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- PDB-5ohm: K33-specific affimer bound to K33 diUb -

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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: 5ohm
タイトルK33-specific affimer bound to K33 diUb
要素
  • K33-specific affimer
  • Polyubiquitin-C
キーワードSIGNALING PROTEIN / ubiquitin / cystatin
機能・相同性
機能・相同性情報


Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation ...Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Regulation of BACH1 activity / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Iron uptake and transport / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Peroxisomal protein import / Degradation of AXIN / Recognition of DNA damage by PCNA-containing replication complex / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Stabilization of p53 / Regulation of TNFR1 signaling / EGFR downregulation / Termination of translesion DNA synthesis / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Hedgehog ligand biogenesis / Negative regulation of FGFR4 signaling / Defective CFTR causes cystic fibrosis / G2/M Checkpoints / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2
類似検索 - 分子機能
: / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / 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 / Polyubiquitin-C
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
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: 3.8 Å
データ登録者Michel, M.A. / Komander, D.
引用ジャーナル: Mol. Cell / 年: 2017
タイトル: Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling.
著者: Michel, M.A. / Swatek, K.N. / Hospenthal, M.K. / Komander, D.
履歴
登録2017年7月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年10月4日Provider: repository / タイプ: Initial release
改定 1.12017年10月18日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.22019年1月2日Group: Data collection / Database references / Source and taxonomy
カテゴリ: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
改定 1.32024年1月17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: Polyubiquitin-C
C: Polyubiquitin-C
E: Polyubiquitin-C
G: Polyubiquitin-C
I: Polyubiquitin-C
K: Polyubiquitin-C
D: K33-specific affimer
H: K33-specific affimer
L: K33-specific affimer
B: K33-specific affimer
F: K33-specific affimer
J: K33-specific affimer
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)134,54414
ポリマ－131,48412
非ポリマー3,0602
水00
1
A: Polyubiquitin-C
C: Polyubiquitin-C
D: K33-specific affimer
B: K33-specific affimer


分子量 (理論値)分子数
合計 (水以外)43,8284
ポリマ－43,8284
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-36 kcal/mol
Surface area14980 Å2
手法PISA
2
E: Polyubiquitin-C
G: Polyubiquitin-C
H: K33-specific affimer
F: K33-specific affimer
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,3585
ポリマ－43,8284
非ポリマー1,5301
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-36 kcal/mol
Surface area15030 Å2
手法PISA
3
I: Polyubiquitin-C
K: Polyubiquitin-C
L: K33-specific affimer
J: K33-specific affimer
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,3585
ポリマ－43,8284
非ポリマー1,5301
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-38 kcal/mol
Surface area14950 Å2
手法PISA
単位格子
Length a, b, c (Å)55.866, 149.604, 73.788
Angle α, β, γ (deg.)90.00, 110.44, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Polyubiquitin-C


分子量: 8675.962 Da / 分子数: 6 / 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, UniProt: P0CG64*PLUS
#2: タンパク質
K33-specific affimer


分子量: 13238.074 Da / 分子数: 6 / 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)
#3: 化合物 ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


分子量: 1529.829 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C69H140O35 / コメント: 沈殿剤*YM

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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: 2.2 Å3/Da / 溶媒含有率: 44.03 %
結晶化温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.4 / 詳細: 20% PEG3350 0.2M potassium thiocyanate

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データ収集

回折平均測定温度: 110 K
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I04-1 / 波長: 0.91741 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2014年12月12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: 0.91741 Å / 相対比: 1
反射解像度: 3.8→48.46 Å / Num. obs: 10962 / % possible obs: 97.9 % / 冗長度: 3.3 % / Rmerge(I) obs: 0.237 / Net I/σ(I): 3.8
反射 シェル解像度: 3.8→4.25 Å / 冗長度: 3.4 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.665 / % possible all: 99.2

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10.1_2155: ???)精密化
XDSデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5OHV

