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- PDB-8ebn: Structure of KLHDC2-EloB/C tetrameric assembly -

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基本情報

登録情報
データベース: PDB / ID: 8ebn
タイトルStructure of KLHDC2-EloB/C tetrameric assembly
要素
  • Elongin-B
  • Elongin-C
  • Kelch domain-containing protein 2
キーワードLIGASE / E3 ligase
機能・相同性
機能・相同性情報


ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation ...ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription corepressor binding / Vif-mediated degradation of APOBEC3G / TP53 Regulates Transcription of DNA Repair Genes / Inactivation of CSF3 (G-CSF) signaling / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Regulation of expression of SLITs and ROBOs / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nuclear body / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
類似検索 - 分子機能
KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Elongin-C / Elongin B / Kelch-type beta propeller / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ubiquitin family ...KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Elongin-C / Elongin B / Kelch-type beta propeller / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
類似検索 - ドメイン・相同性
Elongin-C / Elongin-B / Kelch domain-containing protein 2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.6 Å
データ登録者Scott, D.C. / Schulman, B.A.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01GM125885 米国
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)P30CA021765 米国
引用ジャーナル: Mol Cell / 年: 2023
タイトル: E3 ligase autoinhibition by C-degron mimicry maintains C-degron substrate fidelity.
著者: Daniel C Scott / Moeko T King / Kheewoong Baek / Clifford T Gee / Ravi Kalathur / Jerry Li / Nicholas Purser / Amanda Nourse / Sergio C Chai / Sivaraja Vaithiyalingam / Taosheng Chen / ...著者: Daniel C Scott / Moeko T King / Kheewoong Baek / Clifford T Gee / Ravi Kalathur / Jerry Li / Nicholas Purser / Amanda Nourse / Sergio C Chai / Sivaraja Vaithiyalingam / Taosheng Chen / Richard E Lee / Stephen J Elledge / Gary Kleiger / Brenda A Schulman /
要旨: E3 ligase recruitment of proteins containing terminal destabilizing motifs (degrons) is emerging as a major form of regulation. How those E3s discriminate bona fide substrates from other proteins ...E3 ligase recruitment of proteins containing terminal destabilizing motifs (degrons) is emerging as a major form of regulation. How those E3s discriminate bona fide substrates from other proteins with terminal degron-like sequences remains unclear. Here, we report that human KLHDC2, a CRL2 substrate receptor targeting C-terminal Gly-Gly degrons, is regulated through interconversion between two assemblies. In the self-inactivated homotetramer, KLHDC2's C-terminal Gly-Ser motif mimics a degron and engages the substrate-binding domain of another protomer. True substrates capture the monomeric CRL2, driving E3 activation by neddylation and subsequent substrate ubiquitylation. Non-substrates such as NEDD8 bind KLHDC2 with high affinity, but its slow on rate prevents productive association with CRL2. Without substrate, neddylated CRL2 assemblies are deactivated via distinct mechanisms: the monomer by deneddylation and the tetramer by auto-ubiquitylation. Thus, substrate specificity is amplified by KLHDC2 self-assembly acting like a molecular timer, where only bona fide substrates may bind before E3 ligase inactivation.
履歴
登録2022年8月31日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年2月22日Provider: repository / タイプ: Initial release
改定 1.12023年9月13日Group: Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023年10月25日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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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: Kelch domain-containing protein 2
B: Kelch domain-containing protein 2
C: Elongin-B
D: Elongin-C
E: Elongin-B
F: Elongin-C


分子量 (理論値)分子数
合計 (水以外)143,6986
ポリマ－143,6986
非ポリマー00
水1,20767
1
A: Kelch domain-containing protein 2
B: Kelch domain-containing protein 2
C: Elongin-B
D: Elongin-C
E: Elongin-B
F: Elongin-C

A: Kelch domain-containing protein 2
B: Kelch domain-containing protein 2
C: Elongin-B
D: Elongin-C
E: Elongin-B
F: Elongin-C


