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- PDB-7s01: X-ray structure of the phage AR9 non-virion RNA polymerase holoen... -

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基本情報

登録情報
データベース: PDB / ID: 7s01
タイトルX-ray structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with a forked oligonucleotide containing the P077 promoter
要素
  • (DNA-directed RNA ...) x 5
  • Non-template strand of the forked DNA oligonucleotide (downstream copy)
  • Template strand of the forked DNA oligonucleotide (downstream copy) containing the P077 AR9 promoter motif
キーワードTRANSCRIPTION/DNA / DNA-dependent multisubunit RNA polymerase / sigma factor / deoxyuridine / template strand promoter / RNAP / TRANSCRIPTION / TRANSCRIPTION-DNA complex
機能・相同性
機能・相同性情報


DNA-directed RNA polymerase complex / : / : / : / : / : / : / DNA-directed RNA polymerase activity / ribonucleoside binding / DNA-directed RNA polymerase ...DNA-directed RNA polymerase complex / : / : / : / : / : / : / DNA-directed RNA polymerase activity / ribonucleoside binding / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding / metal ion binding
類似検索 - 分子機能
RNA polymerase Rpb1 funnel domain / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 ...RNA polymerase Rpb1 funnel domain / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / DNA-directed RNA polymerase / DNA-directed RNA polymerase beta subunit / DNA-directed RNA polymerase / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase
類似検索 - 構成要素
生物種Bacillus phage AR9 (ファージ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.4 Å
データ登録者Leiman, P.G. / Sokolova, M.L. / Gordeeva, J. / Fraser, A. / Severinov, K.V.
資金援助1件
組織認可番号国
Not fundedFunded by UTMB
引用ジャーナル: Nat Commun / 年: 2022
タイトル: Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase.
著者: Alec Fraser / Maria L Sokolova / Arina V Drobysheva / Julia V Gordeeva / Sergei Borukhov / John Jumper / Konstantin V Severinov / Petr G Leiman /
要旨: Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template ...Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.
履歴
登録2021年8月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年7月6日Provider: repository / タイプ: Initial release
改定 1.12024年4月3日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 2.02024年5月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / chem_comp / chem_comp_atom / chem_comp_bond / entity / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_conn / struct_conn_type / struct_mon_prot_cis / symmetry
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _cell.angle_beta / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.value / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_percent_reflns_obs / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.percent_reflns_obs / _reflns.pdbx_CC_half / _reflns.pdbx_Rrim_I_all / _reflns.percent_possible_obs / _struct_mon_prot_cis.pdbx_omega_angle / _symmetry.space_group_name_Hall
改定 2.12025年2月12日Group: Refinement description / Structure summary
カテゴリ: pdbx_entry_details / pdbx_refine_tls / pdbx_refine_tls_group
Item: _pdbx_entry_details.has_protein_modification / _pdbx_refine_tls.L[1][1] ..._pdbx_entry_details.has_protein_modification / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details

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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
d: DNA-directed RNA polymerase beta' subunit
c: DNA-directed RNA polymerase beta subunit
D: DNA-directed RNA polymerase
C: DNA-directed RNA polymerase
N: Non-template strand of the forked DNA oligonucleotide (downstream copy)
T: Template strand of the forked DNA oligonucleotide (downstream copy) containing the P077 AR9 promoter motif
t: Non-template strand of the forked DNA oligonucleotide (downstream copy)
n: Template strand of the forked DNA oligonucleotide (downstream copy) containing the P077 AR9 promoter motif
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)340,70810
ポリマ－340,6429
非ポリマー651
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: microscopy, The molecule is a monomer in cryo-EM.
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)176.925, 110.455, 222.379
Angle α, β, γ (deg.)90.00, 98.52, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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要素

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DNA-directed RNA ... , 5種, 5分子 AdcDC

#1: タンパク質 DNA-directed RNA polymerase subunit


分子量: 54917.449 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Bacillus phage AR9 (ファージ) / 遺伝子: AR9_g226 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): Star (DE3) / 参照: UniProt: A0A172JIC8
#2: タンパク質 DNA-directed RNA polymerase beta' subunit


