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- PDB-6byh: Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragme... -

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データを開く


IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 6byh
タイトルUbiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex.
要素
  • Lysine-specific demethylase 2A
  • Polyubiquitin-B
  • S-phase kinase-associated protein 1
キーワードPROTEIN BINDING / Ubiquitination
機能・相同性
機能・相同性情報


[histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / regulation of xenophagy / F-box domain binding / synaptic assembly at neuromuscular junction / regulation of cell cycle process / neural crest cell differentiation / histone H3K36 demethylase activity / unmethylated CpG binding / : ...[histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / regulation of xenophagy / F-box domain binding / synaptic assembly at neuromuscular junction / regulation of cell cycle process / neural crest cell differentiation / histone H3K36 demethylase activity / unmethylated CpG binding / : / regulation of BMP signaling pathway / PcG protein complex / regulation of mitophagy / regulation of centrosome duplication / maintenance of protein location in nucleus / Cul7-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / regulation of TOR signaling / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / ubiquitin ligase activator activity / seminiferous tubule development / regulation of DNA damage checkpoint / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / SCF ubiquitin ligase complex / female gonad development / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / limb development / male meiosis I / ubiquitin ligase complex scaffold activity / histone demethylase activity / centrosome duplication / cilium assembly / cullin family protein binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / ubiquitin-like ligase-substrate adaptor activity / neuron projection morphogenesis / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / regulation of neuron apoptotic process / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / regulation of mitotic cell cycle / 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 / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / regulation of mitochondrial membrane potential / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / positive regulation of protein ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of FZD by ubiquitination / p75NTR recruits signalling complexes / regulation of proteasomal protein catabolic process / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / molecular function activator activity / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLI / Downregulation of TGF-beta receptor signaling
類似検索 - 分子機能
PHD-finger / F-box domain / Jumonji, helical domain / Jumonji helical domain / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. ...PHD-finger / F-box domain / Jumonji, helical domain / Jumonji helical domain / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / SKP1/BTB/POZ domain superfamily / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Leucine-rich repeat domain superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Polyubiquitin-B / S-phase kinase-associated protein 1 / Lysine-specific demethylase 2A
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / 分子置換 / 解像度: 2.61 Å
データ登録者Manczyk, N. / Sicheri, F.
資金援助 カナダ, 1件
組織認可番号国
Canadian Institutes of Health Research (CIHR)FDN 143277 カナダ
引用ジャーナル: Structure / 年: 2018
タイトル: A Structure-Based Strategy for Engineering Selective Ubiquitin Variant Inhibitors of Skp1-Cul1-F-Box Ubiquitin Ligases.
著者: Gorelik, M. / Manczyk, N. / Pavlenco, A. / Kurinov, I. / Sidhu, S.S. / Sicheri, F.
履歴
登録2017年12月20日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年7月18日Provider: repository / タイプ: Initial release
改定 1.12018年8月8日Group: Data collection / Database references / カテゴリ: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
改定 1.22018年9月19日Group: Data collection / Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.page_first
改定 1.32020年1月8日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42020年1月29日Group: Derived calculations / カテゴリ: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
改定 1.52023年10月4日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: S-phase kinase-associated protein 1
B: S-phase kinase-associated protein 1
E: Lysine-specific demethylase 2A
F: Lysine-specific demethylase 2A
G: S-phase kinase-associated protein 1
I: Lysine-specific demethylase 2A
C: Polyubiquitin-B
D: Polyubiquitin-B
H: Polyubiquitin-B


分子量 (理論値)分子数
合計 (水以外)104,2399
ポリマ－104,2399
非ポリマー00
水1,26170
1
A: S-phase kinase-associated protein 1
E: Lysine-specific demethylase 2A
D: Polyubiquitin-B


分子量 (理論値)分子数
合計 (水以外)34,7463
ポリマ－34,7463
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: S-phase kinase-associated protein 1
F: Lysine-specific demethylase 2A
H: Polyubiquitin-B


分子量 (理論値)分子数
合計 (水以外)34,7463
ポリマ－34,7463
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
3
G: S-phase kinase-associated protein 1
I: Lysine-specific demethylase 2A
C: Polyubiquitin-B


分子量 (理論値)分子数
合計 (水以外)34,7463
ポリマ－34,7463
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)60.560, 118.188, 146.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質 S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


