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- PDB-4s3o: PCGF5-RING1B-UbcH5c complex -

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基本情報

登録情報
データベース: PDB / ID: 4s3o
タイトルPCGF5-RING1B-UbcH5c complex
要素
  • E3 ubiquitin-protein ligase RING2
  • Polycomb group RING finger protein 5
  • Ubiquitin-conjugating enzyme E2 D3
キーワードLigase/Transcription / E2 / E3 / RING domain / Ubiquitin RING E3 Ligase / Ligase-Transcription complex
機能・相同性
機能・相同性情報


histone H2AK119 ubiquitin ligase activity / PRC1 complex / RING-like zinc finger domain binding / sex chromatin / random inactivation of X chromosome / PcG protein complex / protein K6-linked ubiquitination / Signaling by BMP / (E3-independent) E2 ubiquitin-conjugating enzyme / SUMOylation of DNA methylation proteins ...histone H2AK119 ubiquitin ligase activity / PRC1 complex / RING-like zinc finger domain binding / sex chromatin / random inactivation of X chromosome / PcG protein complex / protein K6-linked ubiquitination / Signaling by BMP / (E3-independent) E2 ubiquitin-conjugating enzyme / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / protein K11-linked ubiquitination / SUMOylation of RNA binding proteins / anterior/posterior axis specification / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / X chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / germ cell development / ubiquitin conjugating enzyme activity / MLL1 complex / negative regulation of BMP signaling pathway / protein monoubiquitination / ubiquitin ligase complex / SUMOylation of DNA damage response and repair proteins / protein K48-linked ubiquitination / protein autoubiquitination / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / TICAM1, RIP1-mediated IKK complex recruitment / epigenetic regulation of gene expression / Regulation of PTEN gene transcription / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / negative regulation of DNA-binding transcription factor activity / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / euchromatin / Inactivation of CSF3 (G-CSF) signaling / RING-type E3 ubiquitin transferase / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / mitotic cell cycle / Neddylation / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / gene expression / proteasome-mediated ubiquitin-dependent protein catabolic process / endosome membrane / protein ubiquitination / nuclear body / chromatin remodeling / DNA repair / apoptotic process / centrosome / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
: / E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. ...: / E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Ubiquitin-conjugating enzyme E2 D3 / Polycomb group RING finger protein 5 / E3 ubiquitin-protein ligase RING2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2 Å
データ登録者Taherbhoy, A.M. / Cochran, A.G.
引用ジャーナル: Nat Commun / 年: 2015
タイトル: BMI1-RING1B is an autoinhibited RING E3 ubiquitin ligase.
著者: Taherbhoy, A.M. / Huang, O.W. / Cochran, A.G.
履歴
登録2015年3月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年7月15日Provider: repository / タイプ: Initial release
改定 1.12015年7月22日Group: Database references
改定 1.22023年9月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 D3
D: Ubiquitin-conjugating enzyme E2 D3
B: E3 ubiquitin-protein ligase RING2
E: E3 ubiquitin-protein ligase RING2
C: Polycomb group RING finger protein 5
F: Polycomb group RING finger protein 5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)88,35814
ポリマ－87,8356
非ポリマー5238
水2,738152
1
D: Ubiquitin-conjugating enzyme E2 D3
E: E3 ubiquitin-protein ligase RING2
F: Polycomb group RING finger protein 5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,1797
ポリマ－43,9173
非ポリマー2624
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Ubiquitin-conjugating enzyme E2 D3
B: E3 ubiquitin-protein ligase RING2
C: Polycomb group RING finger protein 5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,1797
ポリマ－43,9173
非ポリマー2624
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)54.392, 105.285, 132.417
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
詳細Two biological heterotrimers appear in the asymmetric unit (A,B,C and D,E,F)

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要素

#1: タンパク質 Ubiquitin-conjugating enzyme E2 D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating ...Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / Ubiquitin-protein ligase D3


分子量: 16719.066 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2D3, UBC5C, UBCH5C / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61077, ubiquitin-protein ligase
#2: タンパク質 E3 ubiquitin-protein ligase RING2 / Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3 / Protein DinG ...Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3 / Protein DinG / RING finger protein 1B / RING1b / RING finger protein 2 / RING finger protein BAP-1