5ohv


解像度: 3.8→48.46 Å / SU ML: 0.59 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 33.95 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2825 499 4.55 %
Rwork0.2328 --
obs0.2352 10962 97.59 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 3.8→48.46 Å
タンパク質核酸リガンド溶媒全体
原子数7123 0 36 0 7159
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0037285
X-RAY DIFFRACTIONf_angle_d0.6559931
X-RAY DIFFRACTIONf_dihedral_angle_d11.9484300
X-RAY DIFFRACTIONf_chiral_restr0.0441217
X-RAY DIFFRACTIONf_plane_restr0.0041250
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.18230.35731120.29452648X-RAY DIFFRACTION99
4.1823-4.7870.25481420.2122575X-RAY DIFFRACTION97
4.787-6.02930.28121150.24152571X-RAY DIFFRACTION96
6.0293-48.46420.27261300.21222670X-RAY DIFFRACTION99
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)
12.41641.0558-0.11372.50950.11141.28890.6216-0.4190.30660.4217-0.118-0.325-0.66560.50760.080.725-0.66190.01240.6046-0.35440.125-32.9672-23.549119.3506
22.8640.7627-0.43892.49940.81620.7420.718-0.48370.60940.26090.08920.3287-0.0572-0.09290.71441.6293-1.0776-0.10930.7810.48331.0057-32.4043-25.055322.5693
30.31020.15620.12070.8490.26640.10180.1554-0.58030.01541.04810.4258-0.37220.27280.3437-0.35172.2702-0.5804-0.0371.6149-0.57380.6106-33.5617-30.672328.3508
40.61110.19850.14151.25250.76161.81570.637-0.4031-0.71621.22420.1867-0.24460.96080.2986-0.08741.6716-0.2616-0.66771.0418-0.04220.4103-35.673-36.787322.9399
54.91790.5115-0.9099.85994.37664.88450.155-0.0316-0.89930.25130.0146-0.77850.89961.7516-0.36510.51460.29150.45360.9824-0.68171.0807-26.1783-32.971512.964
63.8746-0.36951.294.17134.40515.39480.5696-1.479-0.84131.79870.0947-1.07191.47811.5997-0.2991.5883-0.0335-0.96291.40330.43711.596-22.3112-33.119421.3759
73.4052-3.56221.51549.48262.69093.85420.651-0.35571.11640.4348-0.3584-0.7589-0.68791.1266-0.17311.1635-1.06510.13551.23190.39090.6301-24.7102-22.024717.194
81.4045-0.3649-1.24470.09480.31741.09890.8703-0.2053-0.0794-0.15040.5679-0.03020.7833-0.1569-0.48541.2997-0.2892-0.36580.66610.10910.8444-36.2675-35.681118.2167
90.49990.73230.06421.523-0.57690.8339-0.3004-0.35810.20081.603-0.52690.85690.9185-0.30790.19230.8093-0.95720.48560.5747-0.08240.9386-52.5287-46.322920.129
106.5665-3.5619-1.09225.2476-1.29181.25170.3905-1.3423-0.7310.8113-0.2741-0.1352-0.16510.1846-0.16671.034-0.64410.03651.25180.13530.6214-52.0526-40.696327.856
110.80270.143-0.94710.3511-0.17891.11440.122-0.27170.10690.062-0.13210.0002-0.12860.24530.0071.0994-0.42011.04581.23520.18310.4922-49.8155-34.591923.0831
124.21891.085-1.44664.8045-3.13674.8343-0.0755-0.14880.03290.2994-0.12590.532-0.0721-0.18740.12081.9520.37650.70681.1077-0.45760.846-59.9717-35.817617.2052
131.54420.2356-0.4460.6271-0.731.18110.23810.15070.76170.6403-0.64270.07040.1359-0.296-0.2630.4484-1.14450.705-0.10470.15461.1929-56.2024-40.193217.8244
141.2794-1.28672.85925.3855-1.10617.16430.18090.32010.0814-0.2104-0.6060.8648-1.0493-1.53920.05070.54380.52730.33250.7394-0.02871.6922-45.0571-0.4505-10.4882
