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- PDB-5eya: TRIM25 RING domain in complex with Ubc13-Ub conjugate -

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基本情報

登録情報
データベース: PDB / ID: 5eya
タイトルTRIM25 RING domain in complex with Ubc13-Ub conjugate
要素
  • Polyubiquitin-B
  • Tripartite motif-containing 25 variant
  • Ubiquitin-conjugating enzyme E2 N
キーワードSIGNALING PROTEIN/Transferase / Complex / E3 ligase / ubiquitination / SIGNALING PROTEIN-Transferase complex
機能・相同性
機能・相同性情報


: / RIG-I binding / regulation of viral entry into host cell / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / suppression of viral release by host / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / host-mediated suppression of symbiont invasion / DNA double-strand break processing ...: / RIG-I binding / regulation of viral entry into host cell / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / suppression of viral release by host / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / host-mediated suppression of symbiont invasion / DNA double-strand break processing / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / Modulation of host responses by IFN-stimulated genes / postreplication repair / response to vitamin D / symbiont entry into host cell via disruption of host cell glycocalyx / TRAF6 mediated IRF7 activation / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / symbiont entry into host cell via disruption of host cell envelope / cytoplasmic pattern recognition receptor signaling pathway / virus tail / ligase activity / RSV-host interactions / ubiquitin conjugating enzyme activity / TRAF6 mediated NF-kB activation / positive regulation of intracellular signal transduction / viral release from host cell / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / positive regulation of DNA-binding transcription factor activity / protein K48-linked ubiquitination / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / regulation of DNA repair / TICAM1, RIP1-mediated IKK complex recruitment / ERAD pathway / negative regulation of TORC1 signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / antiviral innate immune response / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / positive regulation of DNA repair / cellular response to leukemia inhibitory factor / Termination of translesion DNA synthesis / ubiquitin binding / NOD1/2 Signaling Pathway / double-strand break repair via homologous recombination / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Nonhomologous End-Joining (NHEJ) / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / Formation of Incision Complex in GG-NER / positive regulation of NF-kappaB transcription factor activity / FCERI mediated NF-kB activation / G2/M DNA damage checkpoint / PKR-mediated signaling / RING-type E3 ubiquitin transferase / Interleukin-1 signaling / Aggrephagy / response to estrogen / SARS-CoV-1 activates/modulates innate immune responses / Ovarian tumor domain proteases / protein polyubiquitination / cytoplasmic stress granule / Interferon gamma signaling / ubiquitin-protein transferase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / T cell receptor signaling pathway / Processing of DNA double-strand break ends / regulation of protein localization / TRAF3-dependent IRF activation pathway / response to oxidative stress / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / nuclear body / cadherin binding / innate immune response / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol
類似検索 - 分子機能
TRIM25, PRY/SPRY domain / : / zinc finger of C3HC4-type, RING / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / Pectate lyase superfamily protein ...TRIM25, PRY/SPRY domain / : / zinc finger of C3HC4-type, RING / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / Pectin lyase fold / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Pectin lyase fold/virulence factor / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Tail fiber / Ubiquitin-conjugating enzyme E2 N / E3 ubiquitin/ISG15 ligase TRIM25 / E3 ubiquitin/ISG15 ligase TRIM25
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 / 解像度: 2.4 Å
データ登録者Pornillos, O. / Sanchez, J.G.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM112508 米国
引用ジャーナル: Cell Rep / 年: 2016
タイトル: Mechanism of TRIM25 Catalytic Activation in the Antiviral RIG-I Pathway.
著者: Sanchez, J.G. / Chiang, J.J. / Sparrer, K.M. / Alam, S.L. / Chi, M. / Roganowicz, M.D. / Sankaran, B. / Gack, M.U. / Pornillos, O.
履歴
登録2015年11月24日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年8月17日Provider: repository / タイプ: Initial release
改定 1.12017年9月27日Group: Author supporting evidence / Derived calculations / カテゴリ: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
改定 1.22019年12月25日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32024年10月9日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Ubiquitin-conjugating enzyme E2 N
F: Tripartite motif-containing 25 variant
G: Tripartite motif-containing 25 variant
B: Ubiquitin-conjugating enzyme E2 N
C: Polyubiquitin-B
D: Polyubiquitin-B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)70,79310
ポリマ－70,5316
非ポリマー2624
水3,243180
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)53.047, 75.779, 169.101
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A
21chain B
12chain C
22chain D
13chain F
23chain G

