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- PDB-4yfk: Escherichia coli RNA polymerase in complex with squaramide compound 8. -

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基本情報

登録情報
データベース: PDB / ID: 4yfk
タイトルEscherichia coli RNA polymerase in complex with squaramide compound 8.
要素
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA polymerase sigma factor RpoD
キーワードtranscription/transcription inhibitor / switch region / squaramide / transcription-inhibitor complex / transcription-transcription inhibitor complex
機能・相同性
機能・相同性情報


sigma factor antagonist complex / regulation of DNA-templated transcription initiation / sigma factor activity / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / : / : / : / : / : ...sigma factor antagonist complex / regulation of DNA-templated transcription initiation / sigma factor activity / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / : / : / : / : / : / : / DNA-templated transcription initiation / DNA-directed RNA polymerase activity / ribonucleoside binding / DNA-directed RNA polymerase / response to heat / protein dimerization activity / negative regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytosol / cytoplasm
類似検索 - 分子機能
Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 ...Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / 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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / 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 / Helix Hairpins / 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 / 5' to 3' exonuclease, C-terminal subdomain / Helix non-globular / Beta Complex / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / 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 / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A
類似検索 - ドメイン・相同性
Chem-4C6 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta' / RNA polymerase sigma factor RpoD
類似検索 - 構成要素
生物種Escherichia coli O139:H28 (大腸菌)
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: 3.571 Å
データ登録者Molodtsov, V. / Fleming, P.R. / Eyermann, C.J. / Ferguson, A.D. / Foulk, M.A. / McKinney, D.C. / Masse, C.E. / Buurman, E.T. / Murakami, K.S.
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: J.Med.Chem. / 年: 2015
タイトル: X-ray Crystal Structures of Escherichia coli RNA Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with an Improved Fraction Unbound to Human Plasma Protein.
著者: Molodtsov, V. / Fleming, P.R. / Eyermann, C.J. / Ferguson, A.D. / Foulk, M.A. / McKinney, D.C. / Masse, C.E. / Buurman, E.T. / Murakami, K.S.
履歴
登録2015年2月25日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年3月11日Provider: repository / タイプ: Initial release
改定 1.12015年4月8日Group: Database references
改定 1.22015年4月22日Group: Database references
改定 1.32017年9月20日Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
カテゴリ: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
改定 1.42019年12月25日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52023年9月27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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)921,05922
ポリマ－919,81412
非ポリマー1,24610
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)460,53011
ポリマ－459,9076
非ポリマー6235
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area38900 Å2
ΔGint-198 kcal/mol
Surface area157920 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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)460,53011
ポリマ－459,9076
非ポリマー6235
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area37320 Å2
ΔGint-183 kcal/mol
Surface area151440 Å2
手法PISA
単位格子
Length a, b, c (Å)186.105, 206.438, 307.993
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 O139:H28 (strain E24377A / ETEC) (大腸菌)
株: E24377A / ETEC / 遺伝子: rpoA, EcE24377A_3778 / プラスミド: pGEMABC / 詳細 (発現宿主): addgene #45398 / 発現宿主: Escherichia coli #1/H766 (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: A7ZSI4, 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 O139:H28 (strain E24377A / ETEC) (大腸菌)
株: E24377A / ETEC / 遺伝子: rpoB, EcE24377A_4528 / プラスミド: pGEMABC / 詳細 (発現宿主): addgene #45398 / 発現宿主: Escherichia coli #1/H766 (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: A7ZUK1, 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 O139:H28 (strain E24377A / ETEC) (大腸菌)
株: E24377A / ETEC / 遺伝子: rpoC, EcE24377A_4529 / プラスミド: pGEMABC / 詳細 (発現宿主): addgene #45398 / 発現宿主: Escherichia coli #1/H766 (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: A7ZUK2, 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 O139:H28 (strain E24377A / ETEC) (大腸菌)
株: E24377A / ETEC / 遺伝子: rpoZ, EcE24377A_4152 / プラスミド: pACYCDuet-1_Ec_rpoZ / 発現宿主: Escherichia coli #1/H766 (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: A7ZTK1, DNA-directed RNA polymerase

