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- PDB-2jj1: The Structure of F1-ATPase inhibited by piceatannol. -

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基本情報

登録情報
データベース: PDB / ID: 2jj1
タイトルThe Structure of F1-ATPase inhibited by piceatannol.
要素
  • (ATP SYNTHASE SUBUNIT ...) x 2
  • ATP SYNTHASE GAMMA CHAIN
キーワードHYDROLASE / MITOCHONDRION / ATP-BINDING
機能・相同性
機能・相同性情報


Formation of ATP by chemiosmotic coupling / Cristae formation / : / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) ...Formation of ATP by chemiosmotic coupling / Cristae formation / : / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane
類似検索 - 分子機能
ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Pyruvate Kinase; Chain: A, domain 1 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase, F1 complex, gamma subunit conserved site ...ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Pyruvate Kinase; Chain: A, domain 1 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AZIDE ION / PICEATANNOL / PHOSPHATE ION / ATP synthase subunit beta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit alpha, mitochondrial
類似検索 - 構成要素
生物種BOS TAURUS (ウシ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.7 Å
データ登録者Gledhill, J.R. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2007
タイトル: Mechanism of Inhibition of Bovine F1-ATPase by Resveratrol and Related Polyphenols.
著者: Gledhill, J.R. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
履歴
登録2007年7月3日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02007年8月21日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Advisory / Refinement description / Version format compliance
改定 1.22023年12月13日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "IA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "MA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
B: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
C: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
D: ATP SYNTHASE SUBUNIT BETA
E: ATP SYNTHASE SUBUNIT BETA
F: ATP SYNTHASE SUBUNIT BETA
G: ATP SYNTHASE GAMMA CHAIN
H: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
I: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
J: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
K: ATP SYNTHASE SUBUNIT BETA
L: ATP SYNTHASE SUBUNIT BETA
M: ATP SYNTHASE SUBUNIT BETA
N: ATP SYNTHASE GAMMA CHAIN
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)709,92652
ポリマ－702,91214
非ポリマー7,01538
水20,5191139
1
A: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
B: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
C: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
D: ATP SYNTHASE SUBUNIT BETA
E: ATP SYNTHASE SUBUNIT BETA
F: ATP SYNTHASE SUBUNIT BETA
G: ATP SYNTHASE GAMMA CHAIN
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)354,96326
ポリマ－351,4567
非ポリマー3,50719
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area41430 Å2
ΔGint-203.7 kcal/mol
Surface area102300 Å2
手法PISA
2
H: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
I: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
J: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
K: ATP SYNTHASE SUBUNIT BETA
L: ATP SYNTHASE SUBUNIT BETA
M: ATP SYNTHASE SUBUNIT BETA
N: ATP SYNTHASE GAMMA CHAIN
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)354,96326
ポリマ－351,4567
非ポリマー3,50719
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area41280 Å2
ΔGint-210.6 kcal/mol
Surface area102130 Å2
手法PISA
単位格子
Length a, b, c (Å)106.957, 281.176, 138.785
Angle α, β, γ (deg.)90.00, 89.58, 90.00
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21H
12B
22I
13C
23J
14D
24K
15E
25L
16F
26M
17G
27N

NCSドメイン領域:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A24 - 510
2112H24 - 510
1122B23 - 401
2122I23 - 401
1222B410 - 510
2222I410 - 510
1132C13 - 510
2132J13 - 510
1142D9 - 475
2142K9 - 475
1152E9 - 474
2152L9 - 474
1162F9 - 474
2162M9 - 474
1172G1 - 47
2172N1 - 47
1272G67 - 90
2272N67 - 90
1372G105 - 116
2372N105 - 116
1472G127 - 148
2472N127 - 148
1572G159 - 173
2572N159 - 173
1672G201 - 272
2672N201 - 272

NCSアンサンブル:
ID
1
2
3
4
5
6
7

NCS oper: (Code: given
Matrix: (0.99999, -0.00013, -0.00427), (-0.00013, -1, 0.0009), (-0.00427, -0.0009, -0.99999)
ベクター: -53.37192, -0.0484, 69.45826)

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要素

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ATP SYNTHASE SUBUNIT ... , 2種, 12分子 ABCHIJDEFKLM

#1: タンパク質
ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM / ATP SYNTHASE ALPHA CHAIN HEART ISOFORM