分子量: 13247.405 Da / 分子数: 2 / Fragment: RING domain, UNP residues 1-116 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RNF2, BAP1, DING, HIPI3, RING1B / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q99496, 合成酵素; C-N結合を形成; 酸-D-アミノ酸リガーゼ（ペプチド合成）
#3: タンパク質 Polycomb group RING finger protein 5 / RING finger protein 159


分子量: 13950.874 Da / 分子数: 2 / Fragment: RING domain, UNP residues 1-109 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PCGF5, RNF159 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q86SE9
#4: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 152 / 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: 2.16 Å3/Da / 溶媒含有率: 43.01 %
結晶化温度: 277 K / 手法: 蒸気拡散法 / pH: 6.5
詳細: 13.5% PEG 550 MME, 10 mM TCEP, 0.1 M MES pH 6.5, 100 mM KCl, VAPOR DIFFUSION, temperature 277K

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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: ALS / ビームライン: 5.0.2 / 波長: 1.00003 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2013年6月13日
放射モノクロメーター: Si(111) / 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: 1.00003 Å / 相対比: 1
反射解像度: 2→50 Å / Num. all: 52285 / Num. obs: 52191 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 7.2 % / Biso Wilson estimate: 32.06 Å2 / Rsym value: 0.069 / Net I/σ(I): 22.5

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解析

ソフトウェア
名称バージョン分類
BOSデータ収集
PHASER位相決定
PHENIX(phenix.refine: 1.8.2_1309)精密化
HKL-2000データ削減
SCALEPACKデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 3RPG, chains A and C