150.0689-0.0420.31940.75050.34012.04-0.18950.1206-0.0950.3312-0.12050.44990.3692-0.833-0.02280.92950.08711.40471.01190.32621.5135-39.85571.4903-9.6066
161.6336-0.9614-2.11860.57221.24272.7517-0.07170.76890.328-0.0733-0.06860.53760.3376-0.60360.33721.09420.26090.35631.7094-0.35571.7108-54.68152.5962-17.6237
174.36552.7334-3.35611.819-1.42986.85310.066-1.0567-0.29250.77050.72070.32430.4323-0.4446-0.50181.06230.35810.25560.94550.5311.3799-43.97677.5495-18.336
180.4650.6651-0.32613.21571.2071.47280.08290.2195-0.1594-0.2786-0.10710.0720.88960.2575-0.0241.62391.0158-0.69520.8762-0.16020.869-37.87933.7149-22.1004
194.9687-1.0889-5.38360.44110.80026.53420.27710.6702-1.2274-0.49810.14630.38781.25210.7981-0.52120.85580.4951-0.29830.8486-0.61462.1594-43.5558-9.1134-20.0496
202.73961.8761-4.56131.2844-3.12497.60010.99150.94580.2662-0.00220.48590.5231-0.4907-0.6064-1.39291.15130.7351-0.41582.09030.31912.4908-47.9452-2.3802-26.3365
210.7437-0.6941.29720.6857-1.24872.29680.97691.416-0.5158-0.10450.40360.91250.0127-1.1032-1.46171.06070.3415-0.40341.75480.44462.4893-52.3149-4.6461-21.1803
224.16494.2454-1.83314.3291-1.85080.93781.26041.3029-0.5856-0.77550.3471.5138-0.3675-0.7447-1.26931.07840.18540.1050.699-0.26321.142-51.4035-5.7662-11.9405
230.7848-0.05650.43010.3927-0.7231.55790.54680.70410.8036-1.1407-0.7522-0.758-0.31550.2764-0.24531.55070.62950.27440.8233-0.16111.2715-35.6340.0809-20.7783
240.35610.2988-0.47110.8191-1.17491.7333-0.148-0.12010.1629-0.4083-0.6412-0.8681-0.38271.0904-0.42442.2381-0.72661.98361.0889-0.23092.2929-18.4647.9442-23.1345
250.17550.10020.30072.03110.13730.5171-0.3264-0.3770.51610.23620.3412-0.4838-0.8215-0.4540.11191.690.41690.60450.91150.01122.205-24.481714.5727-19.5794
262.03531.2259-0.88340.8039-0.21212.16711.0005-0.48680.23681.1267-0.0460.971-0.1775-0.3802-0.23812.053-0.33340.81350.7744-0.10562.2462-23.91217.7579-13.6077
270.6423-0.7144-0.16280.79430.18150.04150.0874-0.20511.0910.2362-0.25670.3368-0.59090.09570.09981.6994-0.8126-0.28190.94390.02482.3734-18.118413.3099-10.3043
286.3876-0.38765.00985.6865-3.74186.0176-1.18271.64651.05790.2484-0.3655-0.2421-0.70720.69661.47630.5546-0.09330.50841.1453-0.06211.949-9.90419.4919-18.1098
291.043-0.3352-0.10376.92890.31623.70150.3039-0.51410.2531-0.2428-0.4586-0.3542-0.2760.6474-0.80711.2196-0.06360.73850.96590.4651.6928-25.89354.6493-14.4041
301.3067-0.9342-0.88854.1478-3.19394.8158-0.091-0.0125-0.24662.0951-0.3857-0.00890.94031.58150.41722.39780.126-1.16450.702-0.04221.6673-48.9759-2.040826.0632
310.27450.2001-0.57830.35330.05152.25580.71640.42110.472-0.88340.5094-0.5218-1.197-0.7281-0.93473.14470.1724-0.36950.9540.01131.2007-55.2933-7.936923.5206
321.989-2.66531.31523.5797-1.62797.36590.76960.1523-0.47770.5464-1.2039-0.31330.57880.27570.50151.8616-0.14030.13050.250.09152.5479-54.2306-2.074916.3684
330.31530.39380.88092.37140.91172.47910.3610.6873-0.6234-0.4162-0.4555-0.42340.94711.17640.1722.40070.5741-0.12980.8977-0.13091.8169-47.643-7.459512.3461