分子量: 49397.164 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Bacillus phage AR9 (ファージ) / 遺伝子: AR9_g270 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): Star (DE3) / 参照: UniProt: A0A172JIH0
#3: タンパク質 DNA-directed RNA polymerase beta subunit


分子量: 58112.289 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Bacillus phage AR9 (ファージ) / 遺伝子: AR9_g105 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): Star (DE3) / 参照: UniProt: A0A172JI16
#4: タンパク質 DNA-directed RNA polymerase


分子量: 73100.977 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Bacillus phage AR9 (ファージ) / 遺伝子: AR9_g154 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): Star (DE3) / 参照: UniProt: A0A172JI62, DNA-directed RNA polymerase
#5: タンパク質 DNA-directed RNA polymerase


分子量: 76978.383 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Bacillus phage AR9 (ファージ) / 遺伝子: AR9_g089 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): Star (DE3) / 参照: UniProt: A0A172JHZ2, DNA-directed RNA polymerase

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DNA鎖 , 2種, 4分子 NtTn

#6: DNA鎖 Non-template strand of the forked DNA oligonucleotide (downstream copy)


分子量: 4303.829 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Bacillus phage AR9 (ファージ)
#7: DNA鎖 Template strand of the forked DNA oligonucleotide (downstream copy) containing the P077 AR9 promoter motif


分子量: 9764.241 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Bacillus phage AR9 (ファージ)

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非ポリマー , 1種, 1分子

#8: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Zn

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationN

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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: 3.25 Å3/Da / 溶媒含有率: 62.16 %
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: 5
詳細: 1.5 ul aliquot of the AR9 nvRNAP promoter complex (10 mg/mL) was mixed with the same volume of a solution containing 150 mM MIB pH 5, 150 mM LiCl, 13 % PEG 1500 and incubated as a hanging ...詳細: 1.5 ul aliquot of the AR9 nvRNAP promoter complex (10 mg/mL) was mixed with the same volume of a solution containing 150 mM MIB pH 5, 150 mM LiCl, 13 % PEG 1500 and incubated as a hanging drop over the same solution.

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 21-ID-D / 波長: 0.9184 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2017年6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: 0.9184 Å / 相対比: 1
反射解像度: 3.38→50 Å / Num. obs: 59745 / % possible obs: 94 % / Observed criterion σ(I): 1.2 / 冗長度: 2.88 % / Biso Wilson estimate: 111.6 Å2 / Net I/σ(I): 7.94
反射 シェル解像度: 3.38→3.58 Å / 冗長度: 2.58 % / Mean I/σ(I) obs: 1.2 / % possible all: 83.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
Coot0.9.5モデル構築
精密化構造決定の手法: 分子置換
開始モデル: EMD-24763