分子量 (理論値)分子数
合計 (水以外)287,39512
ポリマ－287,39512
非ポリマー00
水21612
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation4_554-y,-x,-z-1/31
Buried area29390 Å2
ΔGint-192 kcal/mol
Surface area85260 Å2
手法PISA
単位格子
Length a, b, c (Å)142.431, 142.431, 140.479
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

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要素

#1: タンパク質 Kelch domain-containing protein 2 / Hepatocellular carcinoma-associated antigen 33 / Host cell factor homolog LCP / Host cell factor- ...Hepatocellular carcinoma-associated antigen 33 / Host cell factor homolog LCP / Host cell factor-like protein 1 / HCLP-1


分子量: 46154.672 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KLHDC2, HCA33 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9Y2U9
#2: タンパク質 Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


分子量: 11748.406 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ELOB, TCEB2 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q15370
#3: タンパク質 Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


分子量: 13945.732 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ELOC, TCEB1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q15369
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 67 / 由来タイプ: 天然 / 式: H2O

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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: 2.86 Å3/Da / 溶媒含有率: 57.03 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: % PEG3350, 0.2 M KSCN, 0.1 M Tris, 0.1M Na/K Tartrate, 2.5% MPD, pH =6.8

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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 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2020年7月30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 Å / 相対比: 1
反射解像度: 2.6→50 Å / Num. obs: 49565 / % possible obs: 98.6 % / 冗長度: 4 % / Biso Wilson estimate: 59.05 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.037 / Rrim(I) all: 0.077 / Χ2: 1.319 / Net I/σ(I): 11.5 / Num. measured all: 197411
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
2.6-2.6940.61349480.8290.3450.7050.50999.6
2.69-2.840.44649490.9040.2510.5130.55899.5
2.8-2.933.90.29949460.9450.170.3450.67598.9
2.93-3.083.70.19548120.9640.1150.2270.79596.2
3.08-3.284.20.14849930.9830.0820.1690.98999.6
3.28-3.534.10.10649870.990.0590.1221.40499.4
3.53-3.8840.07949940.9920.0440.0911.86499.5
3.88-4.453.80.05848820.9940.0340.0682.39696.6
4.45-5.64.10.04650110.9960.0260.0532.24899.1
5.6-5040.0350430.9990.0160.0341.73797.5

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解析

ソフトウェア
名称バージョン分類
HKL-2000データスケーリング
PHENIX1.20.1_4487精密化
PDB_EXTRACT3.27データ抽出
HKL-2000データ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1VCB