345.33610.68782.85831.7358-2.03365.04220.19910.29830.0699-0.3803-0.1215-0.22610.25841.16410.20291.16770.1572-0.28671.56630.281.0811-40.8005-3.763920.0858
351.1953-0.51-1.88221.8342-0.06713.43450.04230.3267-0.21770.1788-0.1981-0.23840.29351.0817-0.40920.9717-0.1604-1.07240.86650.19421.0099-55.48312.086318.0205
360.5048-0.1071-1.12270.70010.5532.62770.5939-0.2942-0.2746-0.1246-0.01511.11951.2346-1.33170.02641.4723-0.7069-0.82810.94240.04891.5998-76.68785.915811.661
370.83290.18460.82210.11310.17990.82840.248-0.6461-0.09420.5925-0.13171.21151.3146-0.935-0.45141.1804-0.2471-0.02981.08750.39781.5206-74.06044.353715.0723
380.8005-0.8954-0.8761.82860.33911.45070.4348-0.08250.1454-0.29990.0289-0.2481-0.23750.0273-0.13891.6898-0.9288-0.61111.32250.76161.3676-74.2505-1.947420.6992
390.7648-0.85710.06091.2618-0.70583.09960.466-0.9032-0.94120.59540.1854-0.92990.5906-0.2879-0.3021.1015-0.5167-0.03481.96660.42491.8052-70.25136.414323.6621
403.95090.69630.34412.6954-0.20850.6080.0966-0.3501-0.27440.06750.1430.38560.2853-0.6097-0.14081.198-1.2208-0.36631.98650.22851.1553-78.21548.167527.7696
412.63173.3742-1.39565.9019-0.63384.04680.7374-1.06810.08311.2274-0.10820.50270.6943-1.5907-0.80440.6916-0.44020.19311.34020.01411.403-75.69459.715320.0974
427.1655-2.28564.06982.4193-0.18523.28820.20990.18870.64680.13890.24510.04010.34670.66220.28520.6249-0.16780.18890.5264-0.05560.8329-49.0747-23.0488-1.6142
434.2359-1.4331-0.08818.3225-0.49176.83590.45750.35031.1350.1008-0.83380.0383-0.5104-1.0711-0.10280.80650.09060.04990.77050.12560.7248-50.2188-19.1657-1.1683
446.33060.04750.00875.98890.78555.6459-0.14530.45941.14960.15240.27930.0241-0.314-0.29490.14430.4426-0.3972-0.32090.4603-0.12420.4971-45.3035-23.61753.2478
453.61710.026-0.11424.54860.79981.5710.3535-0.28210.60010.16620.403-0.0871-0.07740.08580.53970.0874-0.35620.54950.36180.18961.6461-46.143-26.40725.2391
463.5334-2.18690.52192.4273-1.12734.08430.66011.0364-0.3051-0.35570.3903-1.6327-0.20080.9226-0.20520.8314-0.03760.32690.878-0.10840.8476-19.0373-12.8362-1.7668
471.3231-1.63242.4364.43270.17878.67570.35160.27480.49220.88380.0094-1.03580.19441.8625-0.2190.7705-0.1060.09550.6436-0.15991.9052-14.3968-14.89244.5963
482.01560.2043-0.93581.1684-1.52762.72240.10181.00820.5152-0.12360.63960.449-0.053-0.7160.03250.7105-0.79890.5450.5909-0.2011.6534-37.0324-13.4515-1.8194
492.72582.1761.43333.2437-0.02815.866-0.5440.92790.2381-0.21410.6478-0.16140.12180.1386-0.33070.3334-0.27530.29990.6548-0.02721.3581-27.7768-13.34771.4363
502.92340.4281.85423.93851.89973.3257-0.2850.58280.28890.4120.2183-0.65890.05630.52040.07430.4474-0.18840.54910.8322-0.04231.3417-22.7161-11.06142.95
515.9208-0.57915.19140.6326-0.37044.5378-0.08630.329-0.4101-0.7038-0.2019-0.30210.4008-0.1361-0.07350.5657-0.5593-0.11490.7674-0.16160.5918-28.211-9.0455-7.9158
522.9569-0.76752.53222.16520.23223.80760.3809-0.3195-0.1772-0.13750.36780.48950.86150.3451-1.07450.9223-0.4504-0.87961.35280.1370.8363-59.588328.040126.1555
