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- PDB-6cht: HNF4alpha in complex with the corepressor EBP1 fragment -

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基本情報

登録情報
データベース: PDB / ID: 6cht
タイトルHNF4alpha in complex with the corepressor EBP1 fragment
要素
  • Hepatocyte nuclear factor 4-alpha
  • Proliferation-associated protein 2G4
キーワードTRANSCRIPTION / HNF4alpha / EBP1 / nuclear receptor / co-repressor / protein-protein interaction / gene regulation / insulin secretion / diabetes
機能・相同性
機能・相同性情報


regulation of growth hormone receptor signaling pathway / regulation of ornithine metabolic process / regulation of gastrulation / Nephron development / sex differentiation / phospholipid homeostasis / signal transduction involved in regulation of gene expression / triglyceride homeostasis / lipid homeostasis / Regulation of gene expression in beta cells ...regulation of growth hormone receptor signaling pathway / regulation of ornithine metabolic process / regulation of gastrulation / Nephron development / sex differentiation / phospholipid homeostasis / signal transduction involved in regulation of gene expression / triglyceride homeostasis / lipid homeostasis / Regulation of gene expression in beta cells / regulation of lipid metabolic process / response to glucose / regulation of insulin secretion / xenobiotic metabolic process / cholesterol homeostasis / fatty acid binding / positive regulation of cell differentiation / regulation of circadian rhythm / negative regulation of cell growth / Nuclear Receptor transcription pathway / lipid metabolic process / nuclear receptor activity / rRNA processing / blood coagulation / sequence-specific double-stranded DNA binding / azurophil granule lumen / rhythmic process / transcription corepressor activity / glucose homeostasis / regulation of translation / DNA-binding transcription activator activity, RNA polymerase II-specific / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / ribonucleoprotein complex / signaling receptor binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / Neutrophil degranulation / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / nucleolus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm
類似検索 - 分子機能
: / : / PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / : / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like ...: / : / PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / : / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
LAURIC ACID / Hepatocyte nuclear factor 4-alpha / Proliferation-associated protein 2G4
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: 3.174 Å
データ登録者Chi, Y.I. / Singh, P. / Lee, I.K.
資金援助 米国, 1件
組織認可番号国
American Diabetes Association7-08-CD-03 米国
引用ジャーナル: J.Biol.Chem. / 年: 2019
タイトル: ErbB3-binding protein 1 (EBP1) represses HNF4 alpha-mediated transcription and insulin secretion in pancreatic beta-cells.
著者: Han, E.H. / Singh, P. / Lee, I.K. / Urrutia, R. / Chi, Y.I.
履歴
登録2018年2月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年2月27日Provider: repository / タイプ: Initial release
改定 1.12019年10月16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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023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
