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- PDB-4l1u: Crystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5... -

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基本情報

登録情報
データベース: PDB / ID: 4l1u
タイトルCrystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5 CTR Phosphopeptide
要素
  • RNA polymerase-associated protein RTF1 homolog
  • Transcription elongation factor SPT5
キーワードTranscription/Peptide / Tutor / Plus3 / Peptide binding protein / Spt5 CTR binding / Transcription / Paf1 complex / Rtf1 / ORF association region / Chromatin / Transcription-Peptide complex
機能・相同性
機能・相同性情報


blastocyst growth / Cdc73/Paf1 complex / negative regulation of DNA-templated transcription, elongation / endodermal cell fate commitment / DSIF complex / regulation of transcription elongation by RNA polymerase II / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / stem cell population maintenance / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection ...blastocyst growth / Cdc73/Paf1 complex / negative regulation of DNA-templated transcription, elongation / endodermal cell fate commitment / DSIF complex / regulation of transcription elongation by RNA polymerase II / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / stem cell population maintenance / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription elongation-coupled chromatin remodeling / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / Wnt signaling pathway / single-stranded DNA binding / E3 ubiquitin ligases ubiquitinate target proteins / chromatin organization / protein heterodimerization activity / mRNA binding / chromatin binding / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
類似検索 - 分子機能
Plus-3 domain / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Spt5, KOW domain repeat 6 / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / Transcription elongation factor SPT5, second KOW domain ...Plus-3 domain / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Spt5, KOW domain repeat 6 / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / Cathepsin B; Chain A / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Alpha-Beta Complex / Alpha Beta
類似検索 - ドメイン・相同性
Transcription elongation factor SPT5 / RNA polymerase-associated protein RTF1 homolog
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: 2.424 Å
データ登録者Wier, A.D. / Heroux, A. / VanDemark, A.P.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2013
タイトル: Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin.
著者: Wier, A.D. / Mayekar, M.K. / Heroux, A. / Arndt, K.M. / Vandemark, A.P.
履歴
登録2013年6月3日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年10月2日Provider: repository / タイプ: Initial release
改定 1.12013年10月23日Group: Database references
改定 1.22013年11月20日Group: Database references
改定 1.32017年11月15日Group: Refinement description / カテゴリ: software / Item: _software.classification / _software.name
改定 1.42023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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
改定 1.52024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: RNA polymerase-associated protein RTF1 homolog
B: RNA polymerase-associated protein RTF1 homolog
C: RNA polymerase-associated protein RTF1 homolog
D: RNA polymerase-associated protein RTF1 homolog
E: RNA polymerase-associated protein RTF1 homolog
F: RNA polymerase-associated protein RTF1 homolog
G: Transcription elongation factor SPT5
H: Transcription elongation factor SPT5
I: Transcription elongation factor SPT5
J: Transcription elongation factor SPT5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)104,56243
ポリマ－101,40810
非ポリマー3,15433
水1,892105
1
B: RNA polymerase-associated protein RTF1 homolog
G: Transcription elongation factor SPT5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,0649
ポリマ－17,3922
非ポリマー6727
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-83 kcal/mol
Surface area8470 Å2
手法PISA
2
C: RNA polymerase-associated protein RTF1 homolog
H: Transcription elongation factor SPT5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,8687
ポリマ－17,3922
非ポリマー4765
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-40 kcal/mol
Surface area8490 Å2
手法PISA
3
E: RNA polymerase-associated protein RTF1 homolog
I: Transcription elongation factor SPT5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,8727
ポリマ－17,3922
非ポリマー4805
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-74 kcal/mol
Surface area8170 Å2
手法PISA
4
F: RNA polymerase-associated protein RTF1 homolog
J: Transcription elongation factor SPT5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,7726
ポリマ－17,3922
非ポリマー3804
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-43 kcal/mol
Surface area8320 Å2
手法PISA
5
A: RNA polymerase-associated protein RTF1 homolog
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)16,3015
ポリマ－15,9201
非ポリマー3804
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
6
D: RNA polymerase-associated protein RTF1 homolog
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)16,6859
ポリマ－15,9201
非ポリマー7658
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)112.932, 172.514, 58.476
Angle α, β, γ (deg.)90.000, 107.000, 90.000
Int Tables number5
Space group name H-MC121