解像度: 3.4→49.35 Å / SU ML: 0.615 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 34.627
立体化学のターゲット値: GEOSTD + MONOMER LIBRARY + CDL V1.2
Rfactor反射数%反射
Rfree0.293 2830 5 %
Rwork0.239 --
obs0.242 56644 96.9 %
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 mean: 133 Å2
精密化ステップサイクル: LAST / 解像度: 3.4→49.35 Å
タンパク質核酸リガンド溶媒全体
原子数21749 1595 1 0 23345
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00223927
X-RAY DIFFRACTIONf_angle_d0.46932595
X-RAY DIFFRACTIONf_dihedral_angle_d15.4483674
X-RAY DIFFRACTIONf_chiral_restr0.0383632
X-RAY DIFFRACTIONf_plane_restr0.0043914
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.460.49341340.42062561X-RAY DIFFRACTION93
3.46-3.520.37611410.33822683X-RAY DIFFRACTION98
3.52-3.590.38361420.31532701X-RAY DIFFRACTION97
3.59-3.660.37711410.30622661X-RAY DIFFRACTION97
3.67-3.740.41931410.31562703X-RAY DIFFRACTION97
3.74-3.830.31161410.28692671X-RAY DIFFRACTION97
3.83-3.930.34651340.2872559X-RAY DIFFRACTION94
3.93-4.030.3021360.26862590X-RAY DIFFRACTION93
4.03-4.150.35741430.2782730X-RAY DIFFRACTION99
4.15-4.290.32531440.27962738X-RAY DIFFRACTION99
4.29-4.440.31731440.2742731X-RAY DIFFRACTION99
4.44-4.620.28891440.23092735X-RAY DIFFRACTION99
4.62-4.830.29591440.21722728X-RAY DIFFRACTION98
4.83-5.080.28391420.2242705X-RAY DIFFRACTION98
5.08-5.40.27431440.22722730X-RAY DIFFRACTION98
5.4-5.820.32821450.25112750X-RAY DIFFRACTION98
5.82-6.40.30061420.24032699X-RAY DIFFRACTION98
6.4-7.320.33281420.23692710X-RAY DIFFRACTION96
7.32-9.220.20671400.17912652X-RAY DIFFRACTION95
9.22-49.350.19791460.16782777X-RAY DIFFRACTION96
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)
11.986024536320.03874648870580.4882302833665.184223147871.461277198332.358438148070.172988731530.000885805923240.04849854066060.6464430077080.0298200749804-0.137533822401-0.203181098538-0.0466618938385-0.155725373920.976061480106-0.02383405396920.3291115865151.201691426560.1150720765241.22459577447-4.4240.32997.333
22.720115058232.51389798917-1.922052535635.60115528489-1.028356404823.52630457283-0.466586089816-0.200799965642-0.171904656128-0.1320960338140.322755235445-0.4414477883290.2983715899050.1224263331370.07658537927620.568884673180.253920414619-0.02823457309851.206842596910.08563583917351.193696748898.11231.11669.546
32.1970174787-0.4962937466492.468806263552.911735008220.8101841576637.21878410532-0.173126828351-0.3898750482390.3605027856940.3779858658570.1017382113690.0345486529587-1.229429777480.2156444122830.08428274090711.00085671006-0.0242976900694-0.251428513170.841276901618-0.1467433582981.4954512163546.23578.39254.146
45.23098560804-1.94108932718-4.594320619237.38699628842.762411607154.375060771120.3907183877290.2769082543730.1151045687441.03833234811-0.1928461628270.956606063099-0.313873799849-0.0334047002332-0.1099958441270.8651821548450.137402855875-0.1420119464970.9886049629690.04349382821560.86228938323932.34838.45172.371
58.30444403691-0.00539566964159-3.210824972960.2566343366110.6098833561242.73977781715-0.561443549101-0.433324244314-0.9099279179240.136357574040.1436466512640.1527574940250.536954262160.1931093988730.3631266294781.019939214670.314878621125-0.1565791843930.8969265283060.08966348604240.9854332683323.41420.90378.983
62.835093265710.680019339151-2.255862927834.03568136236-0.1212637433173.00078597533-0.336323367639-0.649946057779-0.05349124924570.3724729035660.2809154672880.07706390814780.232726093047-0.0282647698829-0.01390186956790.607890027060.276156023586-0.05917183244531.182080645470.08281338005331.1388050861426.24324.45673.931
71.5737160746-0.471714830516-1.188372044360.6972730703030.7224255350651.51400100467-0.126920642712-0.2388747821570.1082250595730.0397787710582-0.0106630153881-0.2182602916890.1084889570760.218114607680.1394215947790.4646615999710.213148932522-0.1919328246710.94156983750.05030258473231.2921478213455.38235.2632.631
