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- PDB-9d1z: Structure of G75Q Ubiquitin bound to KLHDC3-EloB/C -

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基本情報

登録情報
データベース: PDB / ID: 9d1z
タイトルStructure of G75Q Ubiquitin bound to KLHDC3-EloB/C
要素
  • Elongin-B
  • Elongin-C
  • Kelch domain-containing protein 3
  • Ubiquitin
キーワードLIGASE / KLHDC3 / Ubiquitin / C-degron / Cullin-RING / E3
機能・相同性
機能・相同性情報


XBP1(S) activates chaperone genes / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / elongin complex / reciprocal meiotic recombination / 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 ...XBP1(S) activates chaperone genes / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / elongin complex / reciprocal meiotic recombination / 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 / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / Tat-mediated elongation of the HIV-1 transcript / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / Formation of HIV-1 elongation complex containing HIV-1 Tat / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / ubiquitin-like ligase-substrate adaptor activity / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / Formation of HIV elongation complex in the absence of HIV Tat / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / RNA Polymerase II Transcription Elongation / Activated NOTCH1 Transmits Signal to the Nucleus / Formation of RNA Pol II elongation complex / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / RNA Polymerase II Pre-transcription Events / PINK1-PRKN Mediated Mitophagy / TNFR1-induced NF-kappa-B signaling pathway / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / NOTCH3 Activation and Transmission of Signal to the Nucleus / Regulation of signaling by CBL / NIK-->noncanonical NF-kB signaling / SCF-beta-TrCP mediated degradation of Emi1 / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Fanconi Anemia Pathway / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR2 signaling / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Peroxisomal protein import / Negative regulation of FGFR4 signaling
類似検索 - 分子機能
: / Kelch motif / 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 ...: / Kelch motif / 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 domain signature. / Ubiquitin domain / Ubiquitin conserved site / 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
Polyubiquitin-C / Elongin-C / Elongin-B / Kelch domain-containing protein 3
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: 1.88 Å
データ登録者Schulman, B.A. / Scott, D.C.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute on Aging (NIH/NIA)AG011085 米国
引用ジャーナル: Nat Commun / 年: 2024
タイトル: Structural basis for C-degron selectivity across KLHDCX family E3 ubiquitin ligases.
著者: Daniel C Scott / Sagar Chittori / Nicholas Purser / Moeko T King / Samuel A Maiwald / Kelly Churion / Amanda Nourse / Chan Lee / Joao A Paulo / Darcie J Miller / Stephen J Elledge / J Wade ...著者: Daniel C Scott / Sagar Chittori / Nicholas Purser / Moeko T King / Samuel A Maiwald / Kelly Churion / Amanda Nourse / Chan Lee / Joao A Paulo / Darcie J Miller / Stephen J Elledge / J Wade Harper / Gary Kleiger / Brenda A Schulman /
要旨: Specificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend on E3 ligases binding to peptide-like sequences - termed N- or C-degrons - at the ...Specificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend on E3 ligases binding to peptide-like sequences - termed N- or C-degrons - at the termini of substrates. However, our knowledge of structural features distinguishing closely related C-degron substrate-E3 pairings is limited. Here, by systematically comparing ubiquitylation activities towards a suite of common model substrates, and defining interactions by biochemistry, crystallography, and cryo-EM, we reveal principles of C-degron recognition across the KLHDCX family of Cullin-RING ligases (CRLs). First, a motif common across these E3 ligases anchors a substrate's C-terminus. However, distinct locations of this C-terminus anchor motif in different blades of the KLHDC2, KLHDC3, and KLHDC10 β-propellers establishes distinct relative positioning and molecular environments for substrate C-termini. Second, our structural data show KLHDC3 has a pre-formed pocket establishing preference for an Arg or Gln preceding a C-terminal Gly, whereas conformational malleability contributes to KLHDC10's recognition of varying features adjacent to substrate C-termini. Finally, additional non-consensus interactions, mediated by C-degron binding grooves and/or by distal propeller surfaces and substrate globular domains, can substantially impact substrate binding and ubiquitylatability. Overall, the data reveal combinatorial mechanisms determining specificity and plasticity of substrate recognition by KLDCX-family C-degron E3 ligases.
履歴
登録2024年8月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年11月20日Provider: repository / タイプ: Initial release
改定 1.12025年2月5日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name