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タンパク質 , 1種, 2分子 FL

#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 / プラスミド: pGEMD / 発現宿主: Escherichia coli #1/H766 (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P00579

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非ポリマー , 3種, 10分子

#6: 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: 4 / 由来タイプ: 合成 / 式: Mg
#7: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn
#8: 化合物 ChemComp-4C6 / 3,5-dimethyl-N-{2-[4-(4-methylbenzyl)piperidin-1-yl]-3,4-dioxocyclobut-1-en-1-yl}-1,2-oxazole-4-sulfonamide / N-[2-[4-(4-メチルベンジル)ピペリジノ]-3,4-ジオキソ-1-シクロブテニル]-3,5-ジメチルイソオキサ(以下略)


分子量: 443.516 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C22H25N3O5S

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶マシュー密度: 3.22 Å3/Da / 溶媒含有率: 61.75 %
結晶化温度: 300 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1M HEPES-HCL, 0.2M CaACETATE, 15% PEG400 / PH範囲: 7

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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: 0.9179 Å
検出器タイプ: ADSC QUANTUM 270 / 検出器: CCD / 日付: 2014年6月11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: 0.9179 Å / 相対比: 1
反射解像度: 3.5→30 Å / Num. obs: 133199 / % possible obs: 96.8 % / 冗長度: 5.1 % / Net I/σ(I): 12.8

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解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: 1.9_1692)精密化
HKL-2000データスケーリング
PHASER位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 4IGC

