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- PDB-5w1s: X-ray crystal structure of Escherichia coli RNA polymerase and Tr... -

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基本情報

登録情報
データベース: PDB / ID: 5w1s
タイトルX-ray crystal structure of Escherichia coli RNA polymerase and TraR complex
要素
  • (DNA-directed RNA polymerase subunit ...) x 4
  • Protein TraR
  • RNA polymerase sigma factor RpoD
キーワードTRANSFERASE / RNA polymerase / TraR
機能・相同性
機能・相同性情報


sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / sigma factor activity / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility ...sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / sigma factor activity / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm
類似検索 - 分子機能
Zinc finger, C4 DksA/TraR-type / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Zinc finger, DksA/TraR C4-type conserved site / Zinc finger, DksA/TraR C4-type, bacteria / Prokaryotic dksA C4-type zinc finger. / Zinc finger, DksA/TraR C4-type / Prokaryotic dksA/traR C4-type zinc finger / Prokaryotic dksA C4-type zinc finger profiles. / RNA polymerase sigma factor 70, non-essential domain ...Zinc finger, C4 DksA/TraR-type / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Zinc finger, DksA/TraR C4-type conserved site / Zinc finger, DksA/TraR C4-type, bacteria / Prokaryotic dksA C4-type zinc finger. / Zinc finger, DksA/TraR C4-type / Prokaryotic dksA/traR C4-type zinc finger / Prokaryotic dksA C4-type zinc finger profiles. / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Gyrase A; domain 2 / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Beta Complex / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich
類似検索 - ドメイン・相同性
RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / Protein TraR
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.805 Å
データ登録者Murakami, K.S. / Molodtsov, V.
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)GM087350 米国
引用ジャーナル: Mol. Cell / 年: 2018
タイトル: Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA.
著者: Molodtsov, V. / Sineva, E. / Zhang, L. / Huang, X. / Cashel, M. / Ades, S.E. / Murakami, K.S.
履歴
登録2017年6月4日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年6月14日Provider: repository / タイプ: Initial release
改定 1.12017年9月20日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22018年2月7日Group: 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.title / _citation.year
改定 1.32018年3月14日Group: Database references / カテゴリ: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _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
改定 1.42020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52023年10月4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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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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: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
M: Protein TraR
N: Protein TraR
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)938,56122
ポリマ－938,12014
非ポリマー4418
水00
1
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
M: Protein TraR
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)469,28111
ポリマ－469,0607
非ポリマー2214
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area42780 Å2
ΔGint-204 kcal/mol
Surface area162230 Å2
手法PISA
2
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
N: Protein TraR
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)469,28111
ポリマ－469,0607
非ポリマー2214
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area41140 Å2
ΔGint-196 kcal/mol
Surface area154820 Å2
手法PISA
単位格子
Length a, b, c (Å)186.484, 206.039, 310.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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DNA-directed RNA polymerase subunit ... , 4種, 10分子 ABGHCIDJEK

#1: タンパク質
DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


分子量: 36558.680 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: rpoA, pez, phs, sez, b3295, JW3257 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0A7Z4, DNA-directed RNA polymerase
#2: タンパク質 DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


分子量: 150820.875 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12
遺伝子: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0A8V2, DNA-directed RNA polymerase
#3: タンパク質 DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


分子量: 155366.781 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: rpoC, tabB, b3988, JW3951 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0A8T7, DNA-directed RNA polymerase
#4: タンパク質 DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


分子量: 10249.547 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: rpoZ, b3649, JW3624 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0A800, DNA-directed RNA polymerase

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タンパク質 , 2種, 4分子 FLMN

#5: タンパク質 RNA polymerase sigma factor RpoD / Sigma-70


分子量: 70352.242 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: rpoD, alt, b3067, JW3039 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P00579
#6: タンパク質 Protein TraR


分子量: 9153.373 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: traR, ECOK12F083 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P41065

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非ポリマー , 2種, 8分子

#7: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg
#8: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Zn

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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: 3.18 Å3/Da / 溶媒含有率: 61.29 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1M HEPES-HCL (PH7), 0.2M Ca-ACETATE, 15% PEG400