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要素

#1: タンパク質
RNA polymerase-associated protein RTF1 homolog


分子量: 15920.326 Da / 分子数: 6 / 断片: Plus3, UNP residues 353-484 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KIAA0252, RTF1 / プラスミド: pLC3 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) Codon+RILP / 参照: UniProt: Q92541
#2: タンパク質・ペプチド
Transcription elongation factor SPT5 / hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing ...hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing factor large subunit / DSIF large subunit / Tat-cotransactivator 1 protein / Tat-CT1 protein


分子量: 1471.469 Da / 分子数: 4 / 断片: CTR, UNP residues 778-790 / 由来タイプ: 合成 / 詳細: This sequence occurs naturally in human Spt5 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: O00267
#3: 化合物...
ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 29 / 由来タイプ: 合成 / 式: SO4
#4: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C3H8O3
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 105 / 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: 2.69 Å3/Da / 溶媒含有率: 54.2 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 4.2
詳細: Sodium acetate, Ammonium sulfate, pH 4.2, vapor diffusion, sitting drop, temperature 293K

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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: NSLS / ビームライン: X25 / 波長: 1.1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2012年8月5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: 1.1 Å / 相対比: 1
反射解像度: 2.424→50 Å / Num. obs: 40281 / % possible obs: 99.9 % / 冗長度: 3.6 % / Rmerge(I) obs: 0.068 / Χ2: 0.665 / Net I/σ(I): 8.8
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.424-2.523.40.37640100.53199.9
2.52-2.623.60.32339920.498199.9
2.62-2.743.40.24840180.533199.9
2.74-2.883.70.18340400.5761100
2.88-3.063.50.12940270.6251100
3.06-3.33.60.08639970.808199.9
3.3-3.633.60.05540350.8831100
3.63-4.153.60.04440360.6891100
4.15-5.233.70.04240440.6981100
5.23-503.60.05940820.794199.9

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位相決定

位相決定手法: 分子置換
Phasing MR
最高解像度最低解像度
Rotation2.42 Å46.92 Å
Translation2.42 Å46.92 Å

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解析

ソフトウェア
名称バージョン分類NB
DENZOデータ削減
SCALEPACKデータスケーリング
PHASER2.5.0位相決定
PHENIX1.8.2_1309精密化
PDB_EXTRACT3.11データ抽出
HKL-2000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: PDB ENTRY 4L1P

