5 / 詳細: 0.1 M MES pH 6.5, 20 % v/v PEG Smear High BCS

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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: ESRF / ビームライン: MASSIF-3 / 波長: 0.9677 Å
検出器タイプ: DECTRIS EIGER X 4M / 検出器: PIXEL / 日付: 2024年9月7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: 0.9677 Å / 相対比: 1
反射解像度: 2.99→59.61 Å / Num. obs: 34725 / % possible obs: 94.03 % / 冗長度: 1.3 % / Biso Wilson estimate: 86.94 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.05497 / Net I/σ(I): 7.77
反射 シェル解像度: 2.99→3.18 Å / 冗長度: 1.3 % / Rmerge(I) obs: 0.6007 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 6058 / CC1/2: 0.774 / % possible all: 96.67

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解析

ソフトウェア
名称バージョン分類
PHENIXdev_5316精密化
XDSデータ削減
XSCALE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 / 解像度: 2.99→59.61 Å / SU ML: 0.5096 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 35.0942
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2732 910 4.95 %
Rwork0.2203 17470 -
obs0.2229 18380 94.03 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 111.1 Å2
精密化ステップサイクル: LAST / 解像度: 2.99→59.61 Å
タンパク質核酸リガンド溶媒全体
原子数6427 0 0 0 6427
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00436529
X-RAY DIFFRACTIONf_angle_d0.7858757
X-RAY DIFFRACTIONf_chiral_restr0.0526973
X-RAY DIFFRACTIONf_plane_restr0.00621124
X-RAY DIFFRACTIONf_dihedral_angle_d12.44332548
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.720475008428
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.729211933112
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.687327224918
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.739132829977
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.180.41761560.35432984X-RAY DIFFRACTION96.67
3.18-3.430.36881700.32452882X-RAY DIFFRACTION94.96
3.43-3.770.38441310.29182905X-RAY DIFFRACTION93.3
3.77-4.320.24711700.23342895X-RAY DIFFRACTION94.13
4.32-5.440.26591290.18342761X-RAY DIFFRACTION88.51
5.44-59.610.21061540.17113043X-RAY DIFFRACTION96.64
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)
19.97918577588-9.40779030169-4.491613319149.598171651236.078728044496.62970188364-1.18363325417-1.972908135191.843378550431.826308910351.85551997487-2.59730992761.12584422345-0.0963465199397-0.7493536128870.880978586597-0.2974389158870.06989403382461.5078763053-0.2182324380391.062387739546.118368547723.1596051130133.9858399006
23.163552609521.02599756918-2.107757392632.675300677840.9721167845498.02697009357-0.129876870891-0.0837186426328-0.299870627039-0.127543988117-0.01799213145120.1826017418631.20061853623-0.08356843218280.7469174378290.5168709490140.1611206412960.05911198262440.6517838829290.00171475098240.95156778672119.4139896418-4.097284810124.37599569535
36.96627528648-2.10249483355-1.389618546372.95036403616-0.6544432047711.689675369491.41470176312-0.9012588098781.32345311132-0.199023818886-0.6920906765120.429803637727-1.18540406241-0.52394121672-0.3014369468990.9831961035140.003591728181360.1165061692611.53847252970.09477120913811.287412472534.2674594725710.258911161128.3612815709
49.84489516120.342956935613-4.300630638313.54259565489-0.2890903881544.71384541896-1.11887344746-1.24518279038-0.09274328604510.3661583865930.8800966325181.028233947290.01426223522160.421280768543-0.4710629030951.11332117103-0.04941137250.0630390856541.26072145815-0.2974705595031.0438631537710.25487511566.9266051660924.5120945539
55.38500487202-0.234223566984-3.015988292591.68091758325-1.684595879569.731044627360.302229928532-0.8916952609110.2250192786810.2894385570190.402141073774-0.03907169418231.161090531161.85767727903-0.9222362979220.4539174433480.0494211634314-0.09050265682450.714708073673-0.04345081866390.87954129169926.2351220933-4.910114555072.1219324619
62.52605403829-1.968040519532.838645275497.82399404906-1.678602569453.273478034050.0931547331616-0.1192121151531.20614974532-0.6462324536260.2373228007871.35213854971-1.1727634363-1.48952664855-0.7798140906320.774427935097-0.01387606770520.1258979051441.22747384789-0.1074300328820.9407782978921.510823402713.7324060413923.8676440307
72.585941262580.389456441883-2.971028517032.264469856540.08669353629757.750821445590.2284426281-0.7661952397440.605232638095-0.0697087645733-0.1253357345650.184210121581-0.137182228754-0.00861265859946-0.2560306797980.579388893961-0.0665835164115-0.07531553579190.774965483103-0.0613820643630.90294540031617.17480703660.528722587859.10651212754