1vcb


解像度: 2.6→46.62 Å / SU ML: 0.4 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 27.37 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2497 2542 5.14 %
Rwork0.2111 46922 -
obs0.2131 49464 98.41 %
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 max: 177.44 Å2 / Biso mean: 74.7516 Å2 / Biso min: 28.57 Å2
精密化ステップサイクル: final / 解像度: 2.6→46.62 Å
タンパク質核酸リガンド溶媒全体
原子数8396 0 0 67 8463
Biso mean---55.66 -
残基数----1080
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.650.44441550.37262575273099
2.65-2.70.35761270.33572611273899
2.7-2.760.31821320.3092617274999
2.76-2.820.29221480.28122570271899
2.82-2.90.31631340.26932650278499
2.9-2.970.35261460.26532583272997
2.97-3.060.3131250.2592463258894
3.06-3.160.29261240.26012644276899
3.16-3.270.28861290.272426482777100
3.27-3.40.30481420.2612624276699
3.4-3.560.29681310.22322654278599
3.56-3.750.23731440.203926242768100
3.75-3.980.1891610.18692632279399
3.98-4.290.20261760.16892523269998
4.29-4.720.21151420.15172528267095
4.72-5.40.19231300.165426812811100
5.4-6.80.24851370.20762659279699
6.8-46.620.24461590.19142636279596
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)
11.49060.23110.83180.7183-0.27740.9324-0.03220.16640.08330.08540.07660.0478-0.17540.113400.4014-0.0750.09290.22560.01680.423314.9297-32.0701-51.2781
21.6201-0.04770.16260.5723-0.09450.70820.1698-0.0243-0.0471-0.0093-0.0206-0.05580.06990.16110.00010.3605-0.03660.04350.2234-0.01810.379317.175-49.2757-42.9308
30.97830.2557-0.21031.1219-0.04990.9060.1638-0.00830.1085-0.0564-0.0725-0.0808-0.20170.3780.02730.3234-0.11530.07190.3828-0.03760.420634.1361-38.2892-44.939
40.3959-0.34610.32430.2035-0.08780.1286-0.1762-0.4247-0.1988-0.17040.17240.3194-0.3165-0.12600.7077-0.15420.04990.62670.00490.646529.7386-18.9723-69.6946
50.9270.2023-0.40790.7428-0.88840.8497-0.7124-0.03140.1838-0.02270.2608-0.1931-0.4583-0.1336-0.00750.7436-0.1113-0.110.6478-0.16580.649222.2859-23.4449-2.7455
60.13010.1125-0.09430.23780.04240.0824-0.8004-0.25780.94350.27470.4091-0.0852-1.11320.2548-0.00081.18080.0989-0.23991.0179-0.1131.103116.0384-10.6181-0.9817
70.98691.374-0.56742.2059-1.41362.1296-0.136-0.15711.73040.21890.69980.24320.2095-0.08151.49870.67210.4104-0.16111.1363-0.78940.95346.9201-12.65668.6104
80.03120.045-0.05970.0188-0.06770.0770.6897-0.28751.7957-0.3325-0.0849-0.1030.00120.1385-0.00091.10320.21060.05331.0608-0.11291.55215.3376-9.87163.1659
9-0.01760.03-0.03790.5-0.3410.3009-0.5582-0.53880.7913-0.21351.0742-0.2804-0.02490.31170.11740.77720.0509-0.061.2642-0.3590.88020.1229-20.61769.1224
103.37410.94721.39690.36690.32771.3576-0.671-1.21111.32960.68260.15120.3546-0.09390.0622-0.07870.8720.0670.1541.5937-0.38430.68140.0668-25.084112.955
110.1298-0.15550.22411.2944-0.35030.9074-0.0714-1.3490.10220.32040.22060.19160.182-0.33520.55180.5797-0.0597-0.06121.8033-0.3110.04198.3982-33.70210.397
120.1709-0.31650.04092.3009-0.10690.0378-0.1584-0.4842-0.11840.26770.0327-0.62810.2718-0.9143-0.12540.6816-0.2038-0.04331.1764-0.03920.283410.0166-36.54716.7944
130.22280.116-0.19520.5221-0.49380.4405-0.2343-0.0705-0.0535-0.08470.1411-0.2750.52920.2697-0.00380.5856-0.0022-0.03510.778-0.08150.578219.5505-34.47576.562