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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: CHESS / ビームライン: F1 / 波長: 0.98 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2017年4月14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: 0.98 Å / 相対比: 1
反射解像度: 3.8→50 Å / Num. obs: 117447 / % possible obs: 100 % / 冗長度: 7.8 % / Rpim(I) all: 0.043 / Net I/σ(I): 17.5
反射 シェル解像度: 3.8→3.87 Å / 冗長度: 7.4 % / Num. unique obs: 5789 / CC1/2: 0.27 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.11.1_2575: ???)精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4YG2

4yg2


解像度: 3.805→49.836 Å / SU ML: 0.61 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 30.49
Rfactor反射数%反射
Rfree0.2624 3844 1.7 %
Rwork0.2077 --
obs0.2086 225641 99.62 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 3.805→49.836 Å
タンパク質核酸リガンド溶媒全体
原子数56817 0 8 0 56825
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00557685
X-RAY DIFFRACTIONf_angle_d1.06877823
X-RAY DIFFRACTIONf_dihedral_angle_d17.74635675
X-RAY DIFFRACTIONf_chiral_restr0.0528859
X-RAY DIFFRACTIONf_plane_restr0.00610210
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8051-3.85320.37961350.37177749X-RAY DIFFRACTION95
3.8532-3.90390.40421430.37388224X-RAY DIFFRACTION99
3.9039-3.95740.38631380.35788106X-RAY DIFFRACTION98
3.9574-4.01390.3931440.34558177X-RAY DIFFRACTION100
4.0139-4.07380.38531430.32218267X-RAY DIFFRACTION100
4.0738-4.13740.31171430.30438312X-RAY DIFFRACTION100
4.1374-4.20520.32041400.28448224X-RAY DIFFRACTION100
4.2052-4.27770.29711420.27528248X-RAY DIFFRACTION100
4.2777-4.35540.33241440.26548214X-RAY DIFFRACTION100
4.3554-4.43910.32061460.25748269X-RAY DIFFRACTION100
4.4391-4.52970.21861460.23668253X-RAY DIFFRACTION100
4.5297-4.62810.29411430.23378223X-RAY DIFFRACTION100
4.6281-4.73570.27321420.23018240X-RAY DIFFRACTION100
4.7357-4.8540.31091430.22178228X-RAY DIFFRACTION100
4.854-4.98520.29681440.22148226X-RAY DIFFRACTION100
4.9852-5.13170.26581420.22098256X-RAY DIFFRACTION100
5.1317-5.29720.22871440.21548236X-RAY DIFFRACTION100
5.2972-5.48630.26811460.21958302X-RAY DIFFRACTION100
5.4863-5.70560.25111470.22078205X-RAY DIFFRACTION100
5.7056-5.96490.30591440.23088226X-RAY DIFFRACTION100
5.9649-6.27880.28641430.22658278X-RAY DIFFRACTION100
6.2788-6.67130.33851440.21868246X-RAY DIFFRACTION100
6.6713-7.18510.24621410.20558255X-RAY DIFFRACTION100
7.1851-7.90550.26141410.18178255X-RAY DIFFRACTION100
7.9055-9.04360.1941420.15488224X-RAY DIFFRACTION100
9.0436-11.37160.19711410.15078211X-RAY DIFFRACTION100
11.3716-49.840.24931330.17518143X-RAY DIFFRACTION99
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6943.6854-1.11126.5325-1.09221.52410.1109-0.834-0.01260.7427-0.5258-0.16070.3801-0.09050.31982.14570.0917-0.00651.9892-0.22651.314296.78529.51738.7272
24.2068-2.7522-1.06743.7834-2.30154.26310.1208-0.7719-0.167-0.42950.493-0.3557-0.9131-0.5226-0.68051.99750.0874-0.09472.7829-0.49632.09766.862357.087722.8582