分子量: 18808.096 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SKP1, EMC19, OCP2, SKP1A, TCEB1L / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P63208
#2: タンパク質・ペプチド Lysine-specific demethylase 2A / CXXC-type zinc finger protein 8 / F-box and leucine-rich repeat protein 11 / F-box protein FBL7 / F- ...CXXC-type zinc finger protein 8 / F-box and leucine-rich repeat protein 11 / F-box protein FBL7 / F-box protein Lilina / F-box/LRR-repeat protein 11 / JmjC domain-containing histone demethylation protein 1A / [Histone-H3]-lysine-36 demethylase 1A


分子量: 5952.017 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KDM2A, CXXC8, FBL7, FBXL11, JHDM1A, KIAA1004 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q9Y2K7, [histone H3]-dimethyl-L-lysine36 demethylase
#3: タンパク質 Polyubiquitin-B


分子量: 9986.385 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0CG47
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 70 / 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: 2.51 Å3/Da / 溶媒含有率: 51.03 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6 / 詳細: 0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500

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データ収集

回折平均測定温度: 93.15 K
放射光源由来: 回転陽極 / タイプ: RIGAKU FR-E DW / 波長: 1.5418 Å
検出器タイプ: RIGAKU SATURN 944 / 検出器: CCD / 日付: 2016年9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: 1.5418 Å / 相対比: 1
反射解像度: 2.61→50 Å / Num. obs: 32211 / % possible obs: 98.5 % / 冗長度: 6.8 % / Rsym value: 0.102 / Net I/σ(I): 24.7
反射 シェル解像度: 2.61→2.7 Å / 冗長度: 5.2 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 2735 / Rsym value: 1 / % possible all: 85.4

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.12_2829: ???)精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1UBQ, 5JH5, 5IBK