80.1442457873180.303314025789-0.2710975360340.830173444466-0.3669208875530.7849973573090.08579302502020.181383937007-0.1306948150990.259785164719-0.04872823868820.360577140953-0.148710409299-0.08114536227840.03417383914810.4678484322810.172701227386-0.2895576185371.23161184982-0.04316359212931.446074597811.64129.09223.502
90.8706595575771.43872533539-0.5748334816845.49968902396-1.334661866960.8966687453680.119465525502-0.226297438292-0.1584155204130.359305961879-0.0855999617088-0.0699510217434-0.146465913045-0.290135653201-0.03582723964450.4499158810180.0784270565629-0.137784653771.064912992220.06837922103461.307472268524.51917.83941.191
102.712130295471.06145478329-3.167672923928.88218023852-1.918012949977.666702798550.180948692193-0.5759184226930.03321977390270.7712541292010.3043823083771.024337386260.293435261363-0.777669068612-0.4803675207330.749600916608-0.100698951511-0.0866527247651.201649105990.03937024443811.30470043286-4.295-8.95850.896
111.043636707710.0521122080705-0.3563179244720.855202633459-0.3463349521951.881028187110.00334763889597-0.206551320347-0.07939692897920.277220859752-0.1775848005150.06994139110820.0330616365633-0.1483585358940.2107480521930.479733903653-0.0470183310448-0.02865402525450.8446073541210.04883863937561.205333698536.94722.35839.6
122.892192822580.575954108332-2.61000792816.254576618210.1853356399976.10081391543-0.44620922791-0.368423269057-0.7274562285040.0240081323933-0.00216926242449-0.2151862819970.516098905155-0.1218811464260.3292427134980.5534746171430.0696349414080.08051492388510.6514111922460.07061313166421.2041921354214.11910.99925.796
132.656423553261.658553533522.173057829521.306126669441.103983973935.16476966336-0.03609436739830.4093801530570.202918272929-0.17173238282-0.219457540144-0.6434044110760.2421577989460.4228499379230.2338277300380.5330368630390.1713614536450.06067509818761.103676604450.1145713010551.5802676112375.59320.1636.027
143.394320950980.943802405614-2.124140082030.255855834384-0.5832781141311.453344023590.1402454014740.1926338277050.0318748310226-0.17704915202-0.308473511051-0.5381615797720.5659906283520.6718893846910.02628571936440.5634240931230.344372486122-0.2148228139131.10002751733-0.01436198511221.3534907548373.13418.48121.18
154.856131104612.58980211036-3.500603664432.56901025511-1.466711470083.1104521321-0.3903605741530.00619896835766-0.603694143334-0.3049095253570.000299742289292-0.3620095313890.6249314527840.2708224974990.3256382900660.707863794370.156527082266-0.1160318618540.6729127726010.01779694118721.1892984653342.8681.436.663
163.77461592907-0.1413796376434.989113315560.751676389630.8695074388678.05729257012-0.516285805009-0.04288930454070.001718089389260.275403724067-0.2160539955450.3952523391250.4987930885950.5322352014950.6567839582730.7946077683860.1175010187420.0264398324390.7133968394930.2099099662461.2381665756837.3810.62533.549
172.23074831838-2.8652259498-0.111625458155.51856462171-0.5651614223280.572857556561-0.274946033094-0.174508378575-0.582870319170.09340505971660.0469500705928-0.4195181742170.757589923410.6445215188580.1227411908380.9935670372320.5653259404730.2048914573661.176305033450.3588698120151.7275827815166.0222.30643.69
183.238023136421.26760436758-0.5033177388945.696524461260.07904688440786.29990747872-0.111914214881-0.726854035178-0.04803769456340.2412932377810.1076192026010.6649241995290.2913239875170.002100838925490.02874989682110.6314869209950.158976846512-0.03629624014240.867719694340.06693938110111.5727853211721.075-21.69223.72