31.06262.49550.09147.20450.4372-0.3667-0.42840.1205-0.25950.34740.45750.10750.9659-0.6116-0.01572.4224-0.56690.48762.16940.23811.51171.4458-5.948835.3246
4-0.22461.1202-1.0452.7591-4.30795.80350.5055-0.3018-0.23250.176-0.7401-0.4312-0.84081.63740.2161.872-0.3638-0.07121.56680.11871.7196134.49342.9878-8.1041
51.8067-1.0764-1.08293.72881.81460.87520.26731.1991-0.4628-1.62180.1643-1.095-0.37350.2392-0.57582.7593-0.11780.07683.3088-0.3392.343139.056916.6964-41.2724
60.78181.96831.53263.0425-0.65584.1149-0.11950.5716-0.2848-0.5386-0.0343-0.32730.50220.56370.11640.91780.0167-0.05351.480.12741.38128.449822.7375-6.4664
71.858-0.08350.58650.48490.58991.0096-0.0574-0.16190.4470.44910.1006-0.0666-0.0313-0.045-0.01581.0038-0.0571-0.03851.5115-0.03261.2175112.545837.287616.75
81.42671.9294-3.63175.5255-2.30818.18870.2404-0.44680.60.0112-0.26230.5023-0.3669-0.61520.00790.5410.0650.09771.1307-0.07031.35977.862129.8849-18.4302
90.5923-0.0776-0.19411.2089-0.28762.4478-0.0685-0.04380.0285-0.1212-0.0861-0.1138-0.0532-0.39850.18920.8466-0.07040.19511.1651-0.05991.376484.82925.5149-22.3984
101.504-0.10341.4660.7953-0.60881.7810.3409-0.0768-0.91880.1789-0.0783-0.07480.97580.2599-0.15181.73420.15130.23561.39910.0421.697398.1432-7.1581-5.9435
113.9653-2.2665-2.1915.17842.82445.9655-0.14790.4165-0.5024-0.326-0.1446-0.60870.80830.34440.13811.2447-0.11780.26891.1633-0.08811.325688.5133-1.2734-36.6833
126.1651.04412.7263.6318-2.39234.0208-0.1722-1.1633-0.6330.05461.25051.54460.2493-1.5769-0.73171.7806-0.15910.20452.0691-0.02992.585360.337813.5315-2.9681
132.9222-3.56751.6246.53592.41268.8154-0.0514-0.3186-2.14050.26120.3248-1.4316-1.15330.424-0.57731.5682-0.1117-0.21241.8167-0.06332.667741.835224.5731-16.8348
142.2971-4.58873.50348.1705-6.11263.86690.41940.11360.2788-0.3973-0.5643-0.125-0.49260.58820.19162.6023-0.25570.66631.4344-0.01582.004495.832276.1315-67.2336
158.37855.19015.55936.08363.84283.56832.089-1.0708-2.6281-1.0623-0.36110.5951-1.6771-1.8556-1.94233.1624-0.2-0.49072.10080.25843.222274.832559.8419-84.1432
160.7780.1024-1.11220.60090.00612.8990.0734-0.2159-0.1627-0.4283-0.1577-0.2417-0.87970.36040.17511.7672-0.13410.1111.4754-0.03182.062995.897360.1402-38.9823
174.4682-5.68153.38716.3614-3.00947.43741.04120.45550.3992-1.7792-0.6271-1.08850.1912-0.398-0.471.78850.01390.03911.5715-0.35211.691556.843164.427-1.9511
18-1.00392.75640.49124.03645.2542.72250.4668-0.15450.327-1.1857-0.43671.74540.0921-1.37160.07651.5079-0.090.582.59320.63362.9874-14.129-39.1602-29.1991
19-0.12332.95581.01647.87761.46180.84570.1859-0.88790.84430.4119-0.3868-2.0154-0.8343-1.21670.45952.58570.91150.59122.6951-0.12972.71631.7773-3.3562-9.397
203.9452-4.9601-3.89026.88667.09575.4464-0.11650.2676-0.0406-1.4969-0.14161.6998-0.4953-0.18770.35932.5528-0.25-0.30141.70220.18251.883111.509-57.2577-83.0354
