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- PDB-6u9d: Saccharomyces cerevisiae acetohydroxyacid synthase -

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基本情報

登録情報
データベース: PDB / ID: 6u9d
タイトルSaccharomyces cerevisiae acetohydroxyacid synthase
要素(Acetolactate synthase ...) x 2
キーワードTRANSFERASE / AHAS / pyruvate / FAD / dioxygen
機能・相同性
機能・相同性情報


acetolactate synthase regulator activity / acetolactate synthase complex / acetolactate synthase / branched-chain amino acid biosynthetic process / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / mitochondrial nucleoid / enzyme regulator activity ...acetolactate synthase regulator activity / acetolactate synthase complex / acetolactate synthase / branched-chain amino acid biosynthetic process / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / mitochondrial nucleoid / enzyme regulator activity / flavin adenine dinucleotide binding / magnesium ion binding / mitochondrion
類似検索 - 分子機能
: / Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / : / AHAS small subunit-like ACT domain / Acetolactate synthase/Transcription factor NikR, C-terminal / Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain ...: / Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / : / AHAS small subunit-like ACT domain / Acetolactate synthase/Transcription factor NikR, C-terminal / Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain / ACT domain / Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / ACT domain profile. / ACT domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / ACT-like domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Chem-60G / ADENOSINE-5'-TRIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / THIAMINE DIPHOSPHATE / Acetolactate synthase small subunit, mitochondrial / Acetolactate synthase catalytic subunit, mitochondrial / Acetolactate synthase small subunit, mitochondrial
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.194 Å
データ登録者Guddat, L.W. / Lonhienne, T.
資金援助 オーストラリア, 1件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)Grant numbers 1087713 & 1147297 オーストラリア
引用ジャーナル: Nature / 年: 2020
タイトル: Structures of fungal and plant acetohydroxyacid synthases.
著者: Thierry Lonhienne / Yu Shang Low / Mario D Garcia / Tristan Croll / Yan Gao / Quan Wang / Lou Brillault / Craig M Williams / James A Fraser / Ross P McGeary / Nicholas P West / Michael J ...著者: Thierry Lonhienne / Yu Shang Low / Mario D Garcia / Tristan Croll / Yan Gao / Quan Wang / Lou Brillault / Craig M Williams / James A Fraser / Ross P McGeary / Nicholas P West / Michael J Landsberg / Zihe Rao / Gerhard Schenk / Luke W Guddat /
要旨: Acetohydroxyacid synthase (AHAS), also known as acetolactate synthase, is a flavin adenine dinucleotide-, thiamine diphosphate- and magnesium-dependent enzyme that catalyses the first step in the ...Acetohydroxyacid synthase (AHAS), also known as acetolactate synthase, is a flavin adenine dinucleotide-, thiamine diphosphate- and magnesium-dependent enzyme that catalyses the first step in the biosynthesis of branched-chain amino acids. It is the target for more than 50 commercial herbicides. AHAS requires both catalytic and regulatory subunits for maximal activity and functionality. Here we describe structures of the hexadecameric AHAS complexes of Saccharomyces cerevisiae and dodecameric AHAS complexes of Arabidopsis thaliana. We found that the regulatory subunits of these AHAS complexes form a core to which the catalytic subunit dimers are attached, adopting the shape of a Maltese cross. The structures show how the catalytic and regulatory subunits communicate with each other to provide a pathway for activation and for feedback inhibition by branched-chain amino acids. We also show that the AHAS complex of Mycobacterium tuberculosis adopts a similar structure, thus demonstrating that the overall AHAS architecture is conserved across kingdoms.
履歴
登録2019年9月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年7月15日Provider: repository / タイプ: Initial release
改定 1.12020年7月22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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22020年10月21日Group: Database references / Derived calculations
カテゴリ: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_leaving_atom_flag / _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
改定 1.32021年1月27日Group: Database references / カテゴリ: citation_author / Item: _citation_author.identifier_ORCID
改定 1.42023年10月11日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Acetolactate synthase catalytic subunit, mitochondrial
B: Acetolactate synthase catalytic subunit, mitochondrial
C: Acetolactate synthase small subunit, mitochondrial
D: Acetolactate synthase small subunit, mitochondrial
E: Acetolactate synthase catalytic subunit, mitochondrial
F: Acetolactate synthase catalytic subunit, mitochondrial
G: Acetolactate synthase small subunit, mitochondrial
H: Acetolactate synthase small subunit, mitochondrial
I: Acetolactate synthase catalytic subunit, mitochondrial
J: Acetolactate synthase catalytic subunit, mitochondrial
K: Acetolactate synthase small subunit, mitochondrial
L: Acetolactate synthase small subunit, mitochondrial
M: Acetolactate synthase catalytic subunit, mitochondrial
N: Acetolactate synthase catalytic subunit, mitochondrial
O: Acetolactate synthase small subunit, mitochondrial
P: Acetolactate synthase small subunit, mitochondrial
Q: Acetolactate synthase catalytic subunit, mitochondrial
R: Acetolactate synthase catalytic subunit, mitochondrial
S: Acetolactate synthase small subunit, mitochondrial
T: Acetolactate synthase small subunit, mitochondrial
U: Acetolactate synthase catalytic subunit, mitochondrial
V: Acetolactate synthase catalytic subunit, mitochondrial
W: Acetolactate synthase small subunit, mitochondrial
X: Acetolactate synthase small subunit, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,261,92587
ポリマ－1,236,42024
非ポリマー25,50563
水79344
1
A: Acetolactate synthase catalytic subunit, mitochondrial
B: Acetolactate synthase catalytic subunit, mitochondrial
C: Acetolactate synthase small subunit, mitochondrial
D: Acetolactate synthase small subunit, mitochondrial
E: Acetolactate synthase catalytic subunit, mitochondrial
F: Acetolactate synthase catalytic subunit, mitochondrial
G: Acetolactate synthase small subunit, mitochondrial
H: Acetolactate synthase small subunit, mitochondrial
I: Acetolactate synthase catalytic subunit, mitochondrial
J: Acetolactate synthase catalytic subunit, mitochondrial
K: Acetolactate synthase small subunit, mitochondrial
L: Acetolactate synthase small subunit, mitochondrial
M: Acetolactate synthase catalytic subunit, mitochondrial
N: Acetolactate synthase catalytic subunit, mitochondrial
O: Acetolactate synthase small subunit, mitochondrial
P: Acetolactate synthase small subunit, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)841,59960
ポリマ－824,28016
非ポリマー17,31944
水1629
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area117230 Å2
ΔGint-751 kcal/mol
Surface area228780 Å2
手法PISA
2
Q: Acetolactate synthase catalytic subunit, mitochondrial
R: Acetolactate synthase catalytic subunit, mitochondrial
S: Acetolactate synthase small subunit, mitochondrial
T: Acetolactate synthase small subunit, mitochondrial
U: Acetolactate synthase catalytic subunit, mitochondrial
V: Acetolactate synthase catalytic subunit, mitochondrial
W: Acetolactate synthase small subunit, mitochondrial
X: Acetolactate synthase small subunit, mitochondrial
ヘテロ分子