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASNASNchain AAA3 - 1513 - 151
21GLYGLYASNASNchain BBD3 - 1513 - 151
12METMETGLYGLYchain CCE1 - 761 - 76
22METMETGLYGLYchain DDF1 - 761 - 76
13ZNZNZNZNchain FFG - H101 - 102
23ZNZNZNZNchain GGI - J101 - 102

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質 Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


分子量: 17183.807 Da / 分子数: 2 / 変異: C87K / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2N, BLU / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#2: タンパク質 Tripartite motif-containing 25 variant


分子量: 9504.903 Da / 分子数: 2 / Fragment: UNP residues 12-97 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q59GW5, UniProt: Q14258*PLUS
#3: タンパク質 Polyubiquitin-B


分子量: 8576.831 Da / 分子数: 2 / Fragment: UNP residues 1-76 / 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: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 180 / 由来タイプ: 天然 / 式: H2O
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: 2.41 Å3/Da / 溶媒含有率: 48.95 %
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 / 詳細: 0.2 M Li citrate, 20% PEG 3350

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データ収集

回折平均測定温度: 100 K
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: 0.97 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2014年9月23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: 0.97 Å / 相対比: 1
反射解像度: 2.4→50 Å / Num. obs: 27181 / % possible obs: 98.2 % / 冗長度: 8.1 % / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.066 / Rrim(I) all: 0.191 / Χ2: 0.736 / Net I/av σ(I): 9.625 / Net I/σ(I): 3.9 / Num. measured all: 220683
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.494.80.74323380.7240.3310.8210.45586.4
2.49-2.596.40.7426000.7550.3060.8050.47195.8
2.59-2.77.90.70527250.8580.2650.7550.48499.9
2.7-2.858.90.57527150.9140.2050.6110.525100
2.85-3.0290.41327340.9560.1460.4380.565100
3.02-3.2690.26627370.9850.0940.2820.648100
3.26-3.588.90.17827730.9930.0630.1890.777100
3.58-4.18.80.1327770.9950.0460.1381.148100
4.1-5.178.70.11928030.9920.0430.1270.97100
5.17-508.20.06629790.9990.0240.071.024100