3rpg


解像度: 2→48.919 Å / SU ML: 0.23 / σ(F): 1.34 / 位相誤差: 25.13 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2368 2664 5.1 %
Rwork0.1939 --
obs0.1961 52191 99.8 %
all-52285 -
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
Refine analyzeLuzzati sigma a obs: 0.23 Å
精密化ステップサイクル: LAST / 解像度: 2→48.919 Å
タンパク質核酸リガンド溶媒全体
原子数5405 0 8 152 5565
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0095650
X-RAY DIFFRACTIONf_angle_d1.1437712
X-RAY DIFFRACTIONf_dihedral_angle_d13.0712096
X-RAY DIFFRACTIONf_chiral_restr0.076870
X-RAY DIFFRACTIONf_plane_restr0.006990
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03570.29331510.24262531X-RAY DIFFRACTION99
2.0357-2.07480.28131360.23262580X-RAY DIFFRACTION100
2.0748-2.11720.28611340.22262576X-RAY DIFFRACTION100
2.1172-2.16320.27671260.20712578X-RAY DIFFRACTION100
2.1632-2.21350.25281300.21232554X-RAY DIFFRACTION100
2.2135-2.26890.25951310.20532602X-RAY DIFFRACTION100
2.2689-2.33020.25971550.2152551X-RAY DIFFRACTION100
2.3302-2.39880.28091310.20382600X-RAY DIFFRACTION100
2.3988-2.47620.24761160.20882615X-RAY DIFFRACTION100
2.4762-2.56470.26911330.21392606X-RAY DIFFRACTION100
2.5647-2.66740.27261660.23082520X-RAY DIFFRACTION100
2.6674-2.78880.28321650.22842568X-RAY DIFFRACTION100
2.7888-2.93580.33131310.23442640X-RAY DIFFRACTION100
2.9358-3.11970.26331420.23572611X-RAY DIFFRACTION100
3.1197-3.36050.26021340.22252637X-RAY DIFFRACTION100
3.3605-3.69860.22371470.18932619X-RAY DIFFRACTION100
3.6986-4.23360.17361420.16472666X-RAY DIFFRACTION100
4.2336-5.33280.21171380.14692674X-RAY DIFFRACTION100
5.3328-48.93320.19261560.16672799X-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)
19.7337-5.02674.46145.5421-6.12298.16460.10550.34230.4706-0.1451-0.30260.0853-0.16020.14350.23440.3830.00330.07120.2389-0.11570.32825.65660.0865-17.4949
27.97193.4882.50154.29243.41094.689-0.0963-0.1105-0.15360.0739-0.35680.5361-0.078-0.47210.42540.3220.02090.03770.1779-0.05090.33910.8055-12.0014-17.5484
36.18185.6690.90175.20090.40442.4207-0.13060.2835-0.4936-0.1930.1557-0.16650.02860.065-0.01550.25240.01820.06870.2046-0.08290.28867.0476-15.5369-23.8599
41.27061.1744-0.1446.05422.70635.5413-0.14960.928-0.66460.0254-0.42610.72340.3163-0.44790.39390.4009-0.0520.05810.5994-0.34010.6183-3.9387-25.7376-31.3601
58.6522-0.5378-0.83847.45940.71535.0867-0.02720.1999-0.5149-0.57320.17760.8502-0.2673-0.4583-0.07520.34960.0252-0.01750.40650.04930.2845-16.826-46.7444-18.3712
62.60541.8868-0.42437.1596-0.75445.57410.6695-0.15150.79890.503-0.17540.407-0.79780.3864-0.13840.32280.04650.07930.46920.00580.4241-11.9736-37.0951-13.0889
77.84724.71213.5597.48353.87927.7662-0.33340.50250.85830.015-0.23980.6388-0.2126-0.75110.30540.27880.0622-0.01750.32670.09380.3423-7.8059-37.9335-19.5457
86.30464.67081.97776.66333.17964.3430.10250.045-0.21540.24540.1958-0.44230.11320.3344-0.27870.25780.09150.01950.2697-0.0180.25850.7619-38.8351-13.0468
96.16313.47933.2615.756-0.20693.93840.6984-0.197-0.6910.8029-0.2041-0.490.59270.1926-0.45580.43610.0737-0.07650.32580.03380.3488-2.1143-47.1283-9.2163
102.26061.9933-1.16843.8116-0.9311.29890.4638-0.0704-1.79210.36490.071-1.49161.53570.541-0.64930.7990.1772-0.36230.809-0.21180.786910.7866-43.4776-3.8567
117.9765-0.51713.8676.0247-2.26655.0880.2304-0.6567-0.02361.21940.2144-1.1296-0.34080.6168-0.3280.56860.0303-0.18110.6564-0.24370.629411.0844-30.2584-2.2171
123.15643.88165.27885.10536.8199.2050.425-1.4386-0.0138-0.0662-0.29310.29430.8551-0.6712-0.13410.4029-0.1125-0.03820.44960.01570.258930.3419-4.0324-46.3003