Q: Acetolactate synthase catalytic subunit, mitochondrial
R: Acetolactate synthase catalytic subunit, mitochondrial
S: Acetolactate synthase small subunit, mitochondrial
T: Acetolactate synthase small subunit, mitochondrial
U: Acetolactate synthase catalytic subunit, mitochondrial
V: Acetolactate synthase catalytic subunit, mitochondrial
W: Acetolactate synthase small subunit, mitochondrial
X: Acetolactate synthase small subunit, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)840,65154
ポリマ－824,28016
非ポリマー16,37138
水18010
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area109200 Å2
ΔGint-693 kcal/mol
Surface area224660 Å2
手法PISA
単位格子
Length a, b, c (Å)368.647, 230.307, 183.532
Angle α, β, γ (deg.)90.000, 94.570, 90.000
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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Acetolactate synthase ... , 2種, 24分子 ABEFIJMNQRUVCDGHKLOPSTWX

#1: タンパク質
Acetolactate synthase catalytic subunit, mitochondrial / Acetohydroxy-acid synthase catalytic subunit / ALS


分子量: 70264.992 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: ILV2, SMR1, YMR108W, YM9718.07 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P07342, acetolactate synthase
#2: タンパク質
Acetolactate synthase small subunit, mitochondrial


分子量: 32770.016 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: Ilv2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: B3LU66, UniProt: P25605*PLUS

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非ポリマー , 6種, 107分子

#3: 化合物
ChemComp-TPP / THIAMINE DIPHOSPHATE / チアミンピロりん酸


分子量: 425.314 Da / 分子数: 11 / 由来タイプ: 合成 / 式: C12H19N4O7P2S
#4: 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: 16 / 由来タイプ: 合成 / 式: Mg
#5: 化合物
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / FAD


分子量: 785.550 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C27H33N9O15P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: FAD*YM
#6: 化合物
ChemComp-60G / methyl 2-[(4,6-dimethoxypyrimidin-2-yl)carbamoylsulfamoylmethyl]benzoate / Bensulfuron methyl / ベンスルフロンメチル