改定 1.32024年12月25日Group: Advisory / Derived calculations / Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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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: Hepatocyte nuclear factor 4-alpha
B: Hepatocyte nuclear factor 4-alpha
C: Proliferation-associated protein 2G4
D: Hepatocyte nuclear factor 4-alpha
E: Hepatocyte nuclear factor 4-alpha
F: Proliferation-associated protein 2G4
G: Hepatocyte nuclear factor 4-alpha
H: Hepatocyte nuclear factor 4-alpha
I: Proliferation-associated protein 2G4
J: Hepatocyte nuclear factor 4-alpha
K: Hepatocyte nuclear factor 4-alpha
L: Proliferation-associated protein 2G4
M: Hepatocyte nuclear factor 4-alpha
N: Hepatocyte nuclear factor 4-alpha
P: Hepatocyte nuclear factor 4-alpha
Q: Hepatocyte nuclear factor 4-alpha
S: Hepatocyte nuclear factor 4-alpha
T: Hepatocyte nuclear factor 4-alpha
V: Hepatocyte nuclear factor 4-alpha
W: Hepatocyte nuclear factor 4-alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)450,99928
ポリマ－449,39720
非ポリマー1,6038
水79344
1
A: Hepatocyte nuclear factor 4-alpha
B: Hepatocyte nuclear factor 4-alpha
C: Proliferation-associated protein 2G4
J: Hepatocyte nuclear factor 4-alpha
K: Hepatocyte nuclear factor 4-alpha
L: Proliferation-associated protein 2G4
M: Hepatocyte nuclear factor 4-alpha
N: Hepatocyte nuclear factor 4-alpha
V: Hepatocyte nuclear factor 4-alpha
W: Hepatocyte nuclear factor 4-alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)225,50014
ポリマ－224,69810
非ポリマー8014
水1629
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area23970 Å2
ΔGint-119 kcal/mol
Surface area79300 Å2
手法PISA
2
D: Hepatocyte nuclear factor 4-alpha
E: Hepatocyte nuclear factor 4-alpha
F: Proliferation-associated protein 2G4
G: Hepatocyte nuclear factor 4-alpha
H: Hepatocyte nuclear factor 4-alpha
I: Proliferation-associated protein 2G4
P: Hepatocyte nuclear factor 4-alpha
Q: Hepatocyte nuclear factor 4-alpha
S: Hepatocyte nuclear factor 4-alpha
T: Hepatocyte nuclear factor 4-alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)225,50014
ポリマ－224,69810
非ポリマー8014
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area24180 Å2
ΔGint-111 kcal/mol
Surface area78410 Å2
手法PISA
単位格子
Length a, b, c (Å)139.721, 104.946, 139.563
Angle α, β, γ (deg.)90.00, 90.61, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Hepatocyte nuclear factor 4-alpha / HNF-4-alpha / Nuclear receptor subfamily 2 group A member 1 / Transcription factor 14 / TCF-14 / ...HNF-4-alpha / Nuclear receptor subfamily 2 group A member 1 / Transcription factor 14 / TCF-14 / Transcription factor HNF-4


分子量: 27535.918 Da / 分子数: 16 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HNF4A, HNF4, NR2A1, TCF14 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P41235
#2: タンパク質・ペプチド
Proliferation-associated protein 2G4 / Cell cycle protein p38-2G4 homolog / hG4-1 / ErbB3-binding protein 1


分子量: 2205.511 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: Q9UQ80
#3: 化合物
ChemComp-DAO / LAURIC ACID / ラウリン酸


分子量: 200.318 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C12H24O2
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 44 / 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: 2.28 Å3/Da / 溶媒含有率: 45.98 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.25
詳細: 0.1 m Bis-Tris, 26-28% MPD, 3-4% PEG8000, 20-50 mM Glycine and 10% glycerol

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データ収集