140.48020.2644-0.19660.1559-0.23660.19440.2646-0.3984-0.41280.1559-0.35310.16090.6472-0.22290.00220.5123-0.125-0.00410.49230.08490.420413.785-53.1783-20.5435
150.1213-0.305-0.04940.5331-0.01920.0296-0.0029-0.14480.48580.02790.30120.3795-0.35290.19930.0050.566-0.11850.06490.47010.01290.4088.3568-40.1447-30.3158
160.2522-0.2209-0.00890.75920.11970.47180.3002-0.8634-0.80810.4897-0.36850.09730.2021-0.1975-0.02570.5539-0.18190.0960.65430.1610.5273-11.2281-61.779-7.0989
170.2347-0.5364-0.21351.43230.87660.83110.1802-0.3476-0.26340.1286-0.19940.977-0.1486-0.6536-0.4930.448-0.19590.13990.61510.24080.754-23.3596-63.6337-8.224
181.5919-0.2326-0.13590.01810.00560.0188-0.11950.2535-0.56330.3723-0.28720.97390.3738-0.532-0.15950.7257-0.22230.30330.59310.29120.9194-16.0609-72.9482-5.3755
190.00740.00610.03080.25360.12960.08730.1209-0.4359-0.82851.28960.2088-0.5354-0.10160.45160.05380.8829-0.1774-0.0170.94060.34030.722-5.0661-64.4659-0.9296
200.9225-0.2056-0.35620.19080.0560.4261-0.2950.2538-0.6351-0.1995-0.2338-0.35310.36110.343-0.72370.5906-0.19510.13440.37340.07010.8607-16.1031-71.2063-14.8734
210.425-0.0640.44430.0190.1173.2271-0.0106-0.1407-0.2708-0.1548-0.17010.44910.1332-0.812-0.25730.765-0.18550.22080.24530.06870.6627-1.1072-65.1062-23.8027
220.3424-0.36890.21310.6498-0.87382.32450.4837-0.4022-0.32790.0743-0.24790.34721.3461-0.46250.25670.4282-0.20270.19660.44620.02490.5579-11.7566-54.8071-20.1325
230.06020.0736-0.05170.12660.03030.03740.3521-0.4919-0.0266-0.0391-0.1580.4008-0.41490.30780.00060.5815-0.10510.13940.5326-0.00580.4642-10.076-47.1777-15.3198
240.23730.13590.06220.1009-0.01480.08930.1119-0.03870.4654-0.1950.1033-0.4330.3587-0.05720.00230.4942-0.05030.07620.32540.03830.4506-9.427-49.5202-25.1592
250.4156-0.50430.15220.4591-0.12390.05260.0507-0.8636-0.42440.37940.05280.39840.29690.37060.02340.5656-0.15530.06850.61580.03070.4055-1.5586-53.1038-11.3505
260.21-0.02120.140.12230.12150.32850.3454-0.52640.0213-0.1645-0.27390.02580.2077-0.6668-0.01840.7598-0.15790.08750.65760.08440.52514.4904-51.0369-3.0474
270.4318-0.1892-0.27320.43510.71761.24920.27070.22210.0642-0.0414-0.7384-0.2426-0.1062-0.0946-0.28810.4498-0.19290.13840.39970.05630.42844.9226-50.1293-20.7071
280.0285-0.01280.05780.09020.19070.6035-0.11550.16880.46260.50410.7362-0.00120.2108-0.30980.01630.6092-0.14340.03080.7659-0.00550.473658.7164-30.4204-70.8783
290.1047-0.07350.10170.0921-0.02290.04390.2358-0.05990.92330.16250.1101-0.23240.347-0.21220.01530.581-0.1585-0.04521.05910.06510.555660.9692-32.5474-74.8717
300.18180.04730.05490.51390.13820.2909-0.27820.2346-0.4705-0.46490.2633-0.2580.0552-0.62010.00390.3976-0.26570.15041.42750.14940.473467.4601-38.4517-76.8755
311.04350.19221.73030.70260.02393.04350.691.59570.2289-0.611-0.1566-1.11090.08532.01920.15010.4663-0.33050.07841.29510.17760.830670.8729-30.7442-78.3122
320.0893-0.1291-0.0820.50070.33540.2585-0.40951.0579-0.0456-0.4465-0.1636-0.2817-0.54840.2905-0.54310.8306-0.57410.19440.87540.0470.656861.3904-27.1141-70.5332
330.5017-0.3399-0.01540.08490.03880.1150.08160.52010.1221-0.0232-0.2085-0.0041-1.04720.2926-0.06340.8151-0.08370.14350.87490.27930.583454.569-21.0841-85.6727