83.03225770674-1.255410061841.468647656182.227260929081.309994537845.89069237238-0.3349212585760.220944306974-0.00987984438407-0.02599463052410.427715808898-0.282400839228-0.02747701869391.656551033330.2030227689330.778788734222-0.1687282082560.1010728282360.9931177803950.01765556218171.0239365980943.23086519435.06510172177-6.69540746875
93.83289957176-0.144118772261-0.9895469613953.96172311951-0.8670134747583.99859298583-0.0850589051172-0.5977071881810.4061371899480.752468702016-0.05341100852850.251855846751-0.1555561306660.02790337054040.587290167011.14074986015-0.06032945267580.09678142556411.07989238181-0.08412870923881.1491186799237.515319751215.8735085455-3.73868716734
105.41798577966-5.24559067770.3435963161055.32027167960.4532297726273.1559877361.58873439589-0.05482953969230.696252749823-3.389807587410.511591667883-2.85786710693-2.75802643029-0.306158272902-1.978261838531.1670609758-0.03750052406890.2474565373921.18021728124-0.3047474334561.1482515181615.858781480328.384022691-11.1384462416
112.91357302782-0.80552533085-2.238954845483.06802055371-1.481362089693.35366540420.5274976488561.82168142244-0.1753053024870.03459798316480.2792755511630.160866284963-0.940485922597-1.36333826264-0.927471915640.9386250395030.2349738284160.1224856597311.78751688175-0.182121498310.9005620873585.8437109407340.28309938235.58782443929
121.68496574697-1.430629160081.458905647391.689272898520.3043493959498.344135333230.3582000209150.304989578059-0.3284779608391.286214910120.2219888385890.5436340864481.534771415110.820840620865-0.8083708173631.400814045120.08624715739080.03483811438680.707599666360.1354620979761.0361012903711.920682804632.097594928932.3951291852
134.91512059381.77959659473-4.22056382263.626565902030.4259803212486.81456606072-0.509078158994-0.0804334233125-0.6397616231050.583313864430.3504472424090.124053404794-0.217841710699-2.27493165592-0.0978900876210.96451699694-0.1837618402670.1902529718930.680091443149-0.127086859670.7881946772659.1808679192236.573783157731.6375304754
141.211554565710.6436295983571.369904007151.54851089370.6844312629085.002472956380.0203146320923-0.0598106225189-0.316458853736-0.22708928162-0.21317754270.0109979593804-0.6183331571160.5514651461730.3089262404360.633742512236-0.01172675267290.002127797768240.51626904607-0.01093531655580.78896676511515.128042163234.66653905639.40916071204
153.03707256205-1.1602043670.6103006132038.881810029340.6954833029866.018078437580.527061011219-0.0623755758135-1.23046998631.1114607202-0.4486379071920.2689888999721.87160554201-0.5310490364930.310569411680.677361566272-0.00508513620410.06618228153310.915384997348-0.05930743285240.92150592287711.685187339821.4354152057-2.66275642269
162.643978213031.254865261980.5074148728241.183670560491.153050590978.421223987830.289055142795-0.378378563406-0.1040059871420.487122086723-0.4307231538860.08997091800470.436016559751-0.4758784043120.1115697639420.741896450475-0.03174351193340.02346629641660.585943232975-0.04981965595870.82026216884713.473434051433.755204721915.0834848894
174.11739726456-4.51525335771-2.017220483445.111775932181.402681291052.707205943990.5405627216790.3914470944161.457898649340.1718121568790.397933609706-0.6017186680550.3470225078110.0716384698474-0.7200085579931.10500416985-0.2986422890010.02046090125761.0996217263-0.1805806864451.0641431792827.898159972752.429193456437.2936662286
183.0087922701-1.00106098285-0.6996571844621.746706401431.034404371413.708715928120.189019708292-0.231684153344-0.1452405663050.165412163499-0.275789542972-0.03228396096470.8072638177930.3485063507930.1531469109751.318717167050.0861291564389-0.003996125680660.800349876736-0.002204497012190.84688405655329.626874160240.053414527741.044961405
195.86231663780.8464399280420.6367891633033.86729187129-2.021060027476.07439587505-1.12402241420.050443528372-0.693682229528-0.8896565158070.3866524879060.1783308871431.01367199274-0.3620355250730.4760322615381.24464371271-0.2465220247780.1550061763951.279249398570.07517958509430.99193481135131.554429067842.395732261729.0872089537
204.607538243672.322224496323.638388217346.745376502230.2286575598577.327621576670.43252274592-0.0831771193725-0.07185266263110.0844916500342-0.4147274839310.205177512286-0.584508679076-0.613628091463-0.2404180072630.9385016147720.104697249428-0.09387127770081.05339214741-0.2011008485610.80046962606631.785130432519.168075156861.1214634876
215.217490858090.139055405716-1.805632927640.8285850094821.052251447982.861998438290.0505980391681-0.442971677703-0.598123367474-1.442282265470.4737730113750.48851474357-1.842167932141.99781670942-0.1815104790481.26821894206-0.172244880106-0.2455171097581.252824140950.1348733151391.0017519926541.942091336112.709201512125.5072325405