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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 3
B: Elongin-B
C: Elongin-C
D: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,9868
ポリマ－77,5134
非ポリマー4734
水12,214678
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)114.949, 120.873, 152.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDモデル要素
11A-544-

HOH

21A-873-

HOH

31A-941-

HOH

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要素

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タンパク質 , 4種, 4分子 ABCD

#1: タンパク質 Kelch domain-containing protein 3 / Testis intracellular mediator protein


分子量: 43245.082 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KLHDC3, PEAS / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9BQ90
#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: 1 / 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: 13871.611 Da / 分子数: 1 / 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 (蝶・蛾) / 参照: UniProt: Q15369
#4: タンパク質 Ubiquitin


分子量: 8647.907 Da / 分子数: 1 / Mutation: G75Q / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBC / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0CG48

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非ポリマー , 2種, 682分子

#5: 化合物
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


分子量: 118.174 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C6H14O2 / タイプ: SUBJECT OF INVESTIGATION / コメント: 沈殿剤*YM
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 678 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
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: 3.43 Å3/Da / 溶媒含有率: 64.1 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 10%%KMME, 5% Tacsimate pH=7.0, 0.1M HEPES 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: ALS / ビームライン: 5.0.1 / 波長: 0.97741 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2023年12月19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: 0.97741 Å / 相対比: 1
反射解像度: 1.88→50 Å / Num. obs: 85054 / % possible obs: 100 % / 冗長度: 8.1 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.035 / Rrim(I) all: 0.099 / Χ2: 0.995 / Net I/σ(I): 5.9
反射 シェル

Diffraction-ID: 1 / % possible all: 100

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
1.9-1.977.40.77783780.7890.9390.310.8380.524
1.97-2.058.20.54184770.8930.9710.2020.5780.513
2.05-2.148.30.484230.9380.9840.1480.4270.565
2.14-2.258.30.30884280.9610.990.1140.3290.657
2.25-2.398.30.23484750.9760.9940.0870.250.752
2.39-2.587.80.18384400.9820.9960.070.1960.856
2.58-2.847.70.13284910.990.9980.0510.1421.049
2.84-3.258.70.09685320.9950.9990.0350.1021.447
3.25-4.098.50.07185760.9970.9990.0260.0761.94
4.09-508.10.04888340.99810.0180.0511.498