212.42192.5966-1.45852.3704-3.92892.4095-0.6609-0.5862-0.3888-0.4921-0.4458-0.19440.71410.68031.07872.64470.10050.33732.51440.24941.840844.234-29.4732-101.4897
221.13422.0856-2.29132.4209-3.5643.69720.49040.06240.3144-0.19380.00080.7691-0.35330.1676-0.44232.33820.0797-0.12292.52380.19022.168430.3911-49.5941-88.7469
235.554-0.18322.03126.54380.90597.839-0.47791.40871.3694-1.97240.6230.5662-1.06240.8019-0.07242.45950.00530.08822.43070.92822.061913.2012-31.3731-78.5344
242.0608-0.16921.6312.4662.64311.79840.5968-0.274-0.5874-0.5413-0.4530.34140.2133-1.215-0.11842.2594-0.274-0.13583.18390.79372.5224-2.4451-38.2799-66.8221
250.7103-0.43230.60741.8052-0.71190.4778-0.27550.0568-0.4748-0.00420.46921.18830.13580.1084-0.262.2498-0.14860.07642.39120.39062.249217.2376-57.515-36.1528
265.8318-1.4932.91654.7457-0.13464.9640.00571.3783-1.742-1.29970.51361.0309-0.19060.1528-0.05112.4826-0.2518-0.05222.94820.45922.39253.8717-70.1862-51.7518
271.394-0.73880.72961.8479-0.17370.09620.00790.29920.1627-0.86550.48480.78920.0227-0.3737-0.42881.8989-0.148-0.00662.74550.81022.2718-5.1514-40.5402-55.0736
288.5319-2.1925-7.06746.21952.20975.9388-0.1314-0.1931-0.44530.95740.00440.34060.3804-0.33520.10871.82680.05930.23461.37330.09841.425746.5554-42.5682-35.6126
294.22351.2454-1.02283.5637-0.44854.3799-0.1201-0.1075-0.675-0.5468-0.0756-0.41310.26320.02580.26471.63950.10970.31841.0386-0.05491.253567.467-54.5437-57.7852
302.407-0.90080.18411.95580.65681.1383-0.2723-0.0670.67510.03640.4510.3935-0.337-0.1824-0.17521.7686-0.03610.44151.50220.22291.760725.6859-14.5584-41.6152
313.456-2.2770.96787.3056-3.96385.6628-0.05470.71430.00611.34440.50812.3461-0.02740.33110.07681.488-0.08620.56791.26260.06692.091841.7135-15.9027-39.4225
322.41091.6298-1.05435.9643-4.39437.4848-0.21250.51980.2456-0.54420.1364-0.0656-0.40110.90010.13331.693-0.26130.31711.2199-0.18691.36559.408-13.4221-54.5088
332.7165-4.4652-3.60927.17865.98719.8039-2.1618-2.05830.26732.9963-0.09750.445-0.9661.39351.28053.5237-0.292-0.18692.9231-0.46412.898639.7908-26.5049-14.2054
344.7663-1.8963-3.79174.94763.93124.4135-1.06380.07290.7971-0.05723.44923.44560.9604-1.9073-2.54944.94520.4787-0.1365.12781.49343.58254.0448-29.1536-6.1042
354.8486-5.68031.49247.4945-1.35550.2126-0.2532-0.19210.0301-0.10430.165-0.25910.2423-0.18790.06043.0140.01930.74961.70520.04572.025584.2366-89.3737-72.0777
361.51191.19751.83581.07421.2791.88050.89330.85350.8890.8164-1.05040.04981.04560.3627-0.80213.70340.0773-1.01381.97730.23814.3388111.7046-75.902-60.2333
372.8317-0.9068-1.50871.231-1.0281.9393-0.74340.0071-1.1589-0.49680.16280.0180.5983-0.21850.48652.8251-0.34070.27411.5772-0.14462.072654.0159-77.1753-72.4161
381.9217-1.0274-0.70918.7447-6.35084.71580.2889-0.3288-0.20270.2495-0.7713-0.2290.2711.12550.26131.9133-0.15360.22191.76190.12021.965141.1034-69.2518-17.19
392.5632-1.2243-3.4891.52422.3666.32261.46841.3637-1.5704-2.7434-1.83721.1183-3.1305-0.33450.27073.73170.2972-0.27322.3351-0.10472.3343123.569-16.4735-17.4703