回折平均測定温度: 173 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2015年5月13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 Å / 相対比: 1
反射解像度: 3.15→49.632 Å / Num. obs: 48984 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / 冗長度: 3.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.3
反射 シェル解像度: 3.15→3.2 Å / 冗長度: 2.2 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.7 / % possible all: 76.2

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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: 1PZL

1pzl


解像度: 3.174→49.632 Å / 交差検証法: FREE R-VALUE / σ(F): 294.98 / 位相誤差: 30.93 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射
Rfree0.2742 2700 5.51 %
Rwork0.2622 --
obs0.4142 48984 71.57 %
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: 3.174→49.632 Å
タンパク質核酸リガンド溶媒全体
原子数26226 0 112 44 26382
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00426777
X-RAY DIFFRACTIONf_angle_d0.85636115
X-RAY DIFFRACTIONf_dihedral_angle_d2.90316530
X-RAY DIFFRACTIONf_chiral_restr0.054161
X-RAY DIFFRACTIONf_plane_restr0.0054592
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1746-3.23570.5482200.5352358X-RAY DIFFRACTION10
3.2357-3.30170.5173330.5062570X-RAY DIFFRACTION15
3.3017-3.37350.5348440.501882X-RAY DIFFRACTION23
3.3735-3.45190.5034660.50031162X-RAY DIFFRACTION31
3.4519-3.53820.5091890.49281610X-RAY DIFFRACTION43
3.5382-3.63380.48971120.47571964X-RAY DIFFRACTION52
3.6338-3.74070.48261240.47012350X-RAY DIFFRACTION62
3.7407-3.86130.48171660.4672698X-RAY DIFFRACTION71
3.8613-3.99930.46031700.45613056X-RAY DIFFRACTION80
3.9993-4.15920.4511720.43293331X-RAY DIFFRACTION88
4.1592-4.34840.44691880.43453460X-RAY DIFFRACTION91
4.3484-4.57740.42271840.41063527X-RAY DIFFRACTION93
4.5774-4.86380.36871640.38883549X-RAY DIFFRACTION93
4.8638-5.23870.36211900.36263532X-RAY DIFFRACTION93
5.2387-5.76470.35021990.33883527X-RAY DIFFRACTION92
5.7647-6.59620.3661750.33123585X-RAY DIFFRACTION94
6.5962-8.30040.34411800.38173618X-RAY DIFFRACTION94
8.3004-42.53150.39812290.40883686X-RAY DIFFRACTION94
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)
14.5876-0.23930.50713.17550.17251.886-0.1043-1.83630.05321.70660.10240.56940.305-0.190.02281.3565-0.08950.58241.1544-0.42131.1209-33.6455-2.961312.2409
21.4390.3093-0.24930.0952-0.16180.51920.2780.47620.3616-0.20590.11660.1664-0.25810.0283-0.44591.04710.48790.27431.79710.44331.6531-61.450159.2797-96.3898
30.66950.00770.8254-00.00961.01710.23330.2039-0.52940.37220.2068-0.6420.42580.3037-0.47461.24560.4277-0.46161.9472-0.25331.6917-56.580838.7228-99.1393
42.00962.21281.3124.4347-0.07412.01360.21430.2228-0.1681-0.53640.3732-0.34790.11630.3513-0.57361.24440.52730.05311.9427-0.30211.683-50.503565.5274-100.3955
50.40750.4952-0.94321.1006-1.97314.01560.07750.6011-0.6316-1.0123-0.2651-0.10870.92481.06580.19052.56560.42340.41992.3031-0.55412.1744-51.704450.7191-111.2359
60.4307-1.16930.28183.3538-0.83650.28160.08970.5243-0.5974-0.4852-0.1456-0.34820.59950.96350.05272.12120.71110.76242.1975-0.54432.1066-47.630139.4107-98.9319
70.6981-0.53740.28242.6466-0.26471.07720.04490.6643-0.5044-1.1923-0.2956-0.49740.81931.04610.25252.75170.67150.78492.6153-0.76762.3704-44.39941.5276-112.7225
80.08840.1629-0.36270.5226-1.60065.85150.0621-0.7308-0.78820.68-0.1591-0.9071.33331.63840.11023.41861.70540.64293.24270.94212.1957-38.478954.6844-117.4085