131.4275-1.7573-1.68424.20211.43815.98620.09550.25520.3863-0.54940.17280.122-0.6552-0.0976-0.30890.3117-0.1875-0.07090.52220.02460.463528.748617.6169-42.4183
146.4903-2.9911-0.25542.26332.38716.90860.17750.3557-0.5606-0.2957-0.20371.49330.2873-0.7220.01130.3259-0.0621-0.01380.398-0.01110.401915.597412.4382-25.3123
153.03832.7282-4.49489.6262-4.98616.79570.1322-0.40850.49910.6154-0.01210.0422-0.14120.1673-0.09810.2035-0.00050.00540.2533-0.04810.214120.10254.4325-17.9741
166.42111.50851.63718.50975.27449.14710.1624-0.0975-0.11990.0673-0.097-0.42130.46230.192-0.01190.26290.00580.01890.2832-0.01810.298929.4875-0.4958-26.9276
177.7907-1.49890.8543.4151-4.72637.4361-0.1061-1.0578-0.50770.03030.0384-0.23110.45130.97640.11610.31270.062-0.02840.43010.04080.316726.2228-2.9235-16.7939
188.6963-2.78634.30775.06640.88868.2638-0.19040.1513-1.89550.0820.1087-0.1470.4638-0.01840.07830.51520.00180.17280.2837-0.030.664925.477-9.8631-24.9753
198.0622-5.7251.93854.1196-0.86656.4227-0.0526-0.1293-0.21480.2887-0.2403-0.87820.09221.06430.2760.326-0.00260.06460.5317-0.00530.488534.5466-0.1714-22.6569
203.4255-3.8975-2.85197.1810.70696.51260.4643-0.62821.1289-0.35670.1215-0.7516-0.67480.6835-0.47580.2635-0.09860.00980.3891-0.08520.335526.113815.465-20.7305
213.67412.84964.91489.41662.51876.9063-0.27520.0547-0.15950.11060.2706-0.0272-0.06340.6005-0.04630.25890.0678-0.02170.3119-0.07260.2653-9.2387-68.057212.9778
221.5357-1.5353-1.5783.77751.15886.915-0.1067-0.392-0.1653-0.0970.10550.38640.4379-0.2110.01470.27030.0127-0.01920.13190.0410.3368-26.4799-69.616915.4769
239.7855-4.7759-2.06997.66510.28852.09560.2831-0.31110.50840.2992-0.12630.4941-0.7941-0.1008-0.17770.60670.0931-0.02880.2683-0.02520.3177-28.5858-53.2869-7.2085
247.51183.7116-4.40338.1233-2.26352.77640.29860.40450.1198-0.4053-0.20430.1060.2004-0.1161-0.11520.4960.0906-0.0770.33210.02060.2232-19.3021-58.0553-15.0692
252.6074-1.73370.42453.6125-3.78365.03680.0415-0.2093-0.358-0.404-0.31180.0780.0140.58540.24150.41460.076-0.07180.3951-0.00710.2258-13.9633-67.4915-6.4324
262.9523-0.9733-4.67142.54211.30649.79630.25640.321-0.6782-0.6503-0.1164-0.30320.7232-0.77220.04820.57110.0861-0.02050.2357-0.07330.3443-12.9088-64.0235-16.0028
272.4629-2.12490.59742.78390.97152.5118-0.61560.2915-0.21510.3433-0.0793-1.741-0.22811.63180.47840.4508-0.00240.02620.63260.06480.7209-4.552-62.2057-11.1154
282.3701-1.17672.2341.7115-3.79448.51241.03570.7831-0.90060.2856-1.52220.66590.65310.93440.48320.62590.0672-0.02470.54770.01020.8236-4.159-66.7687-7.1309
298.2983-4.4191-2.64787.3483-0.27482.04020.11380.5131-0.5962-0.4867-0.13160.3410.2673-0.18710.0260.5410.0075-0.09890.297-0.06230.2856-24.981-67.0578-11.3403
309.1548-5.65025.84399.446-4.51773.8721-0.5189-0.65080.3011.43290.05140.6138-1.2689-0.02350.46440.566-0.13370.0640.5649-0.09610.495127.154622.9919-27.3531
311.022-0.687-0.72287.9717-1.18141.3463-0.0188-0.00410.2091-0.26170.261-0.1685-0.01620.131-0.24870.2208-0.12610.00970.5052-0.06790.269736.420510.5486-37.5717
321.46322.47261.30785.6071-0.64696.8340.2462-0.3232-0.5987-0.2419-0.1004-1.61090.59291.7893-0.15790.2776-0.01130.00880.7894-0.10060.528345.63384.0602-35.6765
334.8288-4.1357-6.77248.09115.919.5409-0.3112-0.639-0.11410.60070.227-0.2950.9637-0.2802-0.00530.3658-0.0616-0.08070.507-0.00880.262434.93110.1136-37.3663
348.6079-3.7121-3.22737.34851.02187.8203-0.08760.53760.1251-0.65370.19480.5592-0.3146-0.3695-0.0860.2335-0.0513-0.05890.36330.0380.295322.084714.3476-34.2851