分子量: 410.402 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C16H18N4O7S / タイプ: SUBJECT OF INVESTIGATION
#7: 化合物
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP


分子量: 507.181 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / タイプ: SUBJECT OF INVESTIGATION / コメント: ATP, エネルギー貯蔵分子*YM
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 44 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY

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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: 3.19 Å3/Da / 溶媒含有率: 61.99 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: The crystals of Saccharomyces cerevisiae AHAS complex were obtained by the hanging drop vapor diffusion method. The catalytic subunit (70.527 kDa, 70 mg/ml) and regulatory subunit (29.625 ...詳細: The crystals of Saccharomyces cerevisiae AHAS complex were obtained by the hanging drop vapor diffusion method. The catalytic subunit (70.527 kDa, 70 mg/ml) and regulatory subunit (29.625 kDa, 19.8 mg/ml) freshly thawed were mixed together in a ratio of 1:2, giving a solution where the concentration of the RSU was ~ 30% in excess compared to the CSU. The cofactors, inhibitor, and DTT were added to the solution to a final concentration of 2 mM ThDP, 1 mM FAD, 10 mM MgCl2, 1 mM BSM and 5 mM DTT. The crystallization buffer consisted of 0.2 M sodium malonate pH 7 and 20% w/v PEG 3,350. The crystallization drops consisted of equal volumes (1 ul) of well solution and enzyme complex

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データ収集

回折平均測定温度: 100 K / Ambient temp details: Oxford cryostream / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Australian Synchrotron / ビームライン: MX1 / 波長: 0.9537 Å
検出器タイプ: ADSC QUANTUM 210r / 検出器: CCD / 日付: 2018年10月26日 / 詳細: MIRRORS
放射モノクロメーター: SI(III) / 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: 0.9537 Å / 相対比: 1
反射解像度: 3.19→49.115 Å / Num. obs: 250942 / % possible obs: 99.5 % / 冗長度: 7.7 % / Biso Wilson estimate: 68.75 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.054 / Rrim(I) all: 0.151 / Net I/σ(I): 11
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.19-3.257.50.77390467120140.8330.2990.829296.5
17.49-49.116.70.0341010015110.9970.0150.03738.394.4

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
XDSデータ削減
XDS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: BSM complex18 (PDB code 5FEM) and the RSU of Thermotoga maritima16 (PDB code 2FGC).