92.4015-1.32181.09683.6085-0.61521.00210.52510.51770.162-0.7125-0.4228-0.42990.4358-0.4312-0.11111.8110.4456-0.57611.3870.07191.2208-51.899755.1141-87.2658
101.33720.03820.86732.563-0.29562.3972-0.83610.10150.5573-0.78010.68810.5829-0.67140.35350.12072.17870.3218-0.72371.6625-0.62071.8774-17.726251.4922-92.0828
112.4312-0.12651.26985.0569-0.54561.3445-0.7751-0.3718-0.0321-0.27941.25751.1233-0.5616-0.1661-0.47652.22160.6793-0.8741.6217-0.26852.0289-25.671642.8808-90.8085
120.10630.0279-0.26460.414-0.7091.66390.2440.8290.9893-0.821-0.20120.4987-0.9202-0.4684-0.04213.86321.2327-1.03523.16851.23173.8904-29.557345.2449-100.1806
130.227-0.0921-0.07150.2363-0.06541.590.1947-0.2151-0.01460.2524-0.2309-0.0714-0.9776-0.25530.04965.6588-0.4632.00015.66440.89673.0033-26.726653.8548-112.6313
142.1627-2.1361-2.1612.13872.15242.17041.29191.3290.2235-2.5503-1.46740.5204-0.6446-0.57840.17633.65541.6558-0.29443.2397-0.08622.0497-31.249339.1297-115.4269
151.9314-1.82820.51143.2235-0.0350.67310.6011.1586-0.2911-1.0482-0.74340.03890.09840.14940.13670.70020.1671-0.04271.21220.29241.3124-35.726250.4006-77.5351
162.329-2.1522-0.162.06730.3890.7458-0.04520.12390.3104-0.2389-0.2279-0.2435-0.2783-0.16450.18621.15510.5870.25951.20650.08151.0101-7.328957.7746-43.4304
170.24110.01410.3630.0098-0.04471.0246-0.3111-0.0924-0.1425-0.27690.1326-0.4783-0.26420.01340.15261.32080.14650.42831.46370.80871.7845-2.402265.7821-50.2046
180.85280.14721.15170.11480.23191.57180.10270.0423-0.0797-0.3362-0.1718-0.25010.12150.2150.10381.30940.24680.52831.05830.50461.5353-10.273547.8184-54.6206
190.2535-0.21650.11982.02990.41470.20160.804-0.34820.0780.198-0.3035-0.5215-0.79720.3563-0.47652.1628-0.62180.0291.60930.94032.77722.386265.6682-56.73
203.87910.96691.12313.68240.62740.67210.9074-0.87830.25410.7312-1.0287-0.8694-0.44180.86880.13052.2343-0.90080.2691.82010.77612.84198.013776.013-59.2208
213.75051.22955.3984.8077-0.18358.63532.90930.435-1.67650.5219-1.7996-0.54221.2381.6135-1.11022.1346-0.0633-0.42632.09921.06293.314613.918861.1387-65.5448
221.61681.33670.62361.22010.07712.65480.10670.41640.439-0.631-0.0091-0.9764-0.29830.6617-0.13640.8090.27070.35280.7750.1621.2608-16.801761.7523-53.5867
233.0821-3.14230.77994.3466-2.34624.38940.20381.06860.5088-1.6364-0.4589-0.40020.08870.26290.25071.767-0.25-0.09661.5760.27931.028-11.951359.9107-86.7492
244.8582-3.90732.32853.2812-1.38295.487-0.40750.41730.6844-1.0752-0.0224-1.0699-0.30190.09980.41861.5806-0.21490.07991.55570.29721.384-10.085370.2049-80.8951
254.793-4.5978-1.21336.3108-2.11167.0834-0.19660.94691.7554-0.6981-0.0793-1.4364-1.75720.1290.27731.9996-0.1755-0.15741.18730.59081.813-12.573381.1113-83.7962
262.0347-0.04960.84440.5411-0.02710.95040.38330.4020.1375-0.4843-0.3957-0.29230.8150.68470.0212.09940.31170.57040.90710.01611.2561-14.383980.5981-73.153
270.70030.0974-0.02680.2904-0.03890.25110.32310.277-0.1468-0.4204-0.4279-0.21541.08130.85450.10782.69590.85810.65111.67060.34711.4345.413564.7546-77.1307
280.18620.281-0.17832.2416-1.04491.74570.05170.03660.1703-0.1159-0.3473-0.6521-0.26060.21450.29241.47030.18-0.30951.1970.51561.075-23.648867.5994-68.9202
290.5943-0.5421-0.21481.0406-0.25330.4473-0.0396-0.17280.1174-0.3740.3474-0.2126-0.09740.2947-0.30521.4383-0.1372-0.26971.5504-0.44671.1881-61.72534.2088-27.32
300.9789-1.0239-0.2451.91741.15341.6731-0.16870.4332-0.666-0.3070.14810.0795-0.1771-0.0350.01830.9684-0.0592-0.04991.408-0.841.757-65.767111.3587-21.4029