1ubq

5jh5

5ibk


解像度: 2.61→45.09 Å / SU ML: 0.39 / σ(F): 1.33 / 位相誤差: 34.97
Rfactor反射数%反射
Rfree0.294 1640 5.19 %
Rwork0.235 --
obs0.238 31608 96.8 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 2.61→45.09 Å
タンパク質核酸リガンド溶媒全体
原子数6165 0 0 70 6235
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0076274
X-RAY DIFFRACTIONf_angle_d0.8598521
X-RAY DIFFRACTIONf_dihedral_angle_d8.2133793
X-RAY DIFFRACTIONf_chiral_restr0.052998
X-RAY DIFFRACTIONf_plane_restr0.0071087
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6114-2.68830.36381250.30122079X-RAY DIFFRACTION83
2.6883-2.7750.44241130.30992467X-RAY DIFFRACTION96
2.775-2.87420.42071190.33252491X-RAY DIFFRACTION97
2.8742-2.98920.49071300.40692361X-RAY DIFFRACTION94
2.9892-3.12530.47991180.3972468X-RAY DIFFRACTION96
3.1253-3.290.3611500.2782553X-RAY DIFFRACTION100
3.29-3.4960.30921560.24412547X-RAY DIFFRACTION100
3.496-3.76580.2931340.21622579X-RAY DIFFRACTION100
3.7658-4.14460.26211360.22552X-RAY DIFFRACTION99
4.1446-4.74370.27121420.18752519X-RAY DIFFRACTION97
4.7437-5.97440.24121620.20482601X-RAY DIFFRACTION100
5.9744-45.09610.21331550.22751X-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)
12.55280.63540.396.1353.66052.20620.1098-0.87880.21511.00480.6707-0.85481.26790.9985-0.49690.55880.11650.00270.5427-0.0680.5618-8.4628-64.19343.5737
22.2488-5.4028-0.66132.2282.63572.1915-0.0812-0.3857-0.30431.02490.3685-0.3007-0.003-0.4695-0.35370.60670.02990.02170.52830.12390.5229-12.2351-58.580945.7589
32.0715-8.10047.18052.0579-2.35417.2451-1.0407-0.6535-0.40260.8979-0.0104-0.66440.9115-0.8760.19950.48020.05910.1180.56220.12750.7051-22.2624-62.477645.4504
45.2070.77822.65632.7085-0.0155.9681-0.0364-0.3029-0.05350.26320.05320.321-0.13330.1066-0.03550.26430.05240.0880.40640.05080.3837-12.2528-59.070339.1661
55.9709-4.97995.43528.4795-0.17089.2086-0.4128-0.5691-0.02480.48770.09050.6084-0.4174-0.5674-0.12690.4462-0.01120.04520.37010.12690.5801-18.2165-43.353631.9674
64.7878-0.54623.79765.1518-3.74987.9589-0.31530.15950.7031-0.08710.27520.4009-0.386-0.5138-0.17210.29930.00080.0550.26780.04940.4177-19.2467-52.956528.7583
79.9375-4.91174.64847.54280.4345.9824-0.47850.1927-0.2346-0.28550.0420.10760.53140.25830.32560.5967-0.0510.02220.58060.11750.3313-22.2722-49.2259.5472
80.27171.02610.36174.51760.57551.2497-0.1101-1.0009-0.3339-0.86280.5678-0.16821.4839-1.2215-0.5871.3351-0.292-0.52331.16240.23280.8606-34.4354-50.58282.2096
97.1773-1.0774-1.17065.65850.93297.0134-0.3357-1.02490.42040.67150.22230.10710.0035-0.14060.18380.36080.05680.02660.4093-0.0370.3267-17.1737-14.702435.3126
109.1281-2.2086-7.07962.80391.06267.9072-0.4009-0.6609-0.34550.2474-0.0011-0.38460.23980.57990.36860.4602-0.04430.05360.3090.03660.4519-12.4878-31.638325.6481
113.82310.2892-4.47060.5652-0.22777.6491-0.28390.5402-0.2927-0.22390.0993-0.21520.6493-0.34270.11910.42730.00160.00240.40920.01570.3375-6.2253-24.226310.1772
125.3528-2.47291.62972.20482.03751.3489-0.3843-0.1232-0.1246-0.76070.71650.49430.2361-0.2703-0.2270.6194-0.0546-0.00270.50850.14430.3614-24.9976-57.561821.5808
135.835-4.4790.05471.9697-3.94792.1868-0.74890.57480.1821-0.94480.22681.6131-2.23750.5721-0.06740.8054-0.1111-0.10350.52390.120.4845-31.0234-45.00415.285
143.69182.63295.15733.8969-1.292.18990.349-0.4575-0.9346-0.91680.4011.75810.3305-2.3622-0.83540.8796-0.128-0.16910.97160.30760.7318-33.5477-53.686817.0796
158.2328-1.18681.11715.09362.083.5436-0.13430.110.5776-0.4215-0.4102-0.0201-0.52850.50690.63480.5265-0.09890.01860.5290.03130.3045-5.148-17.49314.3576
162.0453-8.22693.80829.3436-3.06267.3647-0.3215-0.545-1.8693-1.38530.9877-0.1550.8976-0.3064-0.23840.5593-0.11740.16270.41660.04190.79551.4971-30.05149.1624