5fem

2fgc


解像度: 3.194→49.11 Å / SU ML: 0.39 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 26.07
Rfactor反射数%反射Selection details
Rfree0.2522 1997 0.8 %1997
Rwork0.2049 ---
obs0.2053 250831 99.47 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 234.67 Å2 / Biso mean: 74.3925 Å2 / Biso min: 1.78 Å2
精密化ステップサイクル: final / 解像度: 3.194→49.11 Å
タンパク質核酸リガンド溶媒全体
原子数76015 0 1593 44 77652
Biso mean--59.44 48.52 -
残基数----10005
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00279237
X-RAY DIFFRACTIONf_angle_d0.585107934
X-RAY DIFFRACTIONf_chiral_restr0.02112353
X-RAY DIFFRACTIONf_plane_restr0.00313889
X-RAY DIFFRACTIONf_dihedral_angle_d13.26429101
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.194-3.27360.31311410.27921732797
3.2736-3.36210.32321430.27471767599
3.3621-3.4610.32491380.26281775199
3.461-3.57270.31891460.248717725100
3.5727-3.70030.24671390.23531771499
3.7003-3.84840.28551440.231117732100
3.8484-4.02350.2411390.214617835100
4.0235-4.23550.25791410.194917731100
4.2355-4.50070.24271520.180317822100
4.5007-4.84790.221380.170917834100
4.8479-5.33530.22451430.175917845100
5.3353-6.10610.25481460.207817914100
6.1061-7.68820.25421460.199917916100
7.6882-49.110.2061410.17341801399
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)
11.7113-0.0077-0.98271.20210.28952.30970.06460.14610.3121-0.0447-0.14160.035-0.3176-0.154-0.20190.2306-0.0081-0.06220.40070.04660.3701306.46645.5026175.8783
21.5023-0.26970.05491.5367-0.19351.3225-0.1164-0.4504-0.02970.5456-0.02060.1771-0.07-0.3415-0.04420.45-0.06360.03320.5483-0.02460.3203295.990936.3456202.3215
32.34840.0673-0.67592.70220.01631.5695-0.0160.1645-0.3934-0.1351-0.13010.49050.161-0.5308-0.13680.2339-0.03560.00830.4595-0.00890.4811289.318815.9358176.4454
41.45030.04890.31131.55650.01831.73720.11790.43-0.2782-0.2722-0.1115-0.33060.3120.316-0.21420.32570.06380.05590.4449-0.01250.5222319.699211.0673164.1393
51.3594-0.1027-2.08373.1993-0.31653.27240.35810.37260.24440.33120.0345-0.39880.48910.54670.1580.52190.08620.14690.8339-0.04251.0277238.549939.333153.9268
60.18910.27160.81925.0279-0.62584.26490.0624-0.0774-0.06570.0116-0.04460.49880.1955-0.188-0.01940.28550.0415-0.07320.5928-0.01780.4884283.512846.5305166.3434
72.02741.79250.69758.23053.74763.34970.02910.1655-0.35520.3366-0.06850.03170.26360.0195-0.10270.28610.0266-0.02870.6217-0.00920.4383264.646332.3607146.1499
82.75351.4463-1.45582.5790.38191.48610.09920.02020.44580.3901-0.1893-0.1726-0.23130.29480.26560.85490.19740.22941.3202-0.1580.7022291.29861.0095117.9782
93.62860.0546-3.64845.2981-0.37944.15160.10890.1061-0.0446-0.1124-0.1293-0.09440.0268-0.2573-0.05470.36220.0489-0.14870.6221-0.00880.4837288.947429.1954152.0465
101.384-1.0545-0.64164.899-1.1371.0280.040.2105-0.03570.2509-0.0462-0.26-0.11130.1805-0.02550.31990.0337-0.16580.65940.00290.4539281.803759.1749144.6007
112.1748-0.051.42131.5241-0.26862.625-0.3183-0.32210.490.0946-0.0063-0.0119-0.3072-0.20780.32520.54790.10950.02170.8786-0.02460.5406305.379547.909287.408
121.18830.20160.44641.2462-0.01260.9168-0.0882-0.0847-0.2080.0960.0624-0.44610.32320.29410.04660.61710.1739-0.00650.90010.00130.6548325.416424.615994.539
131.4783-0.36361.3733.7971-0.11052.1401-0.0157-0.3059-0.26550.26580.02730.27060.3327-0.57920.02180.6804-0.00450.11270.9137-0.04920.4694292.967116.427990.2218
141.1157-0.1131-0.06271.04030.07171.4112-0.11060.4989-0.0196-0.3613-0.07360.13890.137-0.62540.00370.7411-0.04710.03041.1956-0.0840.4827285.761730.93461.4883
150.82150.5031.32925.34590.34192.4066-0.00680.6713-0.2632-0.32840.229-0.2967-0.1114-0.10280.14620.6230.0522-0.11990.7830.10820.5987272.429622.9367144.244