310.74810.35020.11571.0040.72222.43960.02350.3152-0.430.1994-0.0930.17570.6259-0.19130.06660.9396-0.1010.03491.3133-0.78862.1316-57.4539-4.7257-12.7753
320.4369-0.26370.10980.1702-0.04420.07060.25930.4781-0.56710.1037-0.08380.9784-0.0381-0.48-0.20011.10260.31360.05321.6214-0.79382.7628-74.66487.975-13.8731
331.3972-1.0995-0.12661.80770.10831.13370.27260.4322-0.41060.0836-0.15040.676-0.1936-0.5263-0.07921.32760.64980.18811.4236-0.47792.1529-71.931124.8467-11.8377
341.1656-0.0313-0.7041.7588-0.14990.89270.17350.01070.16190.3583-0.29721.24740.3035-0.49960.22621.2041-0.0221-0.32571.2442-0.79232.1246-66.41998.2409-8.7366
350.1872-0.13450.14390.1413-0.1540.18620.2448-0.13120.3487-0.1517-0.24240.44220.0778-0.22480.03350.85620.136-0.41260.9978-0.49281.6203-50.09311.7483-23.9971
360.26890.47820.11840.97860.16080.07120.1073-0.2616-0.05260.1697-0.13950.39890.0901-0.12760.08171.81150.38110.52731.5176-0.58521.6214-57.6929.668715.5874
370.8568-0.64940.16540.53430.05170.743-0.4941-0.31660.34480.2320.03310.42490.4486-0.68160.4711.7118-0.33550.63531.2356-0.53711.836-64.02918.81087.0067
380.8772-0.8383-0.49420.91030.36830.6760.16350.1943-0.1858-0.1521-0.39090.7846-0.2304-0.61170.31541.07830.2379-0.00230.8208-0.5911.4114-51.727817.0363-0.2717
390.1670.15890.18960.78160.02130.4189-0.0459-0.03010.0009-0.3345-0.06510.2857-0.0652-0.2482-0.13020.7635-0.3941-0.11450.60860.03410.3271-33.5302-33.6559-8.5627
400.28140.1644-0.12180.7944-0.55880.80120.1141-0.194-0.10720.10060.08060.20780.0052-0.1828-0.06840.1914-0.22250.00220.34880.24910.1766-31.2665-25.8855-12.0864
410.0337-0.0057-0.00490.1874-0.05490.0320.0118-0.1383-0.14440.1297-0.1751-0.26140.01780.2049-0.16230.0429-0.09020.00920.15750.33350.401-15.905-30.1333-13.5394
420.36480.0049-0.09590.9293-0.00240.2975-0.118-0.0494-0.17950.2314-0.07050.30720.1552-0.09310.13870.417-0.36680.05330.31310.09330.1947-26.7284-21.8327-11.9944
430.16360.04090.04420.1366-0.03440.2082-0.0239-0.09710.00350.0333-0.0524-0.0958-0.05510.1005-0.2015-0.3174-0.0916-0.096-0.31930.2164-0.2112-6.3716-4.9685-11.2492
440.47350.1422-0.35740.2548-0.09530.5263-0.0631-0.0594-0.0992-0.056-0.0274-0.09910.10170.13040.23080.0608-0.14540.01770.16970.1115-0.0411-9.983-17.8205-26.087
450.91420.6118-0.15640.8834-0.20790.62380.2659-0.20070.33190.2694-0.10230.4271-0.1721-0.1601-0.21510.306-0.2951-0.02620.42630.19580.4303-21.8432-3.7178-1.5743
461.01810.7977-0.10133.2771-0.08691.050.0558-0.01750.25290.3010.00870.2774-0.2121-0.131-0.07841.0955-0.29930.21190.91510.4330.9831-30.5689-31.50748.7696
472.47030.03371.6360.02980.10291.30240.13840.6179-0.1242-0.6479-0.05940.57760.26150.0898-0.04861.5910.4399-0.5361.0131-0.30930.9517-33.526816.1334-54.6824
480.4690.13960.50090.04540.18650.85530.13850.4484-0.1778-0.3105-0.22170.20540.05770.12-0.02291.49760.5045-0.660.8911-0.23760.9628-38.452121.9442-62.1059
491.1561-0.43710.57210.61040.02051.8245-0.16130.21780.0432-0.25260.14440.0712-0.0377-0.00420.04221.29190.2223-0.68960.649-0.25851.0075-38.748129.1835-50.3589
500.0525-0.0401-0.12750.07430.18580.48620.28110.2365-0.3382-0.5919-0.33560.43960.0824-0.44120.01943.1360.3536-1.68031.3975-0.42062.7472-57.744821.7357-55.9928
511.6828-0.7350.51621.1433-0.85811.21930.18680.2279-0.1067-0.4213-0.17810.03070.39060.17920.05761.68280.2121-0.8920.7744-0.00171.4153-38.719733.3131-62.6299