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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
PHENIX精密化
PDB_EXTRACT3.15データ抽出
HKL-2000データ削減
PHENIX位相決定
精密化解像度: 2.4→28.966 Å / SU ML: 0.29 / 交差検証法: FREE R-VALUE / σ(F): 0.16 / 位相誤差: 24.32 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2275 1786 7.25 %
Rwork0.1891 22836 -
obs0.1919 24622 89.7 %
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
原子変位パラメータBiso max: 157.93 Å2 / Biso mean: 46.0471 Å2 / Biso min: 13.43 Å2
精密化ステップサイクル: final / 解像度: 2.4→28.966 Å
タンパク質核酸リガンド溶媒全体
原子数4826 0 4 180 5010
Biso mean--26.67 37.82 -
残基数----612
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0064957
X-RAY DIFFRACTIONf_angle_d1.0986733
X-RAY DIFFRACTIONf_chiral_restr0.041757
X-RAY DIFFRACTIONf_plane_restr0.005878
X-RAY DIFFRACTIONf_dihedral_angle_d14.7661887
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A1740X-RAY DIFFRACTION8.074TORSIONAL
12B1740X-RAY DIFFRACTION8.074TORSIONAL
21C902X-RAY DIFFRACTION8.074TORSIONAL
22D902X-RAY DIFFRACTION8.074TORSIONAL
31F856X-RAY DIFFRACTION8.074TORSIONAL
32G856X-RAY DIFFRACTION8.074TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.46490.3916980.28681261135966
2.4649-2.53740.27741160.25911473158976
2.5374-2.61920.26311230.23871585170883
2.6192-2.71270.26941320.23461686181887
2.7127-2.82130.27131340.2281713184789
2.8213-2.94960.27261390.2341784192392
2.9496-3.10490.28051420.21081799194193
3.1049-3.29920.25331420.21121823196594
3.2992-3.55350.23591470.20171870201796
3.5535-3.91030.23441470.17811899204697
3.9103-4.47440.18011530.14161950210398
4.4744-5.63040.17561520.14461935208797
5.6304-28.96850.18431610.16452058221997
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)
11.23940.27510.561.17020.43181.28260.0238-0.0522-0.6344-0.26680.0228-0.52280.5233-0.5701-0.02270.6622-0.5349-0.11540.1939-0.5398-0.2997-25.1007-11.242-15.6566
25.8962-0.7183-2.32581.70870.28661.3448-0.1455-0.37-0.71990.4969-0.0369-0.03520.80460.23560.03590.57990.0105-0.01370.36240.04230.3436-15.7739-11.9078-8.6204
33.21340.99790.28191.1776-0.05591.3672-0.38020.5116-0.32460.04130.2571-0.08740.4508-0.03120.07140.34940.0112-0.02340.3001-0.02520.1958-9.8921-4.1775-6.6646
43.24583.02230.9297.0249-1.76462.48570.391-0.36970.4776-0.0285-0.07560.3523-0.2447-1.2342-0.20010.3887-0.05050.02250.4389-0.05320.1905-26.3841.7104-13.973
53.1860.73291.25071.27650.1162.37170.0257-0.30520.3552-0.0216-0.08180.0643-0.08480.26820.10960.261-0.0135-0.01640.2654-0.05370.2596-12.36036.0226-9.6658
62.39660.12870.05351.82730.322.4171-0.21790.0350.2535-0.01370.1821-0.1790.15391.0626-0.0150.3107-0.0727-0.10830.29250.02220.1905-7.0174.3364-13.7274
73.8496-0.1298-1.13394.1144-1.74174.8180.0354-0.26960.86360.32890.3002-0.1415-0.4620.6576-0.09190.2486-0.0474-0.03640.5388-00.32563.51346.3811-2.9195
83.77121.8594-2.49513.86490.48744.96290.333-0.39870.03280.7563-0.1875-0.11750.43280.13810.04460.5251-0.00850.06850.2017-0.02730.397-21.3296-14.2552-32.3856
91.6394-0.85150.93171.969-0.32841.96270.00150.0557-0.18080.43650.0377-0.0182-0.0187-0.05610.06830.2588-0.0232-0.03560.1613-0.03410.2136-27.3211-4.0284-31.4164
104.4390.7831-0.12543.4186-1.07573.46820.13390.01520.69650.651-0.0638-0.0694-0.0063-0.1203-0.07620.24050.0072-0.02840.1215-0.02580.2446-29.94313.1791-27.7136