172.33635.4742-2.0972.0262-0.1642.0984-0.1488-0.0562-0.4367-0.6469-0.34990.0687-0.28220.34770.27340.6408-0.02910.02320.5906-0.03820.3879-0.5214-20.3424.9019
188.89641.72571.47829.6835.79636.68260.7226-0.9931-0.16940.41790.4156-0.67680.47641.3088-0.54120.7694-0.10640.00511.233-0.01570.54847.3175-22.343713.8976
199.84712.6788-5.25012.1907-9.19138.7926-0.16560.6452-0.0717-1.22430.6374-0.8039-1.5561-0.9006-0.03931.0035-0.01990.13460.5879-0.28170.872-16.9222-27.995163.4329
205.59063.38533.54833.27411.19419.0295-0.75390.03821.1535-0.31170.2373-0.3111-0.2902-0.43250.52880.51240.007-0.04680.8693-0.4931.0432-21.1296-32.132167.5427
212.8291-0.19831.31875.90461.68196.28850.43870.3395-0.3111-0.2738-0.19860.3279-1.05490.6716-0.13720.6085-0.25190.22760.9006-0.51650.923-20.3043-29.370574.2302
221.6495-0.0973-1.78076.7646-3.79813.8167-0.36530.4108-0.7809-1.41320.05720.38270.6923-0.35850.240.6590.00270.08170.7872-0.38240.9304-20.8868-45.833364.3526
231.0059-0.4809-0.79735.1386-1.71161.5398-0.36210.2763-0.7785-0.5052-0.2264-0.47480.64560.41990.24040.80660.12450.29870.6846-0.3291.2052-16.8029-53.039567.1125
243.8879-2.11410.36516.5979-0.79172.0439-0.02290.1559-1.10180.22680.30860.27980.16790.62340.34090.62310.0520.10110.5415-0.29281.1261-23.4865-44.807876.3167
250.75631.0615-0.99216.63441.6232.2261-1.06510.8983-0.7950.16570.27780.67061.3093-1.18580.62620.9218-0.09070.32020.6148-0.51431.4165-27.0673-53.604872.3152
264.4925-3.40813.85952.5795-3.45532.02390.90010.2578-1.4532-0.33290.58350.0439-1.3374-1.7607-1.31390.87880.17130.43920.88880.02741.5517-23.8173-63.079485.431
275.49470.76927.16197.10612.51819.6341-0.7939-2.5426-0.3661-1.2286-1.1218-1.0201-0.2643-1.42431.61021.23310.11670.59951.2018-0.03191.0434-23.8635-58.492892.5831
281.87523.32511.45519.9913.04352.504-1.3353-0.4616-2.17310.5181-0.0850.83120.8842-0.23410.65191.1848-0.09130.51480.5712-0.35472.0284-32.1914-53.171381.8592
290.97891.0603-0.81191.7072-2.83967.0569-0.76761.5292-1.5902-0.7462-0.2666-0.29931.2218-0.36230.79790.83780.17231.56861.41780.78262.8789-35.6118-54.957987.0336
304.30523.15591.61365.95361.3667.1917-0.1828-0.0789-0.5472-0.3866-0.02530.68480.0715-0.45960.30680.3691-0.0450.01090.5939-0.29080.8814-37.0573-27.872382.3572
313.46651.3302-0.2942.0968-1.48553.32560.0331-0.2316-0.06720.8651-0.51230.9192-0.1465-1.09650.67190.5576-0.01090.05940.4993-0.17650.769-32.6869-22.307191.159
324.2918-1.463-3.20654.7916-3.03036.19370.2791-0.0278-0.12290.7860.0337-1.044-0.32160.5819-0.21660.7217-0.0943-0.060.46-0.21460.7677-24.7619-25.154385.6566
339.1089-2.7742-0.57385.7586-3.14597.7167-0.03970.1126-0.4168-0.92230.4516-0.651-0.0818-0.2687-0.26130.3628-0.08970.02090.5333-0.18150.6663-28.6959-20.413882.1735
340.3349-0.9396-2.13362.1687-0.13047.3604-0.03650.3346-0.9955-0.1084-0.20230.36260.1105-0.7720.2620.4229-0.08650.02020.52490.0130.8249-30.0958-72.437933.5261
350.97810.3457-2.4742.01552.8415.9729-0.10510.6966-0.69060.4969-0.31691.33510.4677-0.6540.18640.326-0.01530.01840.6305-0.1290.8252-32.1867-75.800835.9588
364.523.02761.53718.9769-2.92756.55450.14480.4612-1.1596-0.60220.0904-0.60920.95610.5203-0.07190.47920.05020.2040.3836-0.07590.7697-22.1399-81.315532.0716
376.08571.05431.14618.4722-1.49326.18430.4009-0.1325-0.56290.2309-0.3929-0.36510.59360.12120.12060.43120.06770.08050.3942-0.00870.5681-21.7088-78.820937.3608
384.38193.07941.79632.0752.3447.0979-0.1857-0.17160.75750.5961-0.4253-0.1108-0.70320.37410.85210.3893-0.0668-0.11630.37950.00840.5668-0.88522.322131.3537
392.74253.13640.22168.4934-3.0987.76730.10310.03010.1585-0.9024-0.2838-1.14430.48280.98110.65760.69760.15310.18660.48960.10160.43430.7245-10.641619.7981
407.52922.05553.08129.8844-2.22678.1486-0.2453-0.1051.08370.5252-0.0421-1.3935-0.63860.42820.34680.28160.02320.02240.42860.07050.3797-0.75376.055829.0877