538.0178-1.7274-3.36288.3381-1.89822.348-0.5435-0.2635-0.76051.1425-0.88520.0514-0.31540.30211.39611.93080.0499-0.55550.96480.13431.4837-63.166134.409929.7128
542.24270.63360.58942.0680.22882.8193-0.3441-0.51840.33641.0817-0.186-0.4872-0.54660.00220.48171.6862-0.1141-0.02621.57080.38520.9987-45.998317.15828.0363
550.69480.14550.62070.77920.32051.8995-0.0383-0.90690.60490.8469-0.033-0.0879-0.5941-0.19291.65542.21240.0842-1.16671.3799-0.32460.8112-56.142425.636330.4406
561.2470.55370.7853.24251.12742.7297-0.2434-1.07190.42050.9799-0.33-0.4674-0.5228-0.34490.38281.1094-0.1471-0.81991.0358-0.34751.2496-55.280215.859921.6149
573.4559-2.0535-1.92987.92721.52664.54680.67440.11920.4485-1.15780.0047-0.7989-0.72850.3682-0.10551.0368-0.21620.49240.2209-0.33430.7201-31.5633-43.249-3.7352
585.1159-0.3128-1.61124.30621.16173.08580.2799-0.0942-0.19830.2785-0.0671-0.2241-0.12590.13250.41080.4574-0.2037-0.05670.63370.17340.871-35.634-48.7158-3.0313
597.71811.67960.80188.76510.50655.88280.45910.9336-1.0472-0.1426-0.654-0.40480.38770.3536-0.11630.6798-0.01150.03310.6689-0.14360.8819-35.0265-48.4809-0.4601
600.0003-0.04240.0235.90881.79436.35450.1696-1.3596-1.0920.70350.444-0.0857-0.15460.2772-0.680.3823-0.2040.07740.42790.26671.097-39.5235-41.20225.3311
615.01241.72580.59029.03540.77756.3046-0.1740.7604-1.3685-1.24430.5769-1.31641.09780.7586-0.05071.45960.1340.19190.9872-0.35131.6553-25.2992-20.9288-24.5119
621.11-0.4566-0.01563.22540.25212.7364-0.01661.0883-1.026-1.2001-0.3658-1.43020.11160.9332-0.68051.36750.14890.81341.0233-0.35690.9206-24.3033-16.3125-25.1106
631.49581.9517-1.57423.0134-0.30848.80640.1407-0.6273-0.41450.377-0.18370.0845-1.29330.2491-0.36570.29340.0160.05060.46910.04621.3858-51.573919.65142.0575
640.01010.13380.24984.0234-0.99954.96030.5663-0.1577-0.2615-0.04930.1491-0.709-0.5347-0.59770.24360.6845-0.2502-0.23960.26240.40271.3504-54.508817.41421.3727
654.4617-1.8882-4.13377.22092.97848.368-0.0626-0.30290.15130.9-0.10190.22681.25640.30880.31080.6851-0.0792-0.280.58830.12821.2669-55.920114.42277.934
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 22 )
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 34 )
4X-RAY DIFFRACTION4chain 'A' and (resid 35 through 44 )
5X-RAY DIFFRACTION5chain 'A' and (resid 45 through 49 )
6X-RAY DIFFRACTION6chain 'A' and (resid 50 through 59 )
7X-RAY DIFFRACTION7chain 'A' and (resid 60 through 65 )
8X-RAY DIFFRACTION8chain 'A' and (resid 66 through 74 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 22 )
10X-RAY DIFFRACTION10chain 'C' and (resid 23 through 34 )
11X-RAY DIFFRACTION11chain 'C' and (resid 35 through 44 )
12X-RAY DIFFRACTION12chain 'C' and (resid 45 through 54 )
13X-RAY DIFFRACTION13chain 'C' and (resid 55 through 74 )
14X-RAY DIFFRACTION14chain 'E' and (resid 1 through 7 )
15X-RAY DIFFRACTION15chain 'E' and (resid 8 through 16 )
16X-RAY DIFFRACTION16chain 'E' and (resid 17 through 22 )