162.59650.6943-0.92040.978-0.27491.0798-0.18390.4754-0.3431-0.13850.0522-0.17280.19170.0582-0.03910.53570.02080.01660.9346-0.19870.5086276.744835.7537116.8105
170.62920.8522-0.31953.4105-1.78570.97750.2168-0.02780.05920.5205-0.09891.0114-1.0578-0.46980.2130.79670.16890.16161.04550.0390.795256.600187.6657126.4853
180.27740.8169-0.14972.8007-0.45790.08690.94410.6262-0.6509-1.7983-0.565-0.1576-0.06150.19270.30961.21740.0432-0.40831.6449-0.00170.9258262.582170.0471100.5374
190.58110.0073-0.20342.53871.23221.7642-0.10490.4315-0.0438-0.44030.1213-0.1218-0.00730.038-0.13590.4696-0.03340.03471.058-0.02730.4385278.284452.2142110.9585
201.2054-0.4922-1.35634.2958-0.05061.69360.1526-0.24120.3415-0.1171-0.22080.0339-0.35950.3468-0.11210.54880.0335-0.20040.9521-0.05160.6068227.104789.237392.1129
213.1568-0.09890.06032.2563-0.33440.07630.01950.39560.2687-0.5081-0.1161-0.4896-0.28990.4173-0.02231.02240.0044-0.01031.33640.10990.6487252.67380.691672.9516
220.94650.1981-0.2311.48240.09050.9691-0.15070.4920.0901-0.9046-0.10050.1370.01590.23160.01081.27820.0717-0.15951.27960.00360.54231.599373.688462.4629
231.1171-0.2653-0.29691.9034-0.14621.4186-0.0228-0.1783-0.0476-0.0638-0.07340.7470.1484-0.4169-0.05810.4469-0.0129-0.10871.2629-0.20680.7652207.82763.7936100.1638
240.36050.4148-0.13311.1766-0.22040.7720.13850.27630.2022-0.3634-0.06171.1612-0.2296-0.67520.10360.7030.1929-0.3961.4264-0.17381.2995196.941285.329587.5698
251.7360.0611-0.0524.1915-1.47312.00760.2657-0.41370.0260.52970.179-0.08840.24480.36280.03210.77660.03190.03131.1894-0.08310.6002265.886420.6661115.8811
262.4926-1.43340.69442.1999-1.89581.7673-0.13970.1633-0.2079-0.9690.14670.82290.1577-0.4429-0.00650.5645-0.1052-0.16891.18810.15460.704245.422162.656598.7746
270.2357-0.168-0.05852.5855-1.41291.6238-0.01140.4422-0.1685-0.2743-0.05390.07570.1236-0.0896-0.12370.4278-0.0146-0.13951.0287-0.08220.5439242.98450.4415113.7511
280.01020.01010.0040.00980.01650.0128-0.3289-0.103-0.2067-0.3354-0.114-0.52320.12980.71440.03440.91020.12510.05971.4610.16280.8686271.284664.04104.2042
293.24260.11110.23512.29010.49791.00570.429-1.4827-0.16341.04310.0252-0.6764-0.05260.4967-0.17060.69950.0512-0.06321.2804-0.05270.7176271.009279.381155.418
303.80121.20413.39671.11811.27043.0014-0.47490.14670.9687-0.6253-0.38140.5682-0.9729-0.86520.96750.5546-0.02810.06551.1880.02640.7314236.399673.141129.4101
312.0466-0.4793-0.09774.51360.26611.26420.154-0.08640.13420.1038-0.14950.23530.0643-0.0838-0.12020.44560.0117-0.05971.2535-0.00590.634227.793763.7621112.6284
323.3731.699-0.11092.42540.6071.3444-0.0470.48320.3371-0.3124-0.07220.1555-0.2799-0.0945-0.15850.4590.0685-0.1530.94870.15580.5256260.070275.3247119.1893
335.0964-0.07422.4165.7055-1.08931.3514-0.1748-0.36060.0445-0.08780.27890.66570.1966-0.3748-0.36750.9807-0.07480.07291.3861-0.01340.7983227.292852.1849141.5225
342.1431-0.50310.15722.6863-0.26492.20940.06020.16450.3522-0.0739-0.1429-0.423-0.09620.5263-0.01670.2856-0.0666-0.04270.4171-0.01060.4621233.766686.3707176.3874
351.8528-0.4072-0.42971.73260.12641.37440.07660.49260.1368-0.0944-0.31680.6181-0.1884-0.4-0.29840.3106-0.0072-0.08610.5112-0.13290.7421203.154190.2151168.9824
361.34010.11950.84431.3473-0.14041.1849-0.12920.175-0.60190.1081-0.13170.31030.5519-0.1101-0.1060.4241-0.09130.19340.431-0.17010.766212.998360.5224175.0774
374.4768-2.48913.4922.2878-1.33453.13610.24160.2895-1.03890.2712-0.14040.43950.968-0.0148-0.85361.05980.00290.09380.8248-0.01851.0702229.713440.6692175.0818