112.63771.02871.21022.78970.03661.6844-0.07410.21190.35160.18620.0208-0.0493-0.11640.20280.13980.2142-0.0306-0.02050.15080.00270.184-25.49068.4828-32.0363
123.4809-0.85610.80773.77170.0223.9718-0.4567-0.3808-0.3428-0.15750.66190.02440.5405-0.6014-0.25050.2482-0.0227-0.02520.24050.02560.2658-32.8511-14.8656-37.2126
130.69070.35830.42951.5107-0.41640.46310.01820.11280.00290.0523-0.1635-0.01590.19490.17910.0810.27280.0387-0.0510.13640.00820.2402-25.3718-10.6232-48.1396
142.26770.4545-0.65183.432-1.30261.06370.5211-0.1880.3112-0.0736-0.1477-0.3373-0.5178-0.02470.04670.29880.00260.03810.0614-0.00760.2362-22.83252.5093-53.6208
152.97740.8296-0.2816.3267-5.63875.10240.31690.6492-0.1404-1.5191-0.1259-0.4031.1444-0.00990.46780.81540.017-0.00430.2930.07740.3305-27.237413.1204-55.0199
162.50220.1168-0.78761.4087-0.09771.7264-0.13280.1931-0.2404-0.3070.16390.0656-0.0024-0.3396-0.25430.19820.0028-0.080.16020.05040.1941-32.92977.1898-50.8113
175.3018-4.68962.85244.6898-3.39142.9134-0.2199-0.24180.7470.3714-0.0617-0.96130.24970.0976-0.05560.25090.0374-0.03560.2134-0.04660.213-20.62575.879-44.416
180.3817-0.7603-0.67195.27823.05493.0838-0.0816-0.05970.03040.4107-0.1445-0.89720.39650.41330.0880.26960.0474-0.03840.15940.04660.2333-19.1185-12.6513-42.3179
191.3741-2.10161.32196.1451-0.37692.15640.35860.0374-0.1044-0.8311-0.153-1.10690.38790.472-0.05290.7610.0346-0.14120.4326-0.06970.9046-13.2966-27.595-42.7984
204.56861.1487-0.85345.29330.4273.02530.5593-0.1748-0.7329-0.23760.13110.06320.36350.1764-0.22820.47690.1759-0.10870.38570.05840.2666-27.7847-12.9514-64.8463
216.3221-0.39-2.99482.08370.54783.0050.14210.4556-0.2221-0.33280.0855-0.05320.8210.198-0.22670.47410.0396-0.13830.3565-0.06390.3853-37.329-13.8731-71.7737
224.5198-0.69391.43882.1855-0.20481.94490.1994-0.1617-0.11110.16240.02210.09090.10490.1739-0.19480.2911-0.0146-0.03320.22340.04730.1729-43.1126-6.3425-74.0606
230.756-1.36770.7016.22943.46258.1974-0.30540.1457-0.041-0.58420.6646-0.1951-0.5841.0568-0.3020.1891-0.03350.0260.2567-0.01170.2395-26.5327-0.1885-67.1161
242.3087-0.19141.49641.6469-0.36472.1276-0.20720.19770.30820.0413-0.09380.0468-0.0771-0.19390.22280.18860.0244-0.00770.26630.01990.2024-40.67294.0182-71.4059
252.2232-0.28981.54172.3185-0.14481.0221-0.1239-0.55420.46580.3907-0.07760.2563-0.156-1.06020.12360.31390.1422-0.00250.5201-0.08710.3339-49.41486.0275-69.786
262.2869-0.431-0.24913.70580.95993.42530.08150.4236-0.1571-0.3492-0.07680.73070.1586-0.8619-0.12110.26470.0142-0.07480.60330.06260.2526-56.9979-0.8707-79.758
272.5166-0.742-0.22421.73910.94980.78730.0197-0.828-0.85120.4268-0.23990.22020.6895-0.2254-0.30470.4168-0.1546-0.14440.32820.07520.1472-43.034-13.1945-50.2718
280.21290.0502-0.05560.0126-0.01330.0127-0.0432-0.05180.09420.1733-0.05960.37870.0037-0.2351-0.13610.1198-0.36190.06160.93430.14740.5839-56.503-9.9688-45.3713
295.0212.45632.47552.40390.88312.9340.066-0.1202-0.25290.5786-0.2030.1198-0.026-0.64940.04360.2992-0.12060.02470.4396-0.00810.2395-46.0448-4.4769-45.4953
306.48170.8531.85680.5302-0.3681.49830.2013-0.19361.27360.18480.32030.34050.0205-0.6780.46330.2331-0.0046-0.15290.2712-0.02460.3217-44.21270.4526-51.8195