521.3065-0.192-0.01610.66980.38320.24890.0402-0.128-0.17750.707-0.2908-0.6024-0.2631-0.09410.16831.48580.157-0.65340.6497-0.04731.4352-63.429954.0365-55.4092
535.5802-3.99261.50074.5698-3.31763.3426-0.0156-0.10310.00270.2670.1403-0.11860.23160.1015-0.11881.31520.1025-0.76630.62790.00671.3406-48.742150.4915-46.3684
540.87120.04910.70680.15150.06370.5750.13160.0525-0.1784-0.0978-0.08010.08110.1237-0.1024-0.09971.33940.1954-0.85080.8375-0.211.3686-64.70447.6016-66.1374
550.4737-0.0050.45370.12890.2350.88430.214-0.0889-0.3355-0.0037-0.0020.11910.4032-0.4048-0.14981.82-0.1124-1.00390.9871-0.15121.6872-61.037536.5643-51.0741
560.7569-0.697-0.12580.71840.28860.46690.33960.173-0.0929-0.16770.0311-0.05680.40760.2154-0.21761.54320.6798-0.66131.0861-0.47641.198-47.386148.3282-68.1596
571.51430.6108-0.7162.5108-3.63025.3153-0.51770.48270.0859-1.13820.2720.15-0.36970.07860.24352.10580.045-0.18182.2213-0.33380.6573-38.112120.8993-78.5702
580.3232-0.0256-0.07310.7414-0.54110.45580.06350.28490.29540.12560.01420.2074-0.2015-0.0265-0.06760.8455-0.1683-0.06670.83230.56581.3898-38.84297.4834-65.5319
591.943-1.10930.35161.1831-1.04921.37080.1310.36980.0737-0.61550.05010.446-0.1793-0.3199-0.25451.18840.1085-0.15230.49080.33741.0525-51.723287.2807-72.3177
600.17010.05040.29740.56790.06390.5711-0.00610.08240.0420.03590.1082-0.008-0.006-0.08750.04331.0103-0.0867-0.59730.53190.20520.9727-47.740493.7375-56.3557
610.4976-0.19430.09041.080.061.12910.01680.0509-0.035-0.3209-0.02090.2462-0.0205-0.1299-0.09920.8126-0.1866-0.31620.43610.30160.5029-48.490290.0086-55.1501
621.59620.3972-1.73812.3319-1.72642.66530.0343-0.0649-0.18180.06380.0121-0.3589-0.07610.1972-0.0741.1068-0.2555-0.31890.613-0.01911.4976-31.991686.3324-72.1319
630.35690.21930.24750.94030.27360.946-0.03230.12020.2044-0.21630.0760.6109-0.1055-0.33090.04710.2484-0.0258-0.14740.18920.04430.3202-44.936162.2835-40.1428
640.708-0.16850.15181.6659-0.08591.348-0.15580.09150.0267-0.2834-0.15690.47190.0479-0.42590.07670.1433-0.0472-0.01660.3637-0.0330.2417-45.415872.4649-43.0205
652.18750.04790.30890.5074-0.35420.380.0155-0.27150.17780.11580.0301-0.02230.1086-0.1149-0.05240.4476-0.0049-0.37640.32690.05890.9512-60.231382.7915-46.093
660.61360.6444-0.2030.8252-0.4760.5467-0.00130.0182-0.2304-0.16580.0274-0.18020.1540.02640.22480.5553-0.3681-0.23790.55880.36160.5292-35.303868.3685-57.0938
670.20830.035-0.16670.0582-0.02660.1334-0.1917-0.1101-0.18040.16030.1557-0.2347-0.14130.22140.03031.430.1055-1.00063.1930.10462.5818-25.952196.5886-65.1931
681.1472-0.19150.39760.6563-0.09060.69130.144-0.27140.07020.2118-0.03110.3520.0625-0.30590.0470.41370.0255-0.36270.2784-0.14440.8162-22.758340.1101-1.9694
690.5943-0.40050.33141.05710.02670.73280.1237-0.0015-0.22990.25680.0428-0.0844-0.132-0.2108-0.04380.5980.316-0.30540.3785-0.29260.5625-23.756338.1746-12.9405
700.2768-0.002-0.00890.29280.08410.10570.05840.13760.0679-0.1594-0.1266-0.1218-0.04150.007-0.01140.02950.1549-0.1244-0.12490.0684-0.0553-21.014313.8166-27.8225
710.343-0.0380.36560.20020.07670.56370.02570.2104-0.0501-0.0146-0.04170.0152-0.0216-0.0434-0.05730.1720.196-0.10520.4753-0.26530.2659-26.896523.797-28.7582
720.4136-0.22530.26490.3524-0.32370.3042-0.06410.16520.1251-0.102-0.036-0.0115-0.13590.08330.08630.49890.1105-0.22050.368-0.20920.4515-8.251530.3085-24.292
730.4433-0.3042-0.19130.62620.26420.5475-0.1549-0.044-0.21610.2439-0.01190.27620.1664-0.15480.22340.26110.23230.01870.3032-0.2520.2781-33.127215.8242-13.3125