340.3903-0.2169-0.11150.24640.04920.0567-0.24230.8517-0.3676-0.3538-0.0445-0.09270.0690.4748-0.00020.6766-0.16610.09830.8792-0.08480.528248.0348-39.0106-81.203
350.6087-0.2431-0.10080.3096-0.1580.1547-0.14620.14160.17020.0977-0.35910.0078-0.21220.4903-0.03910.6645-0.24620.13360.78940.00470.48945.9146-32.8577-78.0864
360.33640.061-0.1701-0.001-0.02030.0986-0.3292-0.3453-0.0559-0.27630.3864-0.3963-0.21520.27340.01150.7926-0.2110.12280.7460.00480.472444.3084-29.2748-62.5924
370.25-0.09310.00610.06330.04870.05090.2730.2557-0.2945-0.00580.0449-0.21430.0456-0.32440.00030.6646-0.15380.03970.77990.10720.52837.1553-27.4324-79.0231
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 94 )A27 - 94
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 221 )A95 - 221
3X-RAY DIFFRACTION3chain 'A' and (resid 222 through 363 )A222 - 363
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 406 )A364 - 406
5X-RAY DIFFRACTION5chain 'B' and (resid 27 through 106 )B27 - 106
6X-RAY DIFFRACTION6chain 'B' and (resid 107 through 148 )B107 - 148
7X-RAY DIFFRACTION7chain 'B' and (resid 149 through 188 )B149 - 188
8X-RAY DIFFRACTION8chain 'B' and (resid 189 through 207 )B189 - 207
9X-RAY DIFFRACTION9chain 'B' and (resid 208 through 233 )B208 - 233
10X-RAY DIFFRACTION10chain 'B' and (resid 234 through 271 )B234 - 271
11X-RAY DIFFRACTION11chain 'B' and (resid 272 through 296 )B272 - 296
12X-RAY DIFFRACTION12chain 'B' and (resid 297 through 340 )B297 - 340
13X-RAY DIFFRACTION13chain 'B' and (resid 341 through 363 )B341 - 363
14X-RAY DIFFRACTION14chain 'B' and (resid 364 through 387 )B364 - 387
15X-RAY DIFFRACTION15chain 'B' and (resid 388 through 406 )B388 - 406
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 23 )C1 - 23
17X-RAY DIFFRACTION17chain 'C' and (resid 24 through 41 )C24 - 41
18X-RAY DIFFRACTION18chain 'C' and (resid 42 through 56 )C42 - 56
19X-RAY DIFFRACTION19chain 'C' and (resid 57 through 72 )C57 - 72
20X-RAY DIFFRACTION20chain 'C' and (resid 73 through 90 )C73 - 90
21X-RAY DIFFRACTION21chain 'C' and (resid 91 through 97 )C91 - 97
22X-RAY DIFFRACTION22chain 'D' and (resid 17 through 27 )D17 - 27
23X-RAY DIFFRACTION23chain 'D' and (resid 28 through 46 )D28 - 46
24X-RAY DIFFRACTION24chain 'D' and (resid 47 through 66 )D47 - 66
25X-RAY DIFFRACTION25chain 'D' and (resid 67 through 83 )D67 - 83
26X-RAY DIFFRACTION26chain 'D' and (resid 84 through 96 )D84 - 96
27X-RAY DIFFRACTION27chain 'D' and (resid 97 through 112 )D97 - 112
28X-RAY DIFFRACTION28chain 'E' and (resid 1 through 8 )E1 - 8
29X-RAY DIFFRACTION29chain 'E' and (resid 9 through 23 )E9 - 23
30X-RAY DIFFRACTION30chain 'E' and (resid 24 through 35 )E24 - 35
31X-RAY DIFFRACTION31chain 'E' and (resid 36 through 56 )E36 - 56
32X-RAY DIFFRACTION32chain 'E' and (resid 57 through 79 )E57 - 79
33X-RAY DIFFRACTION33chain 'E' and (resid 80 through 99 )E80 - 99
34X-RAY DIFFRACTION34chain 'F' and (resid 17 through 47 )F17 - 47
35X-RAY DIFFRACTION35chain 'F' and (resid 48 through 83 )F48 - 83
36X-RAY DIFFRACTION36chain 'F' and (resid 84 through 96 )F84 - 96
37X-RAY DIFFRACTION37chain 'F' and (resid 97 through 112 )F97 - 112

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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