分子量: 55332.219 Da / 分子数: 6 / 断片: RESIDUES 44-553 / 由来タイプ: 天然 / 由来: (天然) BOS TAURUS (ウシ) / 器官: HEART / 参照: UniProt: P19483, EC: 3.6.1.34
#2: タンパク質
ATP SYNTHASE SUBUNIT BETA / ATP SYNTHASE BETA CHAIN


分子量: 51757.836 Da / 分子数: 6 / 断片: RESIDUES 47-528 / 由来タイプ: 天然 / 由来: (天然) BOS TAURUS (ウシ) / 器官: HEART / 参照: UniProt: P00829, EC: 3.6.1.34

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タンパク質 , 1種, 2分子 GN

#3: タンパク質 ATP SYNTHASE GAMMA CHAIN


分子量: 30185.674 Da / 分子数: 2 / 断片: RESIDUES 26-297 / 由来タイプ: 天然 / 由来: (天然) BOS TAURUS (ウシ) / 器官: HEART / 参照: UniProt: P05631, EC: 3.6.1.34

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非ポリマー , 8種, 1177分子

#4: 化合物
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP


分子量: 506.196 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C10H17N6O12P3
コメント: AMP-PNP, エネルギー貯蔵分子類似体*YM
#5: 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: 10 / 由来タイプ: 合成 / 式: Mg
#6: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C3H8O3
#7: 化合物 ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP


分子量: 427.201 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / コメント: ADP, エネルギー貯蔵分子*YM
#8: 化合物 ChemComp-AZI / AZIDE ION / アザイド


分子量: 42.020 Da / 分子数: 2 / 由来タイプ: 合成 / 式: N3
#9: 化合物 ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 2 / 由来タイプ: 合成 / 式: PO4
#10: 化合物 ChemComp-PIT / PICEATANNOL / 4-[(E)-2-(3,5-DIHYDROXYPHENYL)ETHENYL]BENZENE-1,2-DIOL / ピセアタンノ-ル


分子量: 244.243 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C14H12O4
#11: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1139 / 由来タイプ: 天然 / 式: H2O

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詳細

配列の詳細RESIDUE GLN 44 IN UNIPROT SEQUENCE IS MODIFIED TO AN N-TERMINAL PYRROLIDONE CARBOXYLIC ACID RESIDUE ...RESIDUE GLN 44 IN UNIPROT SEQUENCE IS MODIFIED TO AN N-TERMINAL PYRROLIDONE CARBOXYLIC ACID RESIDUE AFTER TRANSIT TO MITOCHONDRION. THIS RESIDUE IS MODELLED HERE AS GLU.

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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: 3.13 Å3/Da / 溶媒含有率: 60.37 % / 解説: NONE
結晶化pH: 8.2 / 詳細: pH 8.2

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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: ESRF / ビームライン: ID14-2 / 波長: 0.933
検出器タイプ: ADSC CCD / 検出器: CCD
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: 0.933 Å / 相対比: 1
反射解像度: 2.7→72.36 Å / Num. obs: 201334 / % possible obs: 90.3 % / 冗長度: 1.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.3
反射 シェル解像度: 2.7→2.85 Å / 冗長度: 1.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.9 / % possible all: 92.5

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解析

ソフトウェア
名称バージョン分類
REFMAC5.2.0019精密化
MOSFLMデータ削減
CCP4データスケーリング
AMoRE位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 1W0J