381.5094-0.45570.03622.03760.09361.1246-0.1527-0.6501-0.38840.9016-0.00030.05310.48450.3606-0.09180.95870.02270.06510.72090.18040.5614227.714960.5467202.903
396.0331-2.79711.7444.8586-1.84833.0041-0.6941-1.07380.50671.5813-0.0167-0.6204-0.05020.2284-0.09061.15680.024-0.24911.20510.03550.6935239.135978.2382211.2374
405.2610.5871-1.53298.89221.83926.802-0.20730.2306-0.25430.0344-0.04990.8193-0.1185-0.48040.20680.5222-0.0126-0.24921.2188-0.0381.0591229.108944.3863115.3689
412.0362-0.5367-1.55846.85923.35293.5296-0.2595-0.2997-0.2986-1.1571-0.65640.94330.3072-1.6508-0.10640.7332-0.053-0.03520.946-0.14680.6414233.100568.7707147.0924
427.40.06710.3055.2895-0.22651.190.1160.3225-0.1965-0.1578-0.08250.2410.1405-0.0609-0.0550.40820.01860.0450.5416-0.03440.355234.39673.6583153.9135
430.5998-0.79420.41366.03080.36640.8130.03340.163-0.15390.4675-0.03380.50690.2416-0.17930.02130.3538-0.04440.08410.7105-0.10610.5701242.649941.3968146.0847
445.44810.38163.62594.7854-2.12743.6049-0.028-0.32540.6412-0.0441-0.3912-0.6920.41831.3703-0.22461.36160.43140.27392.01280.24930.8441243.918779.9709125.5909
450.70370.5771-2.27480.4916-1.90267.40660.3170.5210.1307-0.2171-0.1081-0.0758-0.27920.4111-0.06270.6502-0.0827-0.14561.19710.04440.5905294.938666.4311138.8335
464.11711.3536-0.14090.4544-0.06120.00530.0595-0.17830.38560.213-0.0990.11950.01950.0689-0.13980.4014-0.0189-0.10720.6421-0.02510.7154268.105358.6057164.1578
470.748-0.2914-0.72271.6020.10271.61740.02390.0247-0.12950.1952-0.01610.1049-0.1832-0.0965-0.02870.3860.0280.06010.5639-0.05710.4957239.760657.3828167.3459
481.14590.1695-0.36440.5223-0.00940.94120.1170.06610.17060.0907-0.06350.1712-0.0925-0.0159-0.08530.33080.0581-0.01380.51720.00050.4573257.641868.3404149.2337
491.2899-0.53280.07012.09340.44241.02040.25870.26890.119-0.9691-0.02250.14370.0185-0.2628-0.10680.9214-0.0401-0.09670.37930.14780.502337.4138158.6569145.5412
500.9681-0.1614-0.00931.2092-0.16470.61650.222-0.25631.3314-1.11090.2124-0.6362-0.61760.16280.23521.26-0.14080.5342-0.08730.40641.0105350.8225179.614146.7342
510.699-0.3048-0.24120.21290.02760.86340.1390.35060.3554-1.1080.0561-0.9490.23310.51690.52391.3158-0.18110.93510.4590.07840.874369.3865156.2694140.7943
520.2912-0.3703-0.22610.8080.66630.50090.16310.4223-0.0265-0.9418-0.1301-0.38990.12990.038-0.39631.9519-0.0020.37610.7838-0.25310.8049368.7196130.2442123.9393
530.40290.08250.18930.01440.03620.083-0.13220.5427-0.3992-0.59880.0603-0.30.20830.09260.28551.9050.07150.51160.9899-0.13350.8135368.0598135.4253118.5423
540.77170.05770.19840.3797-0.17210.74390.53270.61180.0631-0.3452-0.13020.14410.2914-0.0620.08372.21120.02770.23431.08630.23480.5957353.9417158.7134112.3456
550.5217-1.579-0.21514.88050.66890.07910.0459-0.2830.07740.2665-0.1581-0.59860.25510.12270.07980.80530.0001-0.11540.6747-0.14490.9171379.3822127.0165200.9897
560.4968-0.66840.05582.5855-1.09261.2467-0.3578-0.0377-0.09660.13910.3145-0.2746-0.14990.78320.2180.40650.1704-0.04470.56390.00230.5447356.1698144.3222174.0326
571.2126-0.4065-0.38492.1089-0.32921.0691-0.2215-0.0063-0.031-0.43080.3419-0.1565-0.10230.35020.06120.5131-0.00060.04090.32190.07910.6909347.7871143.9548160.8526
581.2253-0.480.4431.2554-0.1981.17050.05680.18550.1643-0.1916-0.0399-0.2457-0.16190.16960.00990.4282-0.04940.1520.26940.00160.6911370.4761121.9668169.7218
591.639-2.46330.07053.7769-0.080.012-0.18980.07630.37220.0798-0.07490.0227-0.4825-0.3430.05551.29990.13870.19551.09390.08561.0629336.636140.8982193.1208
601.13920.05640.82340.73830.14120.61160.45680.05630.68040.00490.25640.0681-0.547-0.176-0.62550.81750.03370.14560.6818-0.18430.8486331.432293.9133162.0798