4igc
PDB 未公開エントリ


解像度: 3.571→29.965 Å / SU ML: 0.56 / 交差検証法: FREE R-VALUE / σ(F): 1.38 / 位相誤差: 28.37 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2521 1999 1.5 %
Rwork0.2168 --
obs0.2173 131137 94.64 %
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: 3.571→29.965 Å
タンパク質核酸リガンド溶媒全体
原子数55712 0 70 0 55782
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01856595
X-RAY DIFFRACTIONf_angle_d1.8176393
X-RAY DIFFRACTIONf_dihedral_angle_d18.1621870
X-RAY DIFFRACTIONf_chiral_restr0.0838696
X-RAY DIFFRACTIONf_plane_restr0.00810010
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5711-3.66030.3897950.37876240X-RAY DIFFRACTION64
3.6603-3.7590.3551350.36798905X-RAY DIFFRACTION91
3.759-3.86940.35971380.33979014X-RAY DIFFRACTION92
3.8694-3.9940.34541380.33179010X-RAY DIFFRACTION92
3.994-4.13650.28941420.28199374X-RAY DIFFRACTION95
4.1365-4.30160.2811460.25439536X-RAY DIFFRACTION98
4.3016-4.49680.24431480.22989700X-RAY DIFFRACTION98
4.4968-4.7330.25221480.21759725X-RAY DIFFRACTION99
4.733-5.02820.28231500.21249784X-RAY DIFFRACTION99
5.0282-5.41440.26361480.21529789X-RAY DIFFRACTION99
5.4144-5.95540.27511510.21699853X-RAY DIFFRACTION99
5.9554-6.80830.25531500.21619903X-RAY DIFFRACTION99
6.8083-8.54460.22431530.181710001X-RAY DIFFRACTION100
8.5446-29.96550.18281570.145210224X-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)
10.12590.24440.18930.14890.23680.23060.16840.7934-0.058-0.3914-0.1330.09810.8613-0.1553-01.8490.03020.08111.6363-0.08771.2648-91.161310.5626-46.134
20.6443-0.1597-0.32131.95320.42431.1797-0.19160.15630.447-0.01310.0788-0.3461-0.38480.213201.6499-0.10580.04331.5490.0881.3624-101.406541.9936-34.0716
30.3073-0.04930.05650.424-0.31560.56690.27660.40450.0263-0.9497-0.3266-0.21580.2451-0.25801.9287-0.12920.08571.71330.0061.3887-89.852312.7166-44.9733
40.09990.3552-0.3407-0.12820.43130.0849-0.10370.57-0.22670.10320.0651.0412-0.13990.0376-02.0434-0.0909-0.09312.19120.04341.8616-66.297156.9791-23.3124
50.3193-0.0452-0.16210.1143-0.05780.2413-0.15430.831-0.0230.7143-0.3156-0.1727-0.14280.6279-01.44780.0143-0.06841.5694-0.01561.5163-74.687512.2278-30.3186
60.3542-0.1826-0.26950.2729-0.48520.08820.1499-0.0734-0.0356-0.66080.0550.04230.61750.4366-02.47960.43260.33362.1502-0.27222.0719-68.2365-21.4344-37.724
70.71190.5211-0.25860.2102-0.02530.5484-0.2650.09020.5182-0.5255-0.1084-1.49940.22120.1558-01.76540.12940.49341.6901-0.16291.6653-74.608510.0008-32.9274
81.7938-0.3082-0.6531.21370.56330.71960.0882-0.2720.3201-0.0822-0.14550.2047-0.6741-0.6177-01.44050.1491-0.0911.5482-0.08041.337-131.868143.04589.1992
90.3368-0.05670.28261.0585-0.88940.2370.2873-0.3415-0.51150.945-0.21290.78690.3009-0.0337-02.4762-0.02680.31642.2104-0.06821.9128-141.65519.468849.3507
100.6543-0.47260.40180.74-0.85040.1983-0.3405-0.68710.02860.87810.31350.0949-0.1293-0.382601.34930.07810.00671.9415-0.12961.4052-134.289230.453629.8532
111.1273-1.0481-0.74132.32410.36962.3276-0.0545-0.3316-0.01060.21730.04510.1910.3276-0.356601.0062-0.0715-0.10371.3421-0.05231.2361-127.507420.80843.3071
121.4824-0.0150.03841.45030.17091.08310.02630.23120.4294-0.2504-0.01210.0148-0.3028-0.1109-01.06460.0157-0.00061.35930.02731.1534-110.9739.3296-15.1972
130.6718-0.2584-0.35670.7194-0.33790.27290.0641-0.10770.5884-0.22840.04770.2468-0.0792-0.188701.53910.09480.06071.5997-0.01551.7828-116.442360.2984-13.6848
141.32660.94490.60421.45680.54611.267-0.05020.40470.1687-0.45780.11190.13630.0773-0.047801.136-0.04040.01361.305-0.05981.1328-110.636618.4256-21.0196
150.63980.2277-1.41461.15710.5870.77040.0524-0.10620.4592-0.0921-0.0649-0.0420.02110.2856-01.02240.0162-0.04961.28860.00441.2139-77.762230.091518.0917