195.045772017963.550109644493.701711688013.303001254313.471159062993.63788332776-0.298268280898-0.177689742883-0.588041045794-0.2472770530850.56650761501-0.0222214355803-0.3911836469670.128773936148-0.2446962646420.8212275594410.04481881332810.223064405731.059975282590.1855918034781.5692915262832.457-10.75631.886
202.230817927120.123746933217-1.6974702641.093147503640.8423835668682.06956849728-0.31345220813-0.585685079719-0.6764662368380.047290663047-0.1206524234380.01937624792011.1024188615-0.00399639590920.2455636183841.328854070830.4004126714910.2352583500210.9562397055790.2897804007241.4052570806452.7196.06655.35
213.546922054214.829042595110.4297433384699.245076332153.170431709662.67565160737-0.139536407015-0.158698921528-0.1466737214370.382772599289-0.2549999417410.6799427803030.6945823641020.1645701986650.3545915154010.6081457368050.133123171863-0.1630422236590.6849772829170.01802833329011.3770060469924.3611.75812.553
221.91917741128-2.85453330371-1.68292163954.541011843762.079956414042.03153491093-0.1438263890330.22242092733-0.06131949987620.1470333885120.1109109536690.2778685048620.3855084265290.2500853075330.01496262708760.432259127770.0342023793557-0.1262266619280.8894422429610.1515997492581.1202083083913.51643.09910.69
230.601073712945-0.653922256302-0.2642197107883.646191027341.94416025763.17250332407-0.0105168307833-0.024426455780.331166085733-0.2311532167890.0381356564150.161935682661-0.533944383065-0.100920174052-0.0123501921110.3662136555350.0216246690969-0.1907504427260.724278187790.07011684963081.1476995496935.36652.03724.603
241.2248607194-0.457942978182-0.2307084985021.569813227030.2069493105951.474640054290.03224571755390.07624243452650.163326201464-0.02541834437460.0122742866761-0.0436125313747-0.182821734147-0.0388853671067-0.05279641035950.3471328707630.0546648445801-0.1783685392890.6837388039930.1118462577161.1176632108425.48243.36415.005
251.406688294430.30828933239-0.5739701460211.67743504493-0.202995922645.29272447116-0.1166020684550.3800882630090.0395389651633-0.6547982840720.08959570440340.2226985503160.416798576119-0.2944749486380.08355121315590.5077399239150.0660834606756-0.1332408908820.955615482446-0.06973918536811.1552574897330.33222.433-10.035
260.452728023505-0.2826969732990.2201452697210.391278510193-0.1890871996620.154367191122-0.008178384597570.109623787980.1822630426850.2329424834670.256751002508-0.298643040812-0.0851422627908-0.06907803603850.5010268107710.1632021967710.227557798528-0.4080614930630.704439479890.03306039062621.3879349640341.76833.69720.12
271.15727662151-0.962747778601-0.24110755413.16148200914-1.841008259042.5230021037-0.262150675174-0.6803338916330.1434964182380.2962287058360.096684690343-0.16652539436-0.3424305012980.4424684783930.08836525872040.6093336904680.306239588723-0.2159498444291.09333959117-0.1068319503971.0913774526849.0536.90350.739
286.86943318423-2.135698991952.224699015062.015547077920.4631021449767.475393687140.214581968293-1.3515384125-0.2451376321-1.2471652527-0.1273849879190.5536911194221.56050063665-1.80118043568-0.2560660873772.29260924753-0.2563670174690.01069429132472.546353866140.1631994778422.6646111239324.04-2.5258.04
290.825899055016-0.708813578181-1.579009804461.342052557172.203365694953.99926002225-0.0348970735329-0.1535529637770.39753665855-0.09821141976390.300386117458-0.0768655368241-0.0588072156693-0.444985056463-0.2431053397653.52153063922-1.02265561472-1.210555085794.274850165750.1855888093244.512021040221.135-22.58861.499
300.2026739653260.375508290444-0.1453373892711.18148921115-1.040098417642.29743827937-0.6773324259570.71552396961-0.515809957066-1.659935050330.5607780448480.705163339804-0.605934884075-0.3378933012360.1433229249433.60648619577-0.28508066262-0.6007513888172.663467335110.03542375000022.5152998143724.543-15.77166.363