1w0j


解像度: 2.7→72.74 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.859 / SU B: 27.075 / SU ML: 0.28 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 5.755 / ESU R Free: 0.382 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor反射数%反射Selection details
Rfree0.269 10244 5.1 %RANDOM
Rwork0.202 ---
obs0.205 191086 90 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK
原子変位パラメータBiso mean: 36.29 Å2
Baniso -1Baniso -2Baniso -3
1--3.88 Å20 Å20.26 Å2
2--1.65 Å20 Å2
3---2.23 Å2
精密化ステップサイクル: LAST / 解像度: 2.7→72.74 Å
タンパク質核酸リガンド溶媒全体
原子数46072 0 436 1139 47647
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.010.02247222
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.99263830
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68656028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52924.1871944
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46158340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.36915346
X-RAY DIFFRACTIONr_chiral_restr0.0820.27416
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0234818
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.223795
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.232580
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.22279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.267330713
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.248548140
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.58718382
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2531015681
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-ID数タイプRms dev position (Å)Weight position
11A1948tight positional0.060.1
12H1948tight positional0.060.1
21B1916tight positional0.060.1
22I1916tight positional0.060.1
31C1980tight positional0.060.1
32J1980tight positional0.060.1
41D1868tight positional0.060.1
42K1868tight positional0.060.1
51E1864tight positional0.050.1
52L1864tight positional0.050.1
61F1864tight positional0.060.1
62M1864tight positional0.060.1
71G668tight positional0.050.1
72N668tight positional0.050.1
11A1767medium positional0.170.3
12H1767medium positional0.170.3
21B1742medium positional0.150.3
22I1742medium positional0.150.3
31C1788medium positional0.170.3
32J1788medium positional0.170.3
41D1671medium positional0.170.3
42K1671medium positional0.170.3
51E1666medium positional0.170.3
52L1666medium positional0.170.3
61F1666medium positional0.20.3
62M1666medium positional0.20.3
71G628medium positional0.180.3
72N628medium positional0.180.3
11A1948tight thermal1.065
12H1948tight thermal1.065
21B1916tight thermal1.035
22I1916tight thermal1.035
31C1980tight thermal1.035
32J1980tight thermal1.035
41D1868tight thermal1.085
42K1868tight thermal1.085
51E1864tight thermal15
52L1864tight thermal15
61F1864tight thermal1.075
62M1864tight thermal1.075
71G668tight thermal0.95
72N668tight thermal0.95
11A1767medium thermal2.1110
12H1767medium thermal2.1110
21B1742medium thermal2.1410
22I1742medium thermal2.1410
31C1788medium thermal2.2210
32J1788medium thermal2.2210
41D1671medium thermal2.2310
42K1671medium thermal2.2310
51E1666medium thermal1.9710
52L1666medium thermal1.9710
61F1666medium thermal2.1310
62M1666medium thermal2.1310
71G628medium thermal1.8710
72N628medium thermal1.8710
LS精密化 シェル解像度: 2.7→2.77 Å / Total num. of bins used: 20 /
Rfactor反射数
Rfree0.36 768
Rwork0.275 14426
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)
12.58260.4825-1.25990.6017-0.10771.6149-0.06940.0918-0.2699-0.2685-0.0487-0.02690.0609-0.00580.1181-0.01530.04130.014-0.104-0.0478-0.0686-12.11281.7818-22.9101
20.3489-0.0449-0.0590.4825-0.08780.4117-0.02760.10230.0298-0.02160.0055-0.02320.01490.03270.0221-0.07360.0320.0079-0.00510.068-0.1306-4.849931.6889-27.7709