161.9817-0.3185-0.89753.2219-0.45573.33390.0257-0.1667-0.19340.394-0.0424-0.0389-0.06410.303301.0975-0.0760.02561.2277-0.15551.27-87.97639.727145.7676
171.01270.08890.45440.72-0.08260.91720.1113-0.177-0.38760.1234-0.1187-0.08510.3984-0.0117-01.18660.02510.12161.2363-0.02871.3817-89.3451-0.105810.6692
180.1137-0.25280.16730.027-0.057-0.0021-0.03380.8047-0.9168-0.57150.1791-0.80290.44820.542-01.73980.05890.1691.6946-0.11452.1818-60.168813.842.8758
19-0.01610.0824-0.0339-0.0391-0.0082-0.09160.72350.6359-0.15740.46290.15780.6405-1.19250.584502.1707-0.37320.07131.83350.04032.1856-41.940124.840716.9646
20-0.0756-0.17040.91550.68590.48750.2051-0.08860.11610.2968-0.1769-0.1734-0.0643-0.587-0.293802.2892-0.18740.45791.7656-0.07361.9555-95.700576.470466.6579
21-0.2632-0.40350.01050.19540.1819-0.11760.2290.0539-0.25670.5238-0.7121-1.1002-0.37971.14202.7727-0.235-0.42812.37680.1222.9608-74.123361.921783.2673
221.4981-0.4202-0.9621.7508-0.31931.93640.26150.29510.16040.0724-0.07580.5663-1.1391-0.555701.4140.04850.18581.50990.03031.7479-105.15360.512639.1219
230.2010.4038-0.03110.0917-0.4046-0.14960.1340.10550.50790.35790.23750.2935-0.48340.2817-01.6002-0.07460.0761.70850.04951.6315-57.24760.85422.0263
240.07480.2080.15540.03840.0292-0.02090.06140.63310.03810.5549-0.3055-0.9315-0.39380.5611-01.5967-0.05660.37791.8543-0.11392.319117.7786-19.605521.2747
250.3145-0.391-0.36640.9982-0.01620.61790.21220.3863-0.2161-0.34080.0125-0.17760.39910.3564-01.58650.11990.20121.9444-0.27222.175912.3756-52.163134.1345
260.3102-0.14070.33270.1038-0.09080.07570.0686-0.09680.55220.0736-0.3556-0.9823-0.2345-0.163701.8972-0.03470.48151.9067-0.12992.122416.3312-21.930120.4403
27-0.0819-0.0254-0.20380.0003-0.39250.2583-0.17021.0751-0.0585-0.1884-0.01831.68880.57560.6684-01.6161-0.0350.11961.8708-0.20741.9785-3.1178-21.709412.427
280.22880.00610.05160.24090.0210.13480.03120.42070.803-0.2679-0.3312-0.73060.250.1745-02.2572-0.18330.541.92370.26192.4951-1.627712.23815.4562
290.3677-0.0155-0.0126-0.01770.14780.1780.77540.27390.5059-0.4627-0.45670.39170.17270.5539-01.8619-0.18350.55592.00840.00791.8452-1.4133-19.427611.6155
300.66850.06510.11361.18970.11051.0387-0.0513-0.4352-0.280.9227-0.2864-0.40190.44440.0525-02.2903-0.0055-0.00711.7642-0.07191.7085-13.0744-56.449180.7648
312.3802-0.1516-0.1971.177-0.33871.0249-0.1274-0.0630.41030.08340.05130.29460.2802-0.478802.0266-0.1004-0.0261.84910.04221.6186-49.0621-24.4023105.0817
320.3679-0.8753-0.8967-0.01670.69580.8067-0.0186-0.4386-0.2937-0.1923-0.1498-0.03550.0992-0.173-02.2368-0.0524-0.07991.7842-0.06141.665-32.1529-45.162291.6249
330.3248-0.273-0.47021.8185-1.18421.19060.0029-0.2429-0.04370.61480.1076-0.12180.00590.1533-01.66580.033-0.04841.6864-0.20791.585-11.4393-33.907874.6651
340.91450.2631-0.23651.053-0.81431.2977-0.122-0.0765-0.31110.04550.1775-0.87520.38490.471101.50940.1227-0.04731.643-0.19841.7769-0.7918-50.879251.0714
350.7624-0.7725-0.50842.0455-0.38710.1444-0.4313-1.0516-0.09050.76440.3803-0.7781-0.10090.064602.11730.103-0.02072.4555-0.24152.05840.7457-72.354156.1815
360.6270.10260.26740.5380.23281.3326-0.0738-0.09680.10280.3950.1463-0.5793-0.00320.594501.4465-0.05660.09531.7101-0.2811.89783.2464-29.640949.0486
370.30780.615-1.17231.43670.28330.66150.10720.3766-0.2489-0.58290.1167-0.27830.1369-0.210301.5694-0.06970.08291.41510.00631.4938-45.3991-43.580235.62
382.6642-0.3759-1.28452.16960.37373.8966-0.15020.2731-0.03870.1087-0.04970.0032-0.176-0.3867-01.5026-0.12220.10881.21280.02161.2061-65.6667-54.24657.4821
391.43410.2542-0.14610.9082-0.07140.80430.0332-0.02120.54530.07310.12290.0328-0.3518-0.0819-01.6012-0.00770.26361.3760.00331.5457-35.3359-12.976343.825