611.9444-0.0327-0.33061.0399-0.30741.8701-0.04470.216-0.1482-0.6512-0.13410.03020.11260.06820.01730.70850.02320.15020.3901-0.0270.6969359.7917129.9943148.5018
621.20080.2954-0.26891.0553-0.02961.4202-0.00070.07730.1269-0.22890.10490.2292-0.1862-0.20740.04190.44730.09380.05270.30690.07060.7399335.6005122.6199171.7075
630.7606-0.3874-1.170.19890.59831.7877-0.02320.2101-0.0961-0.0660.0439-0.0204-0.03590.0451-0.00241.27150.13520.17660.67650.04651.2295368.5171102.3629155.4479
641.48470.2576-0.13930.9119-0.36861.20430.14750.14720.0978-0.0072-0.0490.1864-0.2595-0.2421-0.06440.39590.0137-0.08890.46390.03280.2925336.141464.6338141.3811
650.8682-0.0016-0.02710.61330.24941.09290.15160.7330.2715-0.5667-0.0577-0.1102-0.4215-0.11690.09640.77160.1064-0.00010.89770.19010.313345.997577.1684112.6726
661.0419-0.15960.16821.5588-0.32971.20250.00420.34580.1112-0.1290.032-0.3918-0.17630.2293-0.02170.3994-0.03420.08470.5218-0.01070.3042369.427469.9427135.9253
670.9659-0.00950.4060.64190.02991.11540.13030.2019-0.3331-0.01220.0202-0.0510.39560.0461-0.06310.48730.0317-0.1220.3861-0.09170.4373360.106240.2864146.8182
681.4350.2087-1.08031.4321-0.89381.19360.27990.1389-0.1145-0.23880.3966-0.22960.08690.3514-0.28730.92050.00520.17930.65620.12021.0047374.3061122.6288158.7801
691.51150.58660.67980.61730.60041.38270.02030.23540.015-0.21090.0855-0.21680.01120.14140.05870.41730.02260.06640.2481-0.02160.5231360.925494.3036161.5936
703.4834-0.45520.29366.15580.02424.16930.0740.17610.0310.0221-0.08240.37340.0483-0.15750.03440.50930.1386-0.00680.49460.17940.6105331.618785.8321201.5697
710.7136-0.7003-0.18082.28891.86341.7995-0.35620.07560.12560.21640.25160.41570.3623-0.63080.05070.54890.16270.07390.55540.06760.3509354.294475.6614169.1342
721.7982-0.15040.20732.6040.0251.56610.19340.18850.0508-0.02930.10520.0894-0.0551-0.1755-0.03120.37820.0179-0.02620.3315-0.05940.4366359.278574.2851160.6647
731.2912-0.2687-0.18671.335-0.00420.9758-0.02360.0825-0.0024-0.02690.06530.21320.0432-0.14510.03150.2962-0.01320.0220.2755-0.01460.5727340.195194.2958172.648
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 84 through 315 )A84 - 315
2X-RAY DIFFRACTION2chain 'A' and (resid 316 through 687 )A316 - 687
3X-RAY DIFFRACTION3chain 'B' and (resid 81 through 277 )B81 - 277
4X-RAY DIFFRACTION4chain 'B' and (resid 278 through 687 )B278 - 687
5X-RAY DIFFRACTION5chain 'C' and (resid 42 through 76 )C42 - 76
6X-RAY DIFFRACTION6chain 'C' and (resid 77 through 155 )C77 - 155
7X-RAY DIFFRACTION7chain 'C' and (resid 156 through 294 )C156 - 294
8X-RAY DIFFRACTION8chain 'D' and (resid 43 through 76 )D43 - 76
9X-RAY DIFFRACTION9chain 'D' and (resid 77 through 155 )D77 - 155
10X-RAY DIFFRACTION10chain 'D' and (resid 156 through 292 )D156 - 292
11X-RAY DIFFRACTION11chain 'E' and (resid 85 through 296 )E85 - 296
12X-RAY DIFFRACTION12chain 'E' and (resid 297 through 687 )E297 - 687
13X-RAY DIFFRACTION13chain 'F' and (resid 84 through 278 )F84 - 278
14X-RAY DIFFRACTION14chain 'F' and (resid 279 through 687 )F279 - 687
15X-RAY DIFFRACTION15chain 'G' and (resid 43 through 77 )G43 - 77
16X-RAY DIFFRACTION16chain 'G' and (resid 78 through 295 )G78 - 295
17X-RAY DIFFRACTION17chain 'H' and (resid 42 through 55 )H42 - 55
18X-RAY DIFFRACTION18chain 'H' and (resid 56 through 77 )H56 - 77
19X-RAY DIFFRACTION19chain 'H' and (resid 78 through 293 )H78 - 293
20X-RAY DIFFRACTION20chain 'I' and (resid 84 through 265 )I84 - 265
21X-RAY DIFFRACTION21chain 'I' and (resid 266 through 343 )I266 - 343
22X-RAY DIFFRACTION22chain 'I' and (resid 344 through 687 )I344 - 687
23X-RAY DIFFRACTION23chain 'J' and (resid 84 through 457 )J84 - 457