4l1p


解像度: 2.424→46.923 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8414 / SU ML: 0.28 / σ(F): 1.38 / 位相誤差: 23.56 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2263 1750 4.94 %
Rwork0.1777 --
obs0.1801 40278 99.55 %
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: 148.25 Å2 / Biso mean: 55.4372 Å2 / Biso min: 21.54 Å2
精密化ステップサイクル: LAST / 解像度: 2.424→46.923 Å
タンパク質核酸リガンド溶媒全体
原子数6719 0 169 105 6993
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0096985
X-RAY DIFFRACTIONf_angle_d1.1169391
X-RAY DIFFRACTIONf_chiral_restr0.068997
X-RAY DIFFRACTIONf_plane_restr0.0041170
X-RAY DIFFRACTIONf_dihedral_angle_d17.8672611
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.424-2.48510.2951400.22652565270594
2.4851-2.55230.2721330.216927662899100
2.5523-2.62740.3081460.217427322878100
2.6274-2.71220.27591430.212927202863100
2.7122-2.80910.25741340.213827572891100
2.8091-2.92160.26121530.22127362889100
2.9216-3.05450.27221350.206827452880100
3.0545-3.21550.26611520.196627272879100
3.2155-3.41690.22381440.182527572901100
3.4169-3.68070.20721360.166827502886100
3.6807-4.05090.23261310.158527422873100
4.0509-4.63660.16761390.130327612900100
4.6366-5.83990.19651780.15827262904100
5.8399-46.9230.21871260.184728042930100
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)
15.04830.7881.1791.88320.71345.57990.0292-1.481.02021.4321-0.387-0.9551-1.18030.02730.04770.6321-0.1013-0.13090.5793-0.02150.7028275.7874-0.049179.2185
24.98240.71610.20954.32071.12280.25520.7264-1.7814-0.63431.2204-0.3623-0.37140.1082-0.174-0.11360.394-0.0635-0.02350.5140.09580.3524265.3339-9.401578.2365
32.5676-2.6430.52425.1452-2.6341.82640.0105-0.35870.21440.28650.33370.5694-0.4451-0.028-0.35540.3325-0.0233-0.03350.35720.05950.4697249.9511-10.86271.6449
48.82730.53580.72120.41330.20955.61460.0398-0.28350.4187-0.50080.44-0.4313-0.90780.5903-0.27360.2931-0.0013-0.00590.30080.09670.3591255.8236-3.146569.0058
56.5499-0.17690.64346.8011-1.37945.5321-0.47130.6968-0.7775-0.42190.4673-0.44430.04350.16610.02940.2548-0.10940.08790.4209-0.04920.3648263.9895-13.466165.4827
66.24472.61810.30758.0271-1.89856.2503-0.43880.59870.0883-1.05120.19930.15420.48760.1150.19460.3658-0.14710.00870.5372-0.00260.3972248.8302-18.038359.9895
72.19062.09580.48115.0443-1.47623.2005-0.27061.49890.2539-0.41110.71870.4456-0.45780.3042-0.38740.4105-0.15070.02540.5088-0.0210.3232256.3028-11.633462.1219
88.59173.95782.72373.21330.96720.9242-0.13322.0793-0.617-0.53090.0316-0.42510.62940.74520.08230.4401-0.28160.0431.1619-0.01250.2667266.7806-10.83559.146
99.54263.9218-0.53413.7274-0.99370.6556-0.15550.2467-1.062-0.18680.0102-0.67120.0950.22630.10810.2772-0.0251-0.00780.3290.00240.4037269.7808-13.940770.2075
103.5978-3.08440.26745.75843.01373.7481-0.35620.22990.3758-0.08880.25920.3426-0.85060.3660.19850.2862-0.0834-0.00390.4105-0.02250.3522274.4072-0.548368.8842
112.18341.33880.71073.95750.67025.39880.8597-0.37741.39870.2825-0.11730.6592-0.0375-0.7234-0.78090.5506-0.05590.12760.6190.00550.4564259.86420.348878.6355
123.1505-0.9865-0.33615.7369-1.98375.15080.40030.73480.5894-0.5445-0.07340.7132-0.6883-0.3094-0.26160.4790.08920.05760.42040.08560.4782231.102210.589661.4946
135.0011-0.38270.77515.8116-1.67092.92550.01990.2999-0.5601-1.03010.1580.16820.3331-0.0876-0.18240.3612-0.0470.00320.2908-0.06190.316229.9571-7.945368.0584
145.1242-3.22030.63043.0954-1.71015.325-0.1484-0.5567-0.10090.0002-0.0008-1.5272-0.22760.60450.00520.2488-0.02970.01030.52050.03420.3775238.3975-5.77574.2331
152.0144-0.8466-0.99511.362-0.42943.834-0.0539-0.3203-0.02180.3712-0.29570.8647-0.4299-0.64940.12330.36810.06990.13120.4376-0.130.7079216.36111.377872.8452
162.35480.80732.92875.7529-0.02256.08920.3068-0.91640.78740.2711-0.17380.0458-0.4028-0.1751-0.18860.2895-0.02960.10030.3512-0.00930.2986224.41171.319175.2976
173.56852.54213.03064.58644.73365.02550.6607-0.546-0.5492-0.22740.4203-0.653-0.49820.577-1.09640.4491-0.1424-0.00290.4060.00390.4152225.3876-13.451781.7941
183.1760.33151.33315.5113-0.81674.87530.211-0.13760.05550.3066-0.15630.0866-0.42580.00630.00450.29870.01960.03960.3077-0.06890.2653225.3811-1.707576.3249
190.9088-0.1205-0.76488.38661.41721.05040.02770.02260.57710.3772-0.23380.6276-0.2108-0.05410.23970.5262-0.0050.11090.29390.02830.3669225.104114.510469.7268