743.0138-0.49540.3680.8053-0.17130.4476-0.00350.03930.0735-0.01560.01780.2956-0.0217-0.1322-0.03340.45130.2082-0.09881.503-0.31221.0262-43.051645.2357-5.5881
750.21920.1254-0.27391.4344-0.98920.8620.3881-0.7370.14271.1165-0.4865-0.30560.4737-0.28180.0721.8479-0.86610.14641.9383-0.32171.6565-11.42713.419929.2119
760.75580.6368-0.62313.78370.45880.9050.6705-0.2833-0.98870.7603-0.395-0.23640.8458-0.2348-0.24072.9008-0.9837-0.68212.2678-0.82112.9068-21.51685.37431.9482
770.2012-0.0622-0.68921.10731.08963.06530.6369-0.4002-1.01021.6617-0.5822-0.67951.4819-0.8368-0.06265.4625-2.1988-1.58193.29990.863.0155-25.9159-7.165546.1569
781.6417-1.10781.82674.85851.7714.22690.8829-1.4154-0.79521.9817-0.88640.5320.9585-0.9239-0.01981.7916-0.4122-0.2111.6599-0.23170.9447-19.5582.527521.7435
791.4685-1.3796-0.68185.22181.39883.06930.3864-0.19410.27561.90720.03310.0192-0.01320.1129-0.41362.3906-0.963-0.47111.75180.42242.1616-50.8472-3.548919.338
800.545-0.33620.68332.36531.63583.07670.4766-0.17880.32962.3143-0.0735-0.478-0.07490.5165-0.43623.0223-1.0356-0.56961.58730.09132.3317-45.4746-5.578724.1628
813.23262.4869-1.1835.7217-4.20464.610.6905-1.35341.33962.4041-0.1018-0.09650.54171.0666-0.56892.5020.0747-0.91711.836-0.74032.3813-36.7252-16.563523.4568
822.13381.12510.15571.30511.04141.92611.7663-1.19871.82474.7723-0.58491.4453-1.53740.2032-1.18344.2874-0.17810.17162.4559-1.46193.9601-42.73741.635333.6269
830.6668-0.0218-0.00060.26370.27690.2914-0.7158-0.39750.93-0.61360.1803-0.0292-1.2893-0.08820.53278.7431-1.5132-0.15874.5615-1.4963.5631-41.1134-3.533444.683
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'N' and (resid 324 through 365 )
2X-RAY DIFFRACTION2chain 'P' and (resid 168 through 194 )
3X-RAY DIFFRACTION3chain 'P' and (resid 195 through 214 )
4X-RAY DIFFRACTION4chain 'P' and (resid 215 through 273 )
5X-RAY DIFFRACTION5chain 'P' and (resid 274 through 283 )
6X-RAY DIFFRACTION6chain 'P' and (resid 284 through 295 )
7X-RAY DIFFRACTION7chain 'P' and (resid 296 through 315 )
8X-RAY DIFFRACTION8chain 'P' and (resid 316 through 331 )
9X-RAY DIFFRACTION9chain 'P' and (resid 332 through 367 )
10X-RAY DIFFRACTION10chain 'Q' and (resid 171 through 203 )
11X-RAY DIFFRACTION11chain 'Q' and (resid 204 through 252 )
12X-RAY DIFFRACTION12chain 'Q' and (resid 253 through 295 )
13X-RAY DIFFRACTION13chain 'Q' and (resid 296 through 316 )
14X-RAY DIFFRACTION14chain 'Q' and (resid 317 through 328 )
15X-RAY DIFFRACTION15chain 'Q' and (resid 329 through 366 )
16X-RAY DIFFRACTION16chain 'S' and (resid 168 through 194 )
17X-RAY DIFFRACTION17chain 'S' and (resid 195 through 236 )
18X-RAY DIFFRACTION18chain 'S' and (resid 237 through 262 )
19X-RAY DIFFRACTION19chain 'S' and (resid 263 through 295 )
20X-RAY DIFFRACTION20chain 'S' and (resid 296 through 314 )
21X-RAY DIFFRACTION21chain 'S' and (resid 315 through 331 )
22X-RAY DIFFRACTION22chain 'S' and (resid 332 through 368 )
23X-RAY DIFFRACTION23chain 'T' and (resid 175 through 214 )
24X-RAY DIFFRACTION24chain 'T' and (resid 215 through 226 )
25X-RAY DIFFRACTION25chain 'T' and (resid 227 through 240 )
26X-RAY DIFFRACTION26chain 'T' and (resid 241 through 270 )
27X-RAY DIFFRACTION27chain 'T' and (resid 271 through 324 )
28X-RAY DIFFRACTION28chain 'T' and (resid 325 through 366 )
29X-RAY DIFFRACTION29chain 'V' and (resid 166 through 194 )
30X-RAY DIFFRACTION30chain 'V' and (resid 195 through 242 )