30.40620.2048-0.06351.8983-0.33071.46260.04160.0940.22080.0248-0.0737-0.093-0.08330.01720.0321-0.04480.03060.0198-0.11760.1167-0.0393-0.813662.4979-28.4547
41.7134-0.13260.60050.2760.05792.7791-0.00320.069-0.06020.00420.0554-0.0638-0.02560.0453-0.0522-0.0620.03960.0305-0.15260.0714-0.03413.5806-3.53569.4776
50.28650.05960.28320.3137-0.01210.6984-0.0265-0.00610.0268-0.00760.0008-0.01840.02830.08030.0257-0.09920.044-0.0126-0.0630.1064-0.042821.056223.199122.5537
62.32510.9025-0.57692.58430.43771.17640.2401-0.32060.33560.1042-0.17080.1328-0.25090.1664-0.0692-0.078-0.0396-0.0186-0.1093-0.0163-0.052530.045650.303733.7724
71.52690.2855-0.30791.86410.08910.86510.0479-0.13-0.08550.06030.0256-0.03380.0008-0.0479-0.0735-0.0097-0.01580.0116-0.11750.1089-0.0584-27.9029-4.148416.1664
80.4205-0.20430.09540.2734-0.09290.3802-0.0008-0.0681-0.0338-0.0073-0.0027-0.0042-0.0259-0.06770.0035-0.08350.02160.0161-0.06180.0413-0.0531-34.964727.271818.5794
90.89660.0382-0.44610.7510.08740.7549-0.0811-0.02520.21590.0539-0.0051-0.0403-0.1258-0.120.0862-0.01390.0887-0.0047-0.1261-0.036-0.0122-39.64357.521120.5039
101.546-0.9888-0.27780.69870.59032.6193-0.0560.0075-0.23870.0129-0.03950.0920.1334-0.06880.0956-0.0448-0.0306-0.0178-0.1010.021-0.0671-32.50251.6184-7.0311
110.60980.0846-0.19050.22810.01810.21890.00980.06610.0257-0.03630.00390.0267-0.0076-0.062-0.0137-0.06060.0368-0.0171-0.05210.0572-0.0942-34.565730.3231-12.7253
120.53380.0232-0.05721.58170.07930.78590.1024-0.03920.4441-0.01090.0589-0.02-0.2279-0.0233-0.16140.0210.0580.0239-0.19850.01710.0808-27.911459.9438-6.7474
131.8460.51590.15240.7637-0.76931.0764-0.00560.1273-0.1949-0.2028-0.0966-0.13120.23560.05170.1022-0.04460.0770.0687-0.0444-0.0159-0.07110.65131.6112-15.8133
140.56990.1037-0.07040.0946-0.2030.526-0.02040.0888-0.0050.0295-0.0639-0.08010.01850.08840.0843-0.11510.04090.0116-0.0140.1049-0.059723.822527.8817-11.107
151.9648-0.0444-0.39243.82531.35540.9271-0.03750.03540.5521-0.19750.02720.095-0.57020.35080.0103-0.0594-0.0396-0.0051-0.18630.17370.129632.468657.0473-6.8813
162.43690.51940.52011.2173-0.4841.5583-0.00380.0321-0.23560.08780.05170.06340.07210.0568-0.0479-0.01640.0199-0.0015-0.15720.1257-0.0247-3.3588-4.469525.9746
170.5448-0.06270.19180.3365-0.09810.18040.0306-0.16820.0239-0.0203-0.03540.0186-0.00850.01320.0049-0.05270.03760.0007-0.02320.0653-0.0835-7.310722.651936.7967
180.38440.6275-0.10081.41710.31630.61470.0023-0.08050.18540.07870.05940.0029-0.21190.0483-0.0617-0.00080.0413-0.0457-0.1393-0.0703-0.0181-6.548453.411634.5989
190.60712.25410.23212.29022.28510.60560.0355-0.20140.0541-0.4626-0.09480.2117-0.08970.02140.0593-0.00570.0358-0.0512-0.1301-0.019-0.0644-0.823948.63794.6945
200.1436-0.5283-0.59218.61350.30423.29260.1512-0.25140.26350.20360.2650.0906-0.49420.2552-0.41620.1015-0.00190.1043-0.4743-0.11360.25991.364783.300712.4765
212.0794-0.687-0.38221.34470.39451.5146-0.1279-0.11270.15560.22770.0626-0.04140.0272-0.05330.0653-0.0323-0.0158-0.0349-0.1073-0.0389-0.081441.7481-1.7892.1553
220.376-0.11470.0490.5131-0.01410.1696-0.0247-0.1303-0.03310.00940.00330.007-0.03120.04130.0215-0.0626-0.0303-0.0109-0.01150.06-0.123549.0103-31.667697.0442
230.0241-0.21340.08161.9056-0.87111.91310.0428-0.0588-0.2396-0.0333-0.0614-0.1070.07840.03010.0186-0.0781-0.0207-0.0108-0.08210.1278-0.036553.1207-62.451397.7385
240.4539-0.0019-0.84613.0977-0.61613.06480.01160.0230.12120.1468-0.0765-0.1457-0.05750.05360.065-0.0774-0.0524-0.0585-0.12330.0761-0.027667.21623.53759.7234
250.32550.0177-0.08030.3583-0.00010.5892-0.01010.00960.01750.0013-0.0302-0.05730.0230.07850.0403-0.0931-0.01060.0143-0.06970.0942-0.037974.5848-23.214146.6732