204.9112-5.0990.11875.3614-1.22988.55010.80890.12860.3419-1.4701-0.3433-0.7177-0.02390.3585-0.35840.39920.04240.06130.3266-0.01070.4243240.44563.118863.237
212.14560.08220.38614.43741.21382.4260.1427-0.01090.0635-0.0316-0.1838-0.00020.1865-0.19370.04620.2465-0.0432-0.00810.28370.00680.2611244.7786-35.023571.2057
223.9246-1.123-1.71157.55392.77264.60040.1584-0.3290.04510.30640.0733-0.37940.3250.0948-0.23770.26-0.041-0.07180.34940.03130.3275248.4786-35.172376.0402
232.24310.26880.93894.6054-1.66782.9320.2088-0.3245-0.42790.2676-0.0939-1.0365-0.21420.0612-0.02460.5847-0.0247-0.12120.2934-0.030.5981249.5419-50.93968.7492
247.3276-3.9533-1.23673.05173.14056.76710.7516-0.2040.1119-0.7579-0.23910.4463-0.2458-0.2734-0.47540.4654-0.0137-0.05160.30240.040.4714233.8177-39.590662.6019
255.32551.4661-2.67322.44830.27971.87710.1848-0.76270.03080.1281-0.15320.13690.17590.0338-0.03190.3497-0.0427-0.03870.4279-0.0530.2259210.3868-27.588876.7355
268.34-1.956-0.46771.36270.98612.70460.0784-0.2092-0.4771-0.26320.0005-0.19440.51970.2639-0.04520.36030.0142-0.0850.3123-0.08710.4333222.1394-32.398168.8805
276.39141.316-2.22697.03792.68794.5810.35730.15041.5251-1.1339-0.010.9238-0.6658-0.6848-0.21620.4189-0.0264-0.11050.52210.02410.5952206.4529-15.562865.6657
288.3099-3.0926-0.93622.82893.04016.0076-0.24030.26520.3641-0.27250.652-0.03180.0813-0.485-0.36080.3355-0.06640.0030.39970.06030.2682210.0799-22.986964.6199
297.5257-0.0465-1.16667.897-0.80898.0328-0.5041.45760.9544-1.14560.0692-1.1218-0.0729-0.53960.11940.4148-0.09590.07770.65-0.05920.5534225.2479-18.534659.5624
302.89090.251-0.37184.81830.42633.7664-0.16831.83980.5613-0.55990.7299-0.43840.2654-0.0908-0.35970.4545-0.13580.04540.5514-0.07970.3276217.7159-25.007761.856
317.37014.4086-2.24973.1064-1.43030.7268-0.61120.08390.1403-0.74510.50080.15850.6611-1.31050.02740.5276-0.35230.03630.84850.13090.2022207.2352-25.966159.0476
322.71731.4642-0.08847.15581.66572.89540.19410.29511.29510.05790.22150.0670.1043-0.0769-0.29740.25440.0131-0.07860.3345-0.05490.3225213.0217-18.325869.657
337.93615.16981.8999.88473.75153.60550.15160.23471.06270.5079-0.230.88110.0773-0.00070.13580.3019-0.09150.0370.34820.02750.3487197.0899-25.380770.3088
342.3787-3.05873.00434.796-3.91183.63890.04130.1163-0.999-0.138-0.13250.25360.54120.09540.040.347-0.121-0.02340.6774-0.04860.3189199.5196-35.56869.2005
352.15423.35280.51826.17150.99242.01710.6333-1.0328-0.52370.8759-0.6421-0.5080.6010.9189-0.00180.4986-0.0013-0.0270.6620.10590.3402214.818-36.536678.9889
365.3940.23062.4592.8012-1.13152.00370.1443-1.421-1.0778-0.00390.42860.3496-0.0987-0.3389-0.49430.4759-0.03640.10870.47870.07180.329239.60571.224452.1561
373.7484-2.841-0.06166.41310.30034.0179-0.556-0.31770.72720.2840.2752-0.0391-0.7250.04330.21440.5334-0.0105-0.03910.3377-0.02440.4682233.535619.378243.6496
386.0661-0.9347-1.34194.9484-1.54524.46280.05490.4601-0.9074-0.240.09080.1875-0.0727-0.0877-0.15250.36020.02520.05270.3279-0.10730.3339231.97036.280934.721
394.1242-2.9242-1.06087.2721.0553.93950.25020.2591-0.0192-0.7939-0.38830.5337-0.60580.09530.16650.4507-0.0029-0.04530.3402-0.02310.3115232.200414.010434.2377
402.1898-1.5224-0.97873.85841.03133.68540.1340.5748-0.80950.44430.01910.4660.3075-0.2134-0.2450.3331-0.004-0.01270.3175-0.00920.4742238.9506-3.672940.7689
413.7757-1.4835-0.64275.25033.03776.899-0.2459-0.2070.14730.37630.5148-0.2996-0.16020.8094-0.23790.3762-0.04590.06660.3853-0.02250.3568242.769.072450.7659
422.8981-1.2157-1.28698.18262.25143.0003-0.3453-0.1935-0.20510.34360.3569-0.27870.4340.1473-0.07030.39850.0275-0.03880.37460.06170.3047238.3442-49.006645.7999
436.49890.2989-0.26744.0612.09282.9052-0.06230.60270.6461-0.53810.2208-0.6137-0.1099-0.0951-0.20460.44710.10560.01360.47090.11120.366241.6215-42.094833.8031
446.7985-3.2150.46076.36422.72741.9401-0.05610.9511-0.3995-0.9951-1.2436-0.29150.09860.11680.59890.62960.06780.1080.43530.22940.7661245.859-58.791529.0913
453.2472-2.3970.23826.45690.93894.28830.05290.59650.1206-0.5001-0.2656-0.47010.52650.02180.25060.48140.01860.11460.45630.05160.3797240.2382-48.161934.1273
462.1167-2.3710.06445.6628-1.61682.86370.37380.84571.00280.27360.0683-0.4359-0.37870.0171-0.10160.37680.10520.08580.39180.05310.4848235.0839-32.478840.1717