222.121917514310.6589364504530.5337087815152.896584289143.384732700823.63236609448-0.3063062302310.2428003659190.0108670504433-0.0802762826914-0.1605260026040.3860285603920.0559937860706-0.7656019774830.1232458002470.964890352524-0.07061735749540.02707179482570.7691976466110.1302887376570.78182273873532.259333650512.861706431440.4598631618
231.83415805915-1.67627927766-2.421646716992.736583619890.881907174924.359771151020.447354021575-1.022726454960.05691451872921.40729712411-0.660448009644-0.3299141759781.120894033830.8340301199290.2273097973891.51453124640.0423938217265-0.1419456120871.270029913090.1011208782880.82389962103942.067389780214.639681405462.189895211
243.471488932411.91037263803-0.572430357723.05668857578-0.7476705184135.29646645456-0.2180186062840.3152287130530.3302605217010.306966916493-0.1418985786190.2588348430040.996085065949-0.55374142250.2605821604330.7561210071930.0261060645338-0.006296539405350.6289965452180.02492794141340.75647551026932.28245902611.750450188938.7956144448
251.841256272281.540847849932.318973540196.514748726112.234002174143.001157554990.327520465391-0.506609512542-0.0593025476799-0.498281467321-0.1670878779061.17030265769-0.514010355620.633401790326-0.3666656460581.64709711489-0.296963779924-0.2397252144161.748389653010.1812811870430.96748476421141.273383530824.732351737657.3258102954
264.863465623271.054755046443.88962121834.589420625894.569577196686.37542128499-0.007989170375060.191392851416-2.151311722410.236880085567-0.26780028534-1.104523446182.680182683581.577107260521.541200285471.0916111037-0.2841263602220.240192478251.050743158720.01210762671790.93050642873138.05699672997.633482096542.3834912264
271.43100412643-0.9223996104-0.3911781946576.41120366566-1.181363545994.97543654755-0.5056884263810.147396816770.300919607811.552454037020.2827130884330.1993359590260.9620839139061.599221123230.5275685492710.95709364109-0.1491468366120.007219513285940.742366126518-0.00235234406520.85731351009935.649077046315.485430373842.3322121312
284.356289451530.508697925088-0.08711223069373.57177402872-0.07948679531450.8276427845340.235221062159-0.0982528584304-0.3572812045060.00986060741596-0.0648722682140.2491939802370.9238142243830.270040830440.04045054127611.551910028010.05116132668640.1804241042761.24301128702-0.09936495116391.0616800821938.4392766945-8.5198462234220.7117871903
290.644102213899-0.280497850377-0.08193617840492.80959682567-2.449220967932.36726843403-0.03020689444580.6613621898390.3861940018750.309706957002-0.226923010811-0.3180615006740.3980849949650.1948019822290.4372976923581.82980595080.0355992504351-0.03208020568051.49056518875-0.1158730717221.2255053445443.957019648-9.4014690110132.2653739102
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 5 through 24 )AA5 - 241 - 20
22chain 'A' and (resid 25 through 66 )AA25 - 6621 - 62
33chain 'A' and (resid 67 through 80 )AA67 - 8063 - 76
44chain 'A' and (resid 81 through 94 )AA81 - 9477 - 90
55chain 'A' and (resid 95 through 119 )AA95 - 11991 - 115
66chain 'A' and (resid 120 through 142 )AA120 - 142116 - 138
77chain 'A' and (resid 143 through 195 )AA143 - 195139 - 191
88chain 'B' and (resid 2 through 27 )BB2 - 271 - 26
99chain 'B' and (resid 28 through 80 )BB28 - 8027 - 79
1010chain 'C' and (resid 6 through 24 )CC6 - 241 - 19
1111chain 'C' and (resid 25 through 36 )CC25 - 3620 - 31
1212chain 'C' and (resid 37 through 47 )CC37 - 4732 - 42
1313chain 'C' and (resid 48 through 57 )CC48 - 5743 - 52
1414chain 'C' and (resid 58 through 119 )CC58 - 11953 - 114
1515chain 'C' and (resid 120 through 142 )CC120 - 142115 - 137
1616chain 'C' and (resid 143 through 195 )CC143 - 195138 - 190
1717chain 'D' and (resid 1 through 23 )DD1 - 231 - 23
1818chain 'D' and (resid 24 through 63 )DD24 - 6324 - 58
1919chain 'D' and (resid 64 through 77 )DD64 - 7759 - 72
2020chain 'E' and (resid 5 through 36 )EE5 - 361 - 32
2121chain 'E' and (resid 37 through 47 )EE37 - 4733 - 43
2222chain 'E' and (resid 48 through 70 )EE48 - 7044 - 66
2323chain 'E' and (resid 71 through 93 )EE71 - 9367 - 84
2424chain 'E' and (resid 94 through 128 )EE94 - 12885 - 119
2525chain 'E' and (resid 135 through 142 )EE135 - 142120 - 127
2626chain 'E' and (resid 143 through 152 )EE143 - 152128 - 137
2727chain 'E' and (resid 153 through 195 )EE153 - 195138 - 180
2828chain 'F' and (resid 4 through 51 )FF4 - 511 - 48
2929chain 'F' and (resid 52 through 79 )FF52 - 7949 - 76

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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