314.229773997-4.2269089379-0.6426754565699.73355227664-1.718225248262.121109894080.356378890326-0.3021168151260.568697871921-0.959332797057-0.0411259602195-1.467304362970.742676494750.239624077729-0.2709382167271.30183141405-0.0351101293006-0.02340617153481.77620799491-0.04148890630651.655374909872022.87150.798
326.25655165991-0.5886774594886.045707737510.0762621468713-0.5652373393356.66298303238-0.2935169293-0.4648020559760.706149865889-0.29497352485-0.0645869019962-0.151514298953-0.137945989372-1.016127410410.3186001779642.06326742359-0.112738762711-0.3854380275284.11494686406-0.6081581685473.10708803021-7.57445.26266.186
331.294445205881.19435350352-0.9187514914842.358702200911.100394593614.35809028799-1.192541880290.08016052516560.875075054929-2.614105840641.1805619644-1.16601815648-2.64662618178-0.154612403752-0.1890982201232.93310406241-0.2558385275250.01136135099151.699232210180.2231524765713.031760469286.75268.4271.668
349.968253449798.776515112662.480181275057.734420687232.198699129210.6329371551032.214206940320.1565555223762.005181916131.64256632637-1.463972397191.221723140710.4377584835930.411420353884-0.7413362647442.46704338692-0.08511066174820.1325446026531.927580108820.05090689473172.91937203810.97774.05571.531
352.341388017634.23441082759-0.570745268798.58619771461-2.989188390924.263387904920.420089547044-0.19847460310.372322095903-1.02106672872-0.5663623508710.3832351693240.1958986180280.5950696588070.1453664651111.288745941690.3052092466720.02141920363542.002887003130.06519639050131.89634280928-3.83336.84774.976
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:178 )A2 - 178
2X-RAY DIFFRACTION2( CHAIN A AND RESID 179:295 )A179 - 295
3X-RAY DIFFRACTION3( CHAIN A AND RESID 296:464 )A296 - 464
4X-RAY DIFFRACTION4( CHAIN d AND RESID 1:42 )d1 - 42
5X-RAY DIFFRACTION5( CHAIN d AND RESID 43:120 )d43 - 120
6X-RAY DIFFRACTION6( CHAIN d AND RESID 121:229 )d121 - 229
7X-RAY DIFFRACTION7( CHAIN d AND RESID 230:426 )d230 - 426
8X-RAY DIFFRACTION8( CHAIN c AND RESID 1:64 )c1 - 64
9X-RAY DIFFRACTION9( CHAIN c AND RESID 65:176 )c65 - 176
10X-RAY DIFFRACTION10( CHAIN c AND RESID 177:325 )c177 - 325
11X-RAY DIFFRACTION11( CHAIN c AND RESID 326:417 )c326 - 417
12X-RAY DIFFRACTION12( CHAIN c AND RESID 418:484 )c418 - 484
13X-RAY DIFFRACTION13( CHAIN D AND RESID 1:84 )D1 - 84
14X-RAY DIFFRACTION14( CHAIN D AND RESID 85:140 )D85 - 140
15X-RAY DIFFRACTION15( CHAIN D AND RESID 141:247 )D141 - 247
16X-RAY DIFFRACTION16( CHAIN D AND RESID 248:285 )D248 - 285
17X-RAY DIFFRACTION17( CHAIN D AND RESID 286:394 )D286 - 394
18X-RAY DIFFRACTION18( CHAIN D AND RESID 395:487 )D395 - 487
19X-RAY DIFFRACTION19( CHAIN D AND RESID 488:533 )D488 - 533
20X-RAY DIFFRACTION20( CHAIN D AND RESID 534:631 )D534 - 631
21X-RAY DIFFRACTION21( CHAIN C AND RESID 1:45 )C1 - 45
22X-RAY DIFFRACTION22( CHAIN C AND RESID 46:151 )C46 - 151
23X-RAY DIFFRACTION23( CHAIN C AND RESID 152:256 )C152 - 256
24X-RAY DIFFRACTION24( CHAIN C AND RESID 257:452 )C257 - 452
25X-RAY DIFFRACTION25( CHAIN C AND RESID 453:516 )C453 - 516
26X-RAY DIFFRACTION26( CHAIN C AND RESID 517:549 )C517 - 549
27X-RAY DIFFRACTION27( CHAIN C AND RESID 550:649 )C550 - 649
28X-RAY DIFFRACTION28( CHAIN N AND RESID 1:12 )N1 - 12
29X-RAY DIFFRACTION29( CHAIN N AND RESID 13:13 )N13
30X-RAY DIFFRACTION30( CHAIN T AND RESID 2:6 )T2 - 6
31X-RAY DIFFRACTION31( CHAIN T AND RESID 7:29 )T7 - 29
32X-RAY DIFFRACTION32( CHAIN T AND RESID 30:30 )T30
33X-RAY DIFFRACTION33( CHAIN t AND RESID 1:14 )t1 - 14
34X-RAY DIFFRACTION34( CHAIN n AND RESID 1:10 )n1 - 10
35X-RAY DIFFRACTION35( CHAIN n AND RESID 11:22 )n11 - 22

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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