474.2712-3.85582.19383.3953-3.1495.6489-0.2133-0.39950.0432-0.01070.17930.12570.2811-0.41430.08390.4509-0.0258-0.0880.44890.04040.3885231.5286-45.379150.0008
482.08150.0186-0.29247.0272-1.8186.32090.3162-0.17260.20930.3771-0.32820.4612-0.001-0.8235-0.12690.4146-0.00940.04580.5064-0.04020.5552216.2995-6.827372.5796
492.21970.42530.477.37733.2663.6525-0.0373-1.02050.36670.3388-0.1033-1.1861-1.30451.01070.24570.42-0.1336-0.08130.6212-0.08080.5933258.3094-30.130673.6054
501.67292.18951.44538.2284-0.29322.17170.88730.53040.7871-0.00120.7568-0.1038-1.1834-1.509-1.45470.7210.04010.01180.82650.14330.8762223.80718.995133.0444
515.395-0.4402-2.62552.19841.78488.70981.1486-0.92070.7768-1.8953-1.0075-0.78570.71971.64540.26190.9650.05080.23390.88510.01570.8449252.3241-44.962833.3636
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 349 through 355 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 356 through 365 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 366 through 377 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 378 through 385 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 386 through 410 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 411 through 419 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 420 through 430 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 431 through 437 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 438 through 461 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 462 through 468 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 469 through 483 )A0
12X-RAY DIFFRACTION12chain 'B' and (resid 350 through 362 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 363 through 372 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 373 through 385 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 386 through 396 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 397 through 410 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 411 through 419 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 420 through 448 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 449 through 468 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 469 through 483 )B0
21X-RAY DIFFRACTION21chain 'C' and (resid 350 through 419 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 420 through 448 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 449 through 468 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 469 through 483 )C0
25X-RAY DIFFRACTION25chain 'D' and (resid 349 through 372 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 373 through 385 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 386 through 396 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 397 through 410 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 411 through 419 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 420 through 430 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 431 through 437 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 438 through 448 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 449 through 461 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 462 through 468 )D0
35X-RAY DIFFRACTION35chain 'D' and (resid 469 through 484 )D0
36X-RAY DIFFRACTION36chain 'E' and (resid 349 through 362 )E0
37X-RAY DIFFRACTION37chain 'E' and (resid 363 through 385 )E0
38X-RAY DIFFRACTION38chain 'E' and (resid 386 through 410 )E0
39X-RAY DIFFRACTION39chain 'E' and (resid 411 through 448 )E0
40X-RAY DIFFRACTION40chain 'E' and (resid 449 through 461 )E0
41X-RAY DIFFRACTION41chain 'E' and (resid 462 through 482 )E0
42X-RAY DIFFRACTION42chain 'F' and (resid 349 through 385 )F0
43X-RAY DIFFRACTION43chain 'F' and (resid 386 through 410 )F0
44X-RAY DIFFRACTION44chain 'F' and (resid 411 through 419 )F0
45X-RAY DIFFRACTION45chain 'F' and (resid 420 through 448 )F0
46X-RAY DIFFRACTION46chain 'F' and (resid 449 through 461 )F0
47X-RAY DIFFRACTION47chain 'F' and (resid 462 through 482 )F0
48X-RAY DIFFRACTION48chain 'G' and (resid 781 through 788 )G0
49X-RAY DIFFRACTION49chain 'H' and (resid 780 through 790 )H0
50X-RAY DIFFRACTION50chain 'I' and (resid 783 through 787 )I0
51X-RAY DIFFRACTION51chain 'J' and (resid 782 through 786 )J0

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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