17X-RAY DIFFRACTION17chain 'E' and (resid 23 through 34 )
18X-RAY DIFFRACTION18chain 'E' and (resid 35 through 44 )
19X-RAY DIFFRACTION19chain 'E' and (resid 45 through 49 )
20X-RAY DIFFRACTION20chain 'E' and (resid 50 through 54 )
21X-RAY DIFFRACTION21chain 'E' and (resid 55 through 59 )
22X-RAY DIFFRACTION22chain 'E' and (resid 60 through 65 )
23X-RAY DIFFRACTION23chain 'E' and (resid 66 through 75 )
24X-RAY DIFFRACTION24chain 'G' and (resid 1 through 22 )
25X-RAY DIFFRACTION25chain 'G' and (resid 23 through 34 )
26X-RAY DIFFRACTION26chain 'G' and (resid 35 through 49 )
27X-RAY DIFFRACTION27chain 'G' and (resid 50 through 54 )
28X-RAY DIFFRACTION28chain 'G' and (resid 55 through 65 )
29X-RAY DIFFRACTION29chain 'G' and (resid 66 through 74 )
30X-RAY DIFFRACTION30chain 'I' and (resid 1 through 22 )
31X-RAY DIFFRACTION31chain 'I' and (resid 23 through 34 )
32X-RAY DIFFRACTION32chain 'I' and (resid 35 through 49 )
33X-RAY DIFFRACTION33chain 'I' and (resid 50 through 54 )
34X-RAY DIFFRACTION34chain 'I' and (resid 55 through 65 )
35X-RAY DIFFRACTION35chain 'I' and (resid 66 through 73 )
36X-RAY DIFFRACTION36chain 'K' and (resid 1 through 6 )
37X-RAY DIFFRACTION37chain 'K' and (resid 7 through 22 )
38X-RAY DIFFRACTION38chain 'K' and (resid 23 through 34 )
39X-RAY DIFFRACTION39chain 'K' and (resid 35 through 49 )
40X-RAY DIFFRACTION40chain 'K' and (resid 50 through 54 )
41X-RAY DIFFRACTION41chain 'K' and (resid 55 through 73 )
42X-RAY DIFFRACTION42chain 'D' and (resid 33 through 74 )
43X-RAY DIFFRACTION43chain 'D' and (resid 75 through 90 )
44X-RAY DIFFRACTION44chain 'D' and (resid 91 through 105 )
45X-RAY DIFFRACTION45chain 'D' and (resid 106 through 121 )
46X-RAY DIFFRACTION46chain 'H' and (resid 33 through 52 )
47X-RAY DIFFRACTION47chain 'H' and (resid 53 through 62 )
48X-RAY DIFFRACTION48chain 'H' and (resid 63 through 73 )
49X-RAY DIFFRACTION49chain 'H' and (resid 74 through 86 )
50X-RAY DIFFRACTION50chain 'H' and (resid 87 through 103 )
51X-RAY DIFFRACTION51chain 'H' and (resid 104 through 121 )
52X-RAY DIFFRACTION52chain 'L' and (resid 32 through 52 )
53X-RAY DIFFRACTION53chain 'L' and (resid 53 through 62 )
54X-RAY DIFFRACTION54chain 'L' and (resid 63 through 73 )
55X-RAY DIFFRACTION55chain 'L' and (resid 74 through 103 )
56X-RAY DIFFRACTION56chain 'L' and (resid 104 through 120 )
57X-RAY DIFFRACTION57chain 'B' and (resid 32 through 52 )
58X-RAY DIFFRACTION58chain 'B' and (resid 53 through 73 )
59X-RAY DIFFRACTION59chain 'B' and (resid 74 through 104 )
60X-RAY DIFFRACTION60chain 'B' and (resid 105 through 120 )
61X-RAY DIFFRACTION61chain 'F' and (resid 32 through 73 )
62X-RAY DIFFRACTION62chain 'F' and (resid 74 through 122 )
63X-RAY DIFFRACTION63chain 'J' and (resid 32 through 73 )
64X-RAY DIFFRACTION64chain 'J' and (resid 74 through 105 )
65X-RAY DIFFRACTION65chain 'J' and (resid 106 through 121 )

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万見について

-
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