419.74062.2063-5.50166.35731.21229.76870.53241.17540.1105-0.5956-0.51150.6128-0.643-0.1974-0.37680.40550.0209-0.04320.30210.0430.6372-3.35576.468221.9068
428.00991.9252-6.93354.2184-0.44518.1540.00211.17541.5378-0.11470.22470.6029-0.0861-0.7387-0.1140.3986-0.0294-0.05330.3550.1280.5799-8.33860.522820.9538
438.18763.8279-5.47482.02-2.44163.62180.68090.09281.164-0.2019-0.52661.85620.3924-0.5325-0.14830.44490.0371-0.04090.5197-0.11060.6646-14.21790.893334.5842
447.695-2.02944.04992.018-0.02762.23140.27340.05751.3665-1.0726-0.42681.2461-1.3427-1.48510.39070.55360.0199-0.05690.5712-0.11520.6201-14.99429.466326.8622
458.1992-2.0244-2.66388.27643.73684.84880.3789-0.42870.3438-0.1137-0.53540.3306-0.6567-0.58460.23410.38930.04340.05190.35250.04810.4131-8.5034.943231.4267
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -1 THROUGH 12 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 13 THROUGH 23 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 24 THROUGH 32 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 33 THROUGH 67 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 68 THROUGH 96 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 97 THROUGH 126 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 127 THROUGH 146 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 147 THROUGH 155 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 0 THROUGH 67 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 68 THROUGH 96 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 97 THROUGH 162 )
12X-RAY DIFFRACTION12CHAIN 'E' AND (RESID 887 THROUGH 904 )
13X-RAY DIFFRACTION13CHAIN 'E' AND (RESID 905 THROUGH 915 )
14X-RAY DIFFRACTION14CHAIN 'E' AND (RESID 916 THROUGH 931 )
15X-RAY DIFFRACTION15CHAIN 'F' AND (RESID 887 THROUGH 904 )
16X-RAY DIFFRACTION16CHAIN 'F' AND (RESID 905 THROUGH 913 )
17X-RAY DIFFRACTION17CHAIN 'F' AND (RESID 914 THROUGH 923 )
18X-RAY DIFFRACTION18CHAIN 'F' AND (RESID 924 THROUGH 931 )
19X-RAY DIFFRACTION19CHAIN 'G' AND (RESID 0 THROUGH 7 )
20X-RAY DIFFRACTION20CHAIN 'G' AND (RESID 8 THROUGH 32 )
21X-RAY DIFFRACTION21CHAIN 'G' AND (RESID 33 THROUGH 51 )
22X-RAY DIFFRACTION22CHAIN 'G' AND (RESID 52 THROUGH 86 )
23X-RAY DIFFRACTION23CHAIN 'G' AND (RESID 87 THROUGH 96 )
24X-RAY DIFFRACTION24CHAIN 'G' AND (RESID 97 THROUGH 110 )
25X-RAY DIFFRACTION25CHAIN 'G' AND (RESID 111 THROUGH 131 )
26X-RAY DIFFRACTION26CHAIN 'G' AND (RESID 132 THROUGH 139 )
27X-RAY DIFFRACTION27CHAIN 'G' AND (RESID 140 THROUGH 144 )
28X-RAY DIFFRACTION28CHAIN 'I' AND (RESID 889 THROUGH 915 )
29X-RAY DIFFRACTION29CHAIN 'I' AND (RESID 916 THROUGH 927 )
30X-RAY DIFFRACTION30CHAIN 'C' AND (RESID -2 THROUGH 25 )
31X-RAY DIFFRACTION31CHAIN 'C' AND (RESID 26 THROUGH 42 )
32X-RAY DIFFRACTION32CHAIN 'C' AND (RESID 43 THROUGH 62 )
33X-RAY DIFFRACTION33CHAIN 'C' AND (RESID 63 THROUGH 81 )
34X-RAY DIFFRACTION34CHAIN 'D' AND (RESID -1 THROUGH 16 )
35X-RAY DIFFRACTION35CHAIN 'D' AND (RESID 17 THROUGH 25 )
36X-RAY DIFFRACTION36CHAIN 'D' AND (RESID 26 THROUGH 64 )
37X-RAY DIFFRACTION37CHAIN 'D' AND (RESID 65 THROUGH 83 )
38X-RAY DIFFRACTION38CHAIN 'H' AND (RESID -1 THROUGH 9 )
39X-RAY DIFFRACTION39CHAIN 'H' AND (RESID 10 THROUGH 16 )
40X-RAY DIFFRACTION40CHAIN 'H' AND (RESID 17 THROUGH 30 )
41X-RAY DIFFRACTION41CHAIN 'H' AND (RESID 31 THROUGH 42 )
42X-RAY DIFFRACTION42CHAIN 'H' AND (RESID 43 THROUGH 52 )
43X-RAY DIFFRACTION43CHAIN 'H' AND (RESID 53 THROUGH 57 )
44X-RAY DIFFRACTION44CHAIN 'H' AND (RESID 58 THROUGH 62 )
45X-RAY DIFFRACTION45CHAIN 'H' AND (RESID 63 THROUGH 82 )

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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