31X-RAY DIFFRACTION31chain 'V' and (resid 243 through 262 )
32X-RAY DIFFRACTION32chain 'V' and (resid 263 through 285 )
33X-RAY DIFFRACTION33chain 'V' and (resid 286 through 314 )
34X-RAY DIFFRACTION34chain 'V' and (resid 315 through 352 )
35X-RAY DIFFRACTION35chain 'V' and (resid 353 through 367 )
36X-RAY DIFFRACTION36chain 'W' and (resid 175 through 226 )
37X-RAY DIFFRACTION37chain 'W' and (resid 227 through 316 )
38X-RAY DIFFRACTION38chain 'W' and (resid 317 through 366 )
39X-RAY DIFFRACTION39chain 'A' and (resid 142 through 194 )
40X-RAY DIFFRACTION40chain 'A' and (resid 195 through 262 )
41X-RAY DIFFRACTION41chain 'A' and (resid 263 through 313 )
42X-RAY DIFFRACTION42chain 'A' and (resid 314 through 367 )
43X-RAY DIFFRACTION43chain 'B' and (resid 162 through 285 )
44X-RAY DIFFRACTION44chain 'B' and (resid 286 through 323 )
45X-RAY DIFFRACTION45chain 'B' and (resid 324 through 366 )
46X-RAY DIFFRACTION46chain 'C' and (resid 352 through 358 )
47X-RAY DIFFRACTION47chain 'D' and (resid 142 through 174 )
48X-RAY DIFFRACTION48chain 'D' and (resid 175 through 243 )
49X-RAY DIFFRACTION49chain 'D' and (resid 244 through 283 )
50X-RAY DIFFRACTION50chain 'D' and (resid 284 through 323 )
51X-RAY DIFFRACTION51chain 'D' and (resid 324 through 367 )
52X-RAY DIFFRACTION52chain 'E' and (resid 162 through 203 )
53X-RAY DIFFRACTION53chain 'E' and (resid 204 through 214 )
54X-RAY DIFFRACTION54chain 'E' and (resid 215 through 252 )
55X-RAY DIFFRACTION55chain 'E' and (resid 253 through 323 )
56X-RAY DIFFRACTION56chain 'E' and (resid 324 through 365 )
57X-RAY DIFFRACTION57chain 'F' and (resid 352 through 358 )
58X-RAY DIFFRACTION58chain 'G' and (resid 145 through 214 )
59X-RAY DIFFRACTION59chain 'G' and (resid 215 through 262 )
60X-RAY DIFFRACTION60chain 'G' and (resid 263 through 295 )
61X-RAY DIFFRACTION61chain 'G' and (resid 296 through 352 )
62X-RAY DIFFRACTION62chain 'G' and (resid 353 through 367 )
63X-RAY DIFFRACTION63chain 'H' and (resid 165 through 195 )
64X-RAY DIFFRACTION64chain 'H' and (resid 196 through 285 )
65X-RAY DIFFRACTION65chain 'H' and (resid 286 through 323 )
66X-RAY DIFFRACTION66chain 'H' and (resid 324 through 366 )
67X-RAY DIFFRACTION67chain 'I' and (resid 352 through 358 )
68X-RAY DIFFRACTION68chain 'J' and (resid 145 through 270 )
69X-RAY DIFFRACTION69chain 'J' and (resid 271 through 367 )
70X-RAY DIFFRACTION70chain 'K' and (resid 165 through 243 )
71X-RAY DIFFRACTION71chain 'K' and (resid 244 through 285 )
72X-RAY DIFFRACTION72chain 'K' and (resid 286 through 323 )
73X-RAY DIFFRACTION73chain 'K' and (resid 324 through 366 )
74X-RAY DIFFRACTION74chain 'L' and (resid 352 through 359 )
75X-RAY DIFFRACTION75chain 'M' and (resid 167 through 243 )
76X-RAY DIFFRACTION76chain 'M' and (resid 244 through 295 )
77X-RAY DIFFRACTION77chain 'M' and (resid 296 through 323 )
78X-RAY DIFFRACTION78chain 'M' and (resid 324 through 367 )
79X-RAY DIFFRACTION79chain 'N' and (resid 173 through 195 )
80X-RAY DIFFRACTION80chain 'N' and (resid 196 through 246 )
81X-RAY DIFFRACTION81chain 'N' and (resid 247 through 273 )
82X-RAY DIFFRACTION82chain 'N' and (resid 274 through 295 )
83X-RAY DIFFRACTION83chain 'N' and (resid 296 through 323 )

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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

-
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