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21_5207精密化
HKL-2000データスケーリング
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 / 解像度: 1.88→45.95 Å / SU ML: 0.18 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 18.96 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1903 4189 4.94 %
Rwork0.1686 --
obs0.1697 84718 98.45 %
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
精密化ステップサイクル: LAST / 解像度: 1.88→45.95 Å
タンパク質核酸リガンド溶媒全体
原子数5028 0 32 678 5738
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0075188
X-RAY DIFFRACTIONf_angle_d0.9757049
X-RAY DIFFRACTIONf_dihedral_angle_d14.6151880
X-RAY DIFFRACTIONf_chiral_restr0.061775
X-RAY DIFFRACTIONf_plane_restr0.009909
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90.3023820.27661686X-RAY DIFFRACTION62
1.9-1.930.2931500.23762645X-RAY DIFFRACTION99
1.93-1.950.24171320.232699X-RAY DIFFRACTION99
1.95-1.980.25811280.21112661X-RAY DIFFRACTION99
1.98-20.21851470.19922688X-RAY DIFFRACTION99
2-2.030.2091500.18582679X-RAY DIFFRACTION100
2.03-2.060.21531410.18432693X-RAY DIFFRACTION100
2.06-2.090.21411390.18212692X-RAY DIFFRACTION100
2.09-2.120.20351200.18252726X-RAY DIFFRACTION100
2.12-2.160.19551240.18172704X-RAY DIFFRACTION100
2.16-2.190.21971350.17752697X-RAY DIFFRACTION100
2.19-2.230.19641450.18162701X-RAY DIFFRACTION100
2.23-2.280.21871310.17022679X-RAY DIFFRACTION100
2.28-2.320.1981290.17272761X-RAY DIFFRACTION100
2.32-2.370.19961260.16722696X-RAY DIFFRACTION100
2.37-2.430.1971440.18362698X-RAY DIFFRACTION100
2.43-2.490.22971290.18172716X-RAY DIFFRACTION100
2.49-2.560.21081530.18082705X-RAY DIFFRACTION100
2.56-2.630.21961770.1872679X-RAY DIFFRACTION100
2.63-2.720.22061470.18572705X-RAY DIFFRACTION100
2.72-2.810.22011530.18742718X-RAY DIFFRACTION100
2.81-2.930.22421430.17972705X-RAY DIFFRACTION100
2.93-3.060.17221390.17882756X-RAY DIFFRACTION100
3.06-3.220.1841630.16632722X-RAY DIFFRACTION100
3.22-3.420.15231330.15882740X-RAY DIFFRACTION100
3.42-3.690.1751530.15442727X-RAY DIFFRACTION100
3.69-4.060.14331400.14462777X-RAY DIFFRACTION100
4.06-4.640.13841460.12662768X-RAY DIFFRACTION100
4.64-5.850.18141390.15152795X-RAY DIFFRACTION100
5.85-45.950.21971510.18272911X-RAY DIFFRACTION100
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)
11.6928-0.04810.07851.4344-0.10931.7375-0.03690.084-0.0342-0.06490.04010.2598-0.0565-0.4034-0.00910.1919-0.0146-0.0250.2556-0.00480.209-26.9898-7.2676-14.016
21.45860.1704-0.60542.01540.04382.1373-0.00730.12010.1703-0.15710.04470.3139-0.3613-0.3414-0.00840.24470.0628-0.02370.28710.01190.2596-27.56925.3027-16.4485
31.5060.0671-1.0443.46510.27911.33450.05540.2050.0983-0.3671-0.00390.3562-0.4257-0.3836-0.00740.26070.0908-0.04340.33670.00990.2702-29.90268.8328-17.3748
40.9849-0.3458-0.02171.49440.02590.93490.0580.18170.0835-0.3301-0.0403-0.1267-0.1124-0.0434-0.01540.2932-0.00350.03190.24810.01530.2032-10.68882.972-27.6968
54.58680.54451.35664.34560.65894.5670.07450.0557-0.237-0.3845-0.07450.06610.0988-0.27370.10480.1914-0.00060.02190.1850.0020.2039-16.9726-11.3991-20.1301
61.8336-0.33041.06881.4563-0.80421.71530.0148-0.102-0.2633-0.02850.03870.11180.1709-0.1808-0.06060.2258-0.02340.01680.2188-0.0010.2687-15.4304-22.0951-7.1771
78.0813-0.61162.0693.99232.65463.3880.02821.01840.1874-0.3690.1568-0.092-0.22250.3104-0.08510.16520.00990.02520.29360.02720.351219.0768-23.4196-2.5571