261.3448-1.1391-0.31252.28990.07590.6820.17970.3823-0.2778-0.0039-0.1070.03570.30470.1497-0.0727-0.06760.05880.0077-0.1024-0.0298-0.011283.4829-50.332535.461
271.36-0.6732-0.08550.77140.39731.5299-0.0190.24550.1655-0.0496-0.00570.0314-0.0217-0.03370.02470.00170.041-0.0297-0.11750.1027-0.042325.68464.157153.1134
280.40070.1033-0.11610.3014-0.03790.47750.01020.07950.03870.00710.0030.01040.0248-0.0981-0.0132-0.0846-0.0045-0.0261-0.05390.0398-0.070618.5719-27.266450.7706
291.20350.18110.32820.49910.49121.0461-0.01670.0821-0.17890.0607-0.0348-0.08220.1563-0.15580.0515-0.0444-0.0732-0.0153-0.1363-0.034-0.026113.8379-57.505648.8715
301.1274-0.5856-0.09970.5718-0.05412.6207-0.05440.01110.19190.074-0.10870.049-0.1072-0.00410.1631-0.03680.0186-0.0167-0.09960.0171-0.076921.2466-1.575376.3588
310.4921-0.08780.04780.09670.0670.32830.0161-0.0679-0.04130.01650.00650.01780.0052-0.0615-0.0226-0.0591-0.0248-0.0075-0.0440.0485-0.086519.1871-30.308982.0657
320.7561-0.28610.38761.85650.39970.36940.22920.0143-0.2241-0.05190.04110.00010.2444-0.0399-0.27020.0377-0.0488-0.0268-0.18430.02430.050525.8121-59.920576.0776
331.2106-0.6905-0.53940.8272-0.5381.89080.0779-0.13350.19880.1285-0.0857-0.053-0.17610.08530.0078-0.0643-0.064-0.069-0.064-0.0143-0.041964.4562-1.603885.0844
340.7343-0.08260.02210.3225-0.16460.3894-0.0291-0.0594-0.0089-0.0101-0.0578-0.0756-0.02790.06640.0869-0.1196-0.0286-0.0221-0.01620.1026-0.064677.5771-27.871280.3362
352.4247-0.35010.47272.67411.43630.955-0.028-0.1129-0.6260.0952-0.00330.0650.40910.24450.0312-0.11210.0326-0.0219-0.15820.17580.132286.2062-57.03576.0564
362.70390.2254-0.31651.3323-0.00331.17260.1058-0.04810.1327-0.1045-0.02630.0916-0.10320.1438-0.0795-0.01030.00250.0132-0.15170.1427-0.030450.16324.442743.2748
370.62540.0079-0.22750.3691-0.18870.23350.02960.1503-0.0174-0.0103-0.03910.00580.01110.01470.0096-0.0581-0.0146-0.0027-0.04330.0608-0.078146.1194-22.676132.4852
380.3398-0.34910.25780.94410.3120.7640.04990.0752-0.1653-0.07320.0074-0.11530.23240.0072-0.05740.0021-0.00040.024-0.1445-0.09180.000246.8649-53.443534.7138
390.5414-3.0532-0.368417.54082.34340.4701-0.00510.1091-0.06730.4153-0.02910.16380.07050.01630.03420.0096-0.02450.0079-0.1795-0.0065-0.003652.7935-48.64764.5489
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 95
2X-RAY DIFFRACTION2A96 - 379
3X-RAY DIFFRACTION3A380 - 510
4X-RAY DIFFRACTION4B23 - 95
5X-RAY DIFFRACTION5B96 - 379
6X-RAY DIFFRACTION6B380 - 509
7X-RAY DIFFRACTION7C16 - 95
8X-RAY DIFFRACTION8C96 - 379
9X-RAY DIFFRACTION9C380 - 510
10X-RAY DIFFRACTION10D9 - 82
11X-RAY DIFFRACTION11D83 - 363
12X-RAY DIFFRACTION12D364 - 475
13X-RAY DIFFRACTION13E9 - 82
14X-RAY DIFFRACTION14E83 - 363
15X-RAY DIFFRACTION15E364 - 474
16X-RAY DIFFRACTION16F9 - 82
17X-RAY DIFFRACTION17F83 - 363
18X-RAY DIFFRACTION18F364 - 474
19X-RAY DIFFRACTION19G1 - 30
20X-RAY DIFFRACTION19G220 - 272
21X-RAY DIFFRACTION20G31 - 219
22X-RAY DIFFRACTION21H24 - 95
23X-RAY DIFFRACTION22H96 - 379
24X-RAY DIFFRACTION23H380 - 510
25X-RAY DIFFRACTION24I23 - 95
26X-RAY DIFFRACTION25I96 - 379
27X-RAY DIFFRACTION26I380 - 509
28X-RAY DIFFRACTION27J16 - 95
29X-RAY DIFFRACTION28J96 - 379
30X-RAY DIFFRACTION29J380 - 510
31X-RAY DIFFRACTION30K9 - 82
32X-RAY DIFFRACTION31K83 - 363
33X-RAY DIFFRACTION32K364 - 475
34X-RAY DIFFRACTION33L9 - 82
35X-RAY DIFFRACTION34L83 - 363
36X-RAY DIFFRACTION35L364 - 474
37X-RAY DIFFRACTION36M9 - 82
38X-RAY DIFFRACTION37M83 - 363
39X-RAY DIFFRACTION38M364 - 474
40X-RAY DIFFRACTION39N1 - 30
41X-RAY DIFFRACTION39N220 - 272

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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