40-0.0156-0.0550.0411-0.1718-0.0368-0.0204-0.83670.66650.0616-1.42310.70440.30.3273-1.224-02.8491-0.14530.27152.79490.28292.3528-39.7739-26.822813.6548
41-0.0898-0.00740.08430.0084-0.0228-0.02790.7288-0.49250.4524-0.14550.3707-0.0492-0.07480.219503.9933-0.2739-0.25472.4761-0.43452.6034-55.4671-32.92073.4445
420.05110.8201-0.22240.5368-0.2361-0.34380.14680.1623-0.14050.7049-0.2231-0.18210.59430.1263-02.54790.06370.30311.6764-0.03971.999-81.3742-91.875673.9758
43-0.1615-0.17730.0282-0.1381-0.0093-0.20870.4627-0.17610.2149-0.9724-0.1360.9818-0.1384-0.8197-02.8268-0.2253-0.18652.6611-0.0222.942-105.0555-77.195260.7984
440.8663-0.4199-0.64630.71450.84292.8862-0.4475-0.3235-0.87070.34850.1213-0.19530.33570.630602.00790.11810.12791.38430.07331.754-51.8224-74.70469.0221
450.217-0.7623-0.02950.5012-0.16351.0434-0.39390.4093-0.4794-0.23370.5110.20780.4763-0.0029-01.9350.11010.1571.7871-0.23541.8151-41.6683-73.09789.7746
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 179 )
3X-RAY DIFFRACTION3chain A and (resid 180 through 233 )
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 325 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 49 )
6X-RAY DIFFRACTION6chain 'B' and (resid 50 through 179 )
7X-RAY DIFFRACTION7chain 'B' and (resid 180 through 233 )
8X-RAY DIFFRACTION8chain C and (resid 3 through 158 )
9X-RAY DIFFRACTION9chain C and (resid 159 through 370 )
10X-RAY DIFFRACTION10chain C and (resid 371 through 481 )
11X-RAY DIFFRACTION11chain C and (resid 482 through 703 )
12X-RAY DIFFRACTION12chain C and (resid 704 through 883 )
13X-RAY DIFFRACTION13chain C and (resid 884 through 1037 )
14X-RAY DIFFRACTION14chain C and (resid 1038 through 1252 )
15X-RAY DIFFRACTION15chain C and (resid 1253 through 1342 )
16X-RAY DIFFRACTION16chain 'D' and (resid 8 through 332 )
17X-RAY DIFFRACTION17chain 'D' and (resid 333 through 1376 )
18X-RAY DIFFRACTION18chain 'E' and (resid 2 through 60 )
19X-RAY DIFFRACTION19chain 'E' and (resid 61 through 90 )
20X-RAY DIFFRACTION20chain F and (resid 94 through 262 )
21X-RAY DIFFRACTION21chain F and (resid 263 through 354 )
22X-RAY DIFFRACTION22chain F and (resid 355 through 530 )
23X-RAY DIFFRACTION23chain F and (resid 531 through 612 )
24X-RAY DIFFRACTION24chain 'G' and (resid 7 through 49 )
25X-RAY DIFFRACTION25chain 'G' and (resid 50 through 179 )
26X-RAY DIFFRACTION26chain 'G' and (resid 180 through 233 )
27X-RAY DIFFRACTION27chain 'H' and (resid 6 through 49 )
28X-RAY DIFFRACTION28chain 'H' and (resid 50 through 179 )
29X-RAY DIFFRACTION29chain 'H' and (resid 180 through 233 )
30X-RAY DIFFRACTION30chain 'I' and (resid 3 through 158 )
31X-RAY DIFFRACTION31chain 'I' and (resid 159 through 370 )
32X-RAY DIFFRACTION32chain 'I' and (resid 371 through 481 )
33X-RAY DIFFRACTION33chain 'I' and (resid 482 through 703 )
34X-RAY DIFFRACTION34chain 'I' and (resid 704 through 883 )
35X-RAY DIFFRACTION35chain 'I' and (resid 884 through 1037 )
36X-RAY DIFFRACTION36chain 'I' and (resid 1038 through 1252 )
37X-RAY DIFFRACTION37chain 'I' and (resid 1253 through 1342 )
38X-RAY DIFFRACTION38chain 'J' and (resid 16 through 332 )
39X-RAY DIFFRACTION39chain 'J' and (resid 333 through 1375 )
40X-RAY DIFFRACTION40chain 'K' and (resid 2 through 60 )
41X-RAY DIFFRACTION41chain 'K' and (resid 61 through 80 )
42X-RAY DIFFRACTION42chain 'L' and (resid 94 through 262 )
43X-RAY DIFFRACTION43chain 'L' and (resid 263 through 354 )
44X-RAY DIFFRACTION44chain 'L' and (resid 355 through 530 )
45X-RAY DIFFRACTION45chain 'L' and (resid 531 through 613 )

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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