24X-RAY DIFFRACTION24chain 'J' and (resid 458 through 685 )J458 - 685
25X-RAY DIFFRACTION25chain 'K' and (resid 42 through 66 )K42 - 66
26X-RAY DIFFRACTION26chain 'K' and (resid 67 through 99 )K67 - 99
27X-RAY DIFFRACTION27chain 'K' and (resid 100 through 275 )K100 - 275
28X-RAY DIFFRACTION28chain 'K' and (resid 276 through 295 )K276 - 295
29X-RAY DIFFRACTION29chain 'L' and (resid 41 through 55 )L41 - 55
30X-RAY DIFFRACTION30chain 'L' and (resid 56 through 89 )L56 - 89
31X-RAY DIFFRACTION31chain 'L' and (resid 90 through 155 )L90 - 155
32X-RAY DIFFRACTION32chain 'L' and (resid 156 through 279 )L156 - 279
33X-RAY DIFFRACTION33chain 'L' and (resid 280 through 295 )L280 - 295
34X-RAY DIFFRACTION34chain 'M' and (resid 83 through 296 )M83 - 296
35X-RAY DIFFRACTION35chain 'M' and (resid 297 through 687 )M297 - 687
36X-RAY DIFFRACTION36chain 'N' and (resid 85 through 255 )N85 - 255
37X-RAY DIFFRACTION37chain 'N' and (resid 256 through 296 )N256 - 296
38X-RAY DIFFRACTION38chain 'N' and (resid 297 through 654 )N297 - 654
39X-RAY DIFFRACTION39chain 'N' and (resid 655 through 687 )N655 - 687
40X-RAY DIFFRACTION40chain 'O' and (resid 50 through 66 )O50 - 66
41X-RAY DIFFRACTION41chain 'O' and (resid 67 through 89 )O67 - 89
42X-RAY DIFFRACTION42chain 'O' and (resid 90 through 155 )O90 - 155
43X-RAY DIFFRACTION43chain 'O' and (resid 156 through 279 )O156 - 279
44X-RAY DIFFRACTION44chain 'O' and (resid 280 through 293 )O280 - 293
45X-RAY DIFFRACTION45chain 'P' and (resid 42 through 55 )P42 - 55
46X-RAY DIFFRACTION46chain 'P' and (resid 56 through 84 )P56 - 84
47X-RAY DIFFRACTION47chain 'P' and (resid 85 through 140 )P85 - 140
48X-RAY DIFFRACTION48chain 'P' and (resid 141 through 294 )P141 - 294
49X-RAY DIFFRACTION49chain 'Q' and (resid 84 through 366 )Q84 - 366
50X-RAY DIFFRACTION50chain 'Q' and (resid 367 through 687 )Q367 - 687
51X-RAY DIFFRACTION51chain 'R' and (resid 84 through 255 )R84 - 255
52X-RAY DIFFRACTION52chain 'R' and (resid 256 through 407 )R256 - 407
53X-RAY DIFFRACTION53chain 'R' and (resid 408 through 544 )R408 - 544
54X-RAY DIFFRACTION54chain 'R' and (resid 545 through 650 )R545 - 650
55X-RAY DIFFRACTION55chain 'S' and (resid 43 through 66 )S43 - 66
56X-RAY DIFFRACTION56chain 'S' and (resid 67 through 85 )S67 - 85
57X-RAY DIFFRACTION57chain 'S' and (resid 86 through 150 )S86 - 150
58X-RAY DIFFRACTION58chain 'S' and (resid 151 through 280 )S151 - 280
59X-RAY DIFFRACTION59chain 'S' and (resid 281 through 295 )S281 - 295
60X-RAY DIFFRACTION60chain 'T' and (resid 45 through 77 )T45 - 77
61X-RAY DIFFRACTION61chain 'T' and (resid 78 through 155 )T78 - 155
62X-RAY DIFFRACTION62chain 'T' and (resid 156 through 279 )T156 - 279
63X-RAY DIFFRACTION63chain 'T' and (resid 280 through 291 )T280 - 291
64X-RAY DIFFRACTION64chain 'U' and (resid 84 through 283 )U84 - 283
65X-RAY DIFFRACTION65chain 'U' and (resid 284 through 687 )U284 - 687
66X-RAY DIFFRACTION66chain 'V' and (resid 83 through 277 )V83 - 277
67X-RAY DIFFRACTION67chain 'V' and (resid 278 through 687 )V278 - 687
68X-RAY DIFFRACTION68chain 'W' and (resid 44 through 76 )W44 - 76
69X-RAY DIFFRACTION69chain 'W' and (resid 77 through 292 )W77 - 292
70X-RAY DIFFRACTION70chain 'X' and (resid 49 through 66 )X49 - 66
71X-RAY DIFFRACTION71chain 'X' and (resid 67 through 89 )X67 - 89
72X-RAY DIFFRACTION72chain 'X' and (resid 90 through 150 )X90 - 150
73X-RAY DIFFRACTION73chain 'X' and (resid 151 through 296 )X151 - 296

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万見について

-
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

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