408.6862-0.9525-3.66480.4134-1.88097.4798-1.33262.953-0.06320.6086-1.9364-1.73780.2481-2.2113.52443.1665-0.32750.38953.67670.62334.761328.09681.1038-79.978
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 7:232 )A7 - 232
2X-RAY DIFFRACTION2( CHAIN A AND RESID 233:325 )A233 - 325
3X-RAY DIFFRACTION3( CHAIN B AND RESID 6:233 )B6 - 233
4X-RAY DIFFRACTION4( CHAIN C AND RESID 3:114 )C3 - 114
5X-RAY DIFFRACTION5( CHAIN C AND RESID 115:437 )C115 - 437
6X-RAY DIFFRACTION6( CHAIN C AND RESID 438:703 )C438 - 703
7X-RAY DIFFRACTION7( CHAIN C AND RESID 704:1252 )C704 - 1252
8X-RAY DIFFRACTION8( CHAIN C AND RESID 1253:1342 )C1253 - 1342
9X-RAY DIFFRACTION9( CHAIN D AND RESID 8:613 )D8 - 613
10X-RAY DIFFRACTION10( CHAIN D AND RESID 614:936 )D614 - 936
11X-RAY DIFFRACTION11( CHAIN D AND RESID 1133:1376 )D1133 - 1376
12X-RAY DIFFRACTION12( CHAIN E AND RESID 2:60 )E2 - 60
13X-RAY DIFFRACTION13( CHAIN E AND RESID 61:90 )E61 - 90
14X-RAY DIFFRACTION14( CHAIN F AND RESID 94:262 )F94 - 262
15X-RAY DIFFRACTION15( CHAIN F AND RESID 263:333 )F263 - 333
16X-RAY DIFFRACTION16( CHAIN F AND RESID 334:562 )F334 - 562
17X-RAY DIFFRACTION17( CHAIN F AND RESID 563:612 )F563 - 612
18X-RAY DIFFRACTION18( CHAIN G AND RESID 7:233 )G7 - 233
19X-RAY DIFFRACTION19( CHAIN H AND RESID 6:233 )H6 - 233
20X-RAY DIFFRACTION20( CHAIN I AND RESID 3:114 )I3 - 114
21X-RAY DIFFRACTION21( CHAIN I AND RESID 115:370 )I115 - 370
22X-RAY DIFFRACTION22( CHAIN I AND RESID 371:519 )I371 - 519
23X-RAY DIFFRACTION23( CHAIN I AND RESID 520:623 )I520 - 623
24X-RAY DIFFRACTION24( CHAIN I AND RESID 624:804 )I624 - 804
25X-RAY DIFFRACTION25( CHAIN I AND RESID 805:906 )I805 - 906
26X-RAY DIFFRACTION26( CHAIN I AND RESID 907:979 )I907 - 979
27X-RAY DIFFRACTION27( CHAIN I AND RESID 980:1262 )I980 - 1262
28X-RAY DIFFRACTION28( CHAIN I AND RESID 1263:1342 )I1263 - 1342
29X-RAY DIFFRACTION29( CHAIN J AND RESID 16:307 )J16 - 307
30X-RAY DIFFRACTION30( CHAIN J AND RESID 308:899 )J308 - 899
31X-RAY DIFFRACTION31( CHAIN J AND RESID 900:931 )J900 - 931
32X-RAY DIFFRACTION32( CHAIN J AND RESID 1137:1375 )J1137 - 1375
33X-RAY DIFFRACTION33( CHAIN K AND RESID 2:60 )K2 - 60
34X-RAY DIFFRACTION34( CHAIN K AND RESID 61:73 )K61 - 73
35X-RAY DIFFRACTION35( CHAIN L AND RESID 94:292 )L94 - 292
36X-RAY DIFFRACTION36( CHAIN L AND RESID 293:354 )L293 - 354
37X-RAY DIFFRACTION37( CHAIN L AND RESID 355:511 )L355 - 511
38X-RAY DIFFRACTION38( CHAIN L AND RESID 512:613 )L512 - 613
39X-RAY DIFFRACTION39( CHAIN M AND ( RESID 4:73 OR RESID 101:101 ) )M4 - 73
40X-RAY DIFFRACTION39( CHAIN M AND ( RESID 4:73 OR RESID 101:101 ) )M101
41X-RAY DIFFRACTION40( CHAIN N AND ( RESID 4:72 OR RESID 101:101 ) )N4 - 72
42X-RAY DIFFRACTION40( CHAIN N AND ( RESID 4:72 OR RESID 101:101 ) )N101

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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