84.8442-0.95220.31591.6821-1.16413.2735-0.18810.33910.424-0.059-0.0226-0.3673-0.06160.32950.19650.22440.0301-0.0130.23650.03290.413927.3921-23.56821.4846
92.06670.52890.08341.14410.26020.4095-0.08351.38820.1064-0.5084-0.3396-0.07610.32380.48540.05920.45590.06470.09210.64910.05790.45425.1588-24.1201-11.299
103.626-0.77270.16892.30330.05870.90930.27940.5907-0.128-0.2784-0.13110.01760.31680.15440.05120.25390.04870.0090.2583-0.00460.317218.3845-26.295-3.2939
117.5026-0.6204-0.38648.2109-0.22978.296-0.1682-1.1615-0.10380.50480.3648-0.0341-0.40391.0345-0.21920.28840.0741-0.00680.4970.00610.32732.6237-33.388810.654
121.0242.0059-1.81855.9822-0.72727.31260.1009-0.443-1.41930.45430.03240.87810.6278-0.6089-0.11340.28820.0005-0.00230.2780.04720.65539.6597-36.22045.4814
134.13530.39220.23932.9715-0.21032.385-0.0939-0.4150.260.2696-0.0279-0.3573-0.04210.10390.02540.24530.0571-0.0430.2568-0.01860.31549.9417-17.56578.8047
143.9572-3.4603-1.64693.31620.22624.7283-0.3186-0.76360.91580.57520.3546-0.6774-0.52990.27870.15760.41720.1061-0.08750.5561-0.05020.46578.5192-15.515617.3213
153.75-0.1126-0.0190.6932-0.11023.9759-0.01820.1137-0.0163-0.0562-0.0032-0.0969-0.08810.0294-0.0040.18540.0289-0.01250.17750.02410.2732.6825-22.3358-2.6011
162.16-0.24440.41124.1489-1.00054.50860.19650.7622-0.6291-0.9035-0.09320.47080.5966-0.615-0.12871.2650.0994-0.2071.4242-0.45680.2676-27.8541-10.0545-54.1082
172.5161.0477-1.97066.3119-0.46911.5601-0.43180.6212-1.11890.01840.41220.54170.8995-0.6690.02421.0935-0.0892-0.20020.6092-0.05530.5773-26.4187-12.2584-48.5717
180.04110.043-0.01710.054-0.01590.03530.36090.4682-0.5533-0.1580.03620.26380.1499-0.336-0.27041.03980.0934-0.47691.82160.27760.9003-37.7305-3.1961-58.2029
193.52910.3718-0.1065.94450.89294.86240.21160.3991-0.5139-0.2647-0.33421.41940.8242-1.49780.14760.6812-0.0587-0.18050.942-0.06070.5013-34.107-4.9876-44.8175
204.48620.70851.4740.4975-0.30391.4123-0.40180.64690.8261-0.9431-0.04470.5323-0.9873-0.87770.34261.2870.2769-0.25441.07210.0020.5745-29.01933.6751-52.1984
210.47140.27670.00074.11621.5640.6228-0.07620.866-0.5653-0.842-0.1658-0.0671-0.2532-0.41620.06241.32880.1462-0.20131.4720.10270.4308-28.552-1.2683-59.787
221.030.19280.67520.2489-0.93885.90260.08560.1964-0.0377-0.7861-0.10190.4729-0.1167-0.80380.12390.63240.037-0.1390.4417-0.04210.263-25.6704-4.9246-39.8403
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 294 )
5X-RAY DIFFRACTION5chain 'A' and (resid 295 through 322 )
6X-RAY DIFFRACTION6chain 'A' and (resid 323 through 377 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 9 )
8X-RAY DIFFRACTION8chain 'B' and (resid 10 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 65 )
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 79 )
11X-RAY DIFFRACTION11chain 'B' and (resid 80 through 89 )
12X-RAY DIFFRACTION12chain 'B' and (resid 90 through 97 )
13X-RAY DIFFRACTION13chain 'C' and (resid 15 through 46 )
14X-RAY DIFFRACTION14chain 'C' and (resid 47 through 66 )
15X-RAY DIFFRACTION15chain 'C' and (resid 67 through 112 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 7 )
17X-RAY DIFFRACTION17chain 'D' and (resid 8 through 16 )
18X-RAY DIFFRACTION18chain 'D' and (resid 17 through 22 )
19X-RAY DIFFRACTION19chain 'D' and (resid 23 through 44 )
20X-RAY DIFFRACTION20chain 'D' and (resid 45 through 56 )
21X-RAY DIFFRACTION21chain 'D' and (resid 57 through 65 )
22X-RAY DIFFRACTION22chain 'D' and (resid 66 through 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