354.408-1.9559-1.48014.32713.50368.2538-0.38690.5820.6562-0.82850.01790.3602-0.4378-0.57380.25170.4938-0.1878-0.12870.46810.17110.406924.182917.3686-51.2387
365.0750.4173-1.23483.1737-0.27495.3349-0.08020.48680.0576-0.69170.07960.50210.2432-0.3638-0.02480.46050.0268-0.1510.1918-0.0360.3659-29.3327-70.25080.8135
378.21540.8364-1.40975.29145.93727.42040.2363-0.4987-0.97630.16920.09090.71060.82450.0711-0.17790.42650.0184-0.08790.1643-0.02480.3487-22.4462-76.55088.1573
387.98543.53627.28194.2321.93329.8142-0.07910.8307-1.0806-0.28510.0841-0.04830.380.7323-0.15860.59650.09470.0070.3182-0.10370.5772-17.2616-82.92862.039
395.2254-1.16312.62663.8717-4.96496.8440.32160.7351-0.6334-1.3632-0.4043-0.12150.44970.84980.09250.45330.1143-0.00010.2693-0.05430.3636-14.1833-72.63534.0947
407.051-6.5671-0.76357.7459-0.48816.5436-0.2895-0.00030.4474-0.3902-0.22810.034-0.7461-0.03090.39160.4230.0305-0.14310.1608-0.04570.2834-27.8409-59.24671.6036
418.5543-0.97921.58626.109-2.73715.5332-0.2516-0.83210.09280.18920.36470.5745-0.2567-0.895-0.15450.27150.08470.02460.2309-0.0510.3071-30.2527-60.861718.8742
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 111 )
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 147 )
5X-RAY DIFFRACTION5chain 'D' and (resid 0 through 15 )
6X-RAY DIFFRACTION6chain 'D' and (resid 16 through 28 )
7X-RAY DIFFRACTION7chain 'D' and (resid 29 through 38 )
8X-RAY DIFFRACTION8chain 'D' and (resid 39 through 84 )
9X-RAY DIFFRACTION9chain 'D' and (resid 85 through 111 )
10X-RAY DIFFRACTION10chain 'D' and (resid 112 through 120 )
11X-RAY DIFFRACTION11chain 'D' and (resid 121 through 147 )
12X-RAY DIFFRACTION12chain 'B' and (resid 10 through 16 )
13X-RAY DIFFRACTION13chain 'B' and (resid 17 through 41 )
14X-RAY DIFFRACTION14chain 'B' and (resid 42 through 49 )
15X-RAY DIFFRACTION15chain 'B' and (resid 50 through 60 )
16X-RAY DIFFRACTION16chain 'B' and (resid 61 through 69 )
17X-RAY DIFFRACTION17chain 'B' and (resid 70 through 81 )
18X-RAY DIFFRACTION18chain 'B' and (resid 82 through 96 )
19X-RAY DIFFRACTION19chain 'B' and (resid 97 through 103 )
20X-RAY DIFFRACTION20chain 'B' and (resid 104 through 116 )
21X-RAY DIFFRACTION21chain 'E' and (resid 10 through 16 )
22X-RAY DIFFRACTION22chain 'E' and (resid 17 through 31 )
23X-RAY DIFFRACTION23chain 'E' and (resid 40 through 49 )
24X-RAY DIFFRACTION24chain 'E' and (resid 50 through 60 )
25X-RAY DIFFRACTION25chain 'E' and (resid 61 through 69 )
26X-RAY DIFFRACTION26chain 'E' and (resid 70 through 80 )
27X-RAY DIFFRACTION27chain 'E' and (resid 81 through 90 )
28X-RAY DIFFRACTION28chain 'E' and (resid 91 through 96 )
29X-RAY DIFFRACTION29chain 'E' and (resid 97 through 116 )
30X-RAY DIFFRACTION30chain 'C' and (resid 6 through 16 )
31X-RAY DIFFRACTION31chain 'C' and (resid 17 through 48 )
32X-RAY DIFFRACTION32chain 'C' and (resid 49 through 64 )
33X-RAY DIFFRACTION33chain 'C' and (resid 65 through 72 )
34X-RAY DIFFRACTION34chain 'C' and (resid 73 through 85 )
35X-RAY DIFFRACTION35chain 'C' and (resid 86 through 101 )
36X-RAY DIFFRACTION36chain 'F' and (resid 8 through 35 )
37X-RAY DIFFRACTION37chain 'F' and (resid 36 through 49 )
38X-RAY DIFFRACTION38chain 'F' and (resid 50 through 64 )
39X-RAY DIFFRACTION39chain 'F' and (resid 65 through 72 )
40X-RAY DIFFRACTION40chain 'F' and (resid 73 through 85 )
41X-RAY DIFFRACTION41chain 'F' and (resid 86 through 102 )

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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