312.362-1.343-3.244.3542.87424.76410.432-0.47690.6171-0.3442-0.290.3998-0.5558-0.4566-0.03560.2696-0.0255-0.07330.7644-0.0550.529-54.1014-3.726-57.315
323.15820.9536-0.93362.1221-0.48582.40230.1952-0.04150.00210.10810.04640.70390.2834-0.8052-0.21020.2768-0.0905-0.0490.4677-0.02530.2461-50.4668-7.1051-55.9751
331.9167-0.6712-0.35891.1535-0.21090.7386-0.11210.5-0.4662-0.2235-0.0964-0.07180.3870.20520.00740.37420.0627-0.05120.35-0.01570.282-5.6298-11.2108-31.1325
346.9357-0.39911.85443.0903-0.96494.731-0.01140.68130.2617-0.5209-0.4317-0.16130.13830.69710.42390.39150.1347-0.01810.36890.02060.2679-6.5176-3.5537-35.1472
352.21240.0325-0.39010.54980.29311.4680.26660.20670.3651-0.1239-0.28-0.14060.09211.24990.10190.27360.106-0.09070.56050.04150.345-0.858-4.1838-26.2518
361.9798-0.4267-0.39651.46951.74693.10520.07180.05920.0061-0.1283-0.0527-0.0351-0.07450.635-0.05550.29150.0121-0.0570.22920.05170.2401-8.54541.1606-22.1886
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 17 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 30 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 57 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 67 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 100 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 122 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 123 through 151 )A0
8X-RAY DIFFRACTION8chain 'F' and (resid 6 through 10 )F0
9X-RAY DIFFRACTION9chain 'F' and (resid 11 through 30 )F0
10X-RAY DIFFRACTION10chain 'F' and (resid 31 through 43 )F0
11X-RAY DIFFRACTION11chain 'F' and (resid 44 through 66 )F0
12X-RAY DIFFRACTION12chain 'F' and (resid 67 through 81 )F0
13X-RAY DIFFRACTION13chain 'G' and (resid -2 through 30 )G0
14X-RAY DIFFRACTION14chain 'G' and (resid 31 through 43 )G0
15X-RAY DIFFRACTION15chain 'G' and (resid 44 through 48 )G0
16X-RAY DIFFRACTION16chain 'G' and (resid 49 through 58 )G0
17X-RAY DIFFRACTION17chain 'G' and (resid 59 through 66 )G0
18X-RAY DIFFRACTION18chain 'G' and (resid 67 through 78 )G0
19X-RAY DIFFRACTION19chain 'G' and (resid 79 through 83 )G0
20X-RAY DIFFRACTION20chain 'B' and (resid 3 through 17 )B0
21X-RAY DIFFRACTION21chain 'B' and (resid 18 through 30 )B0
22X-RAY DIFFRACTION22chain 'B' and (resid 31 through 57 )B0
23X-RAY DIFFRACTION23chain 'B' and (resid 58 through 67 )B0
24X-RAY DIFFRACTION24chain 'B' and (resid 68 through 100 )B0
25X-RAY DIFFRACTION25chain 'B' and (resid 101 through 132 )B0
26X-RAY DIFFRACTION26chain 'B' and (resid 133 through 151 )B0
27X-RAY DIFFRACTION27chain 'C' and (resid 1 through 16 )C0
28X-RAY DIFFRACTION28chain 'C' and (resid 17 through 22 )C0
29X-RAY DIFFRACTION29chain 'C' and (resid 23 through 34 )C0
30X-RAY DIFFRACTION30chain 'C' and (resid 35 through 44 )C0
31X-RAY DIFFRACTION31chain 'C' and (resid 45 through 54 )C0
32X-RAY DIFFRACTION32chain 'C' and (resid 55 through 76 )C0
33X-RAY DIFFRACTION33chain 'D' and (resid 1 through 22 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 23 through 34 )D0
35X-RAY DIFFRACTION35chain 'D' and (resid 35 through 65 )D0
36X-RAY DIFFRACTION36chain 'D' and (resid 66 through 76 )D0

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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