[日本語] English
万見
- PDB-4q66: Structure of Exomer bound to Arf1. -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 4q66
タイトルStructure of Exomer bound to Arf1.
要素
  • ADP-ribosylation factor 1
  • Chs5p
  • Protein BCH1
キーワードPROTEIN TRANSPORT / Cargo adaptor / secretory vesicle / small GTP-ase Arf1-binding / trans-Golgi Network
機能・相同性
機能・相同性情報


exomer complex / : / Synthesis of PIPs at the plasma membrane / VxPx cargo-targeting to cilium / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Golgi vesicle transport ...exomer complex / : / Synthesis of PIPs at the plasma membrane / VxPx cargo-targeting to cilium / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Golgi vesicle transport / Golgi to plasma membrane transport / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / small monomeric GTPase / macroautophagy / intracellular protein transport / small GTPase binding / protein transport / GTPase activity / GTP binding / Golgi apparatus / membrane / plasma membrane / cytosol
類似検索 - 分子機能
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #50 / Chs5p-Arf1p binding / ChAPs (Chs5p-Arf1p-binding proteins) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / ADP-ribosylation factor 1-5 / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #50 / Chs5p-Arf1p binding / ChAPs (Chs5p-Arf1p-binding proteins) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / ADP-ribosylation factor 1-5 / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Other non-globular / Rab subfamily of small GTPases / Special / Tetratricopeptide-like helical domain superfamily / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / ADP-ribosylation factor 1 / Protein BCH1 / :
類似検索 - 構成要素
生物種Saccharomyces cerevisiae R008 (パン酵母)
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: 3.354 Å
データ登録者Paczkowski, J.E. / Fromme, J.C.
引用ジャーナル: Dev.Cell / 年: 2014
タイトル: Structural basis for membrane binding and remodeling by the exomer secretory vesicle cargo adaptor.
著者: Paczkowski, J.E. / Fromme, J.C.
履歴
登録2014年4月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年9月17日Provider: repository / タイプ: Initial release
改定 1.12014年12月31日Group: Database references
改定 1.22024年2月28日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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

-
集合体

登録構造単位
A: Chs5p
J: Chs5p
G: Chs5p
D: Chs5p
K: Protein BCH1
E: Protein BCH1
B: Protein BCH1
H: Protein BCH1
F: ADP-ribosylation factor 1
L: ADP-ribosylation factor 1
C: ADP-ribosylation factor 1
I: ADP-ribosylation factor 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)581,63120
ポリマ－579,44512
非ポリマー2,1868
水00
1
A: Chs5p
D: Chs5p
E: Protein BCH1
B: Protein BCH1
F: ADP-ribosylation factor 1
C: ADP-ribosylation factor 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)290,81610
ポリマ－289,7236
非ポリマー1,0934
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
J: Chs5p
G: Chs5p
K: Protein BCH1
H: Protein BCH1
L: ADP-ribosylation factor 1
I: ADP-ribosylation factor 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)290,81610
ポリマ－289,7236
非ポリマー1,0934
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)114.659, 208.168, 155.078
Angle α, β, γ (deg.)90.00, 105.48, 90.00
Int Tables number4
Space group name H-MP1211

-
要素

#1: タンパク質
Chs5p / Protein CAL3


分子量: 41010.398 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae R008 (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: CAL3, Chs5, L8543.18, R008_L12446, YLR330W / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Rosetta 2 / 参照: UniProt: W7PD87
#2: タンパク質
Protein BCH1 / BUD7 and CHS6 homolog 1


分子量: 83972.320 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: BCH1, YMR237W, YM9959.19 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Rosetta 2 / 参照: UniProt: Q05029
#3: タンパク質
ADP-ribosylation factor 1


分子量: 19878.592 Da / 分子数: 4 / Fragment: delta N-17 Arf1, unp residues 18-181 / Mutation: Q71L / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: ARF1, YDL192W, D1244 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P11076
#4: 化合物
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Gpp(NH)p


分子量: 522.196 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C10H17N6O13P3
コメント: GppNHp, GMPPNP, 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: 4 / 由来タイプ: 合成 / 式: Mg

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.08 Å3/Da / 溶媒含有率: 60.04 %
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: 8.5
詳細: Exomer and Arf1 were mixed 2:1 in 200 mM NaCl, 50 mM Tris, 11% PEG 10000, 10% glycerol., pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: CHESS / ビームライン: A1 / 波長: 0.978 Å
検出器タイプ: ADSC QUANTUM 210 / 検出器: CCD / 日付: 2012年7月2日
放射モノクロメーター: Si(111) / 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: 0.978 Å / 相対比: 1
反射解像度: 3.35→50 Å / Num. all: 97079 / Num. obs: 97079 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 2.7 % / Biso Wilson estimate: 100.36 Å2 / Rsym value: 0.086 / Net I/σ(I): 11.35
反射 シェル解像度: 3.35→3.41 Å / 冗長度: 2.6 % / Mean I/σ(I) obs: 1.45 / Rsym value: 0.7 / % possible all: 78

-
解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
PHASER位相決定
PHENIX(phenix.refine: 1.8.4_1496)精密化
HKL-2000データ削減
HKL-2000データスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 3.354→43.169 Å / SU ML: 0.53 / σ(F): 1.34 / 位相誤差: 33.94 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3104 2555 2.63 %
Rwork0.2788 --
obs0.2796 97079 96.96 %
all-97079 -
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 3.354→43.169 Å
タンパク質核酸リガンド溶媒全体
原子数26171 0 132 0 26303
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00226724
X-RAY DIFFRACTIONf_angle_d0.50136098
X-RAY DIFFRACTIONf_dihedral_angle_d9.6899843
X-RAY DIFFRACTIONf_chiral_restr0.0194283
X-RAY DIFFRACTIONf_plane_restr0.0024406
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3542-3.41870.3681150.33844198X-RAY DIFFRACTION78
3.4187-3.48840.35111410.32235253X-RAY DIFFRACTION98
3.4884-3.56420.38761430.32045278X-RAY DIFFRACTION98
3.5642-3.64710.33621440.31885287X-RAY DIFFRACTION98
3.6471-3.73820.36121460.31075298X-RAY DIFFRACTION98
3.7382-3.83930.38011410.30665315X-RAY DIFFRACTION98
3.8393-3.95220.32291420.29265334X-RAY DIFFRACTION99
3.9522-4.07960.35831450.28985345X-RAY DIFFRACTION98
4.0796-4.22530.31211440.27815355X-RAY DIFFRACTION99
4.2253-4.39430.29341440.25565317X-RAY DIFFRACTION99
4.3943-4.59410.30371410.24575327X-RAY DIFFRACTION99
4.5941-4.8360.27511460.23525359X-RAY DIFFRACTION99
4.836-5.13860.24741440.24375308X-RAY DIFFRACTION99
5.1386-5.53460.2931430.27035368X-RAY DIFFRACTION98
5.5346-6.09020.33571430.29935321X-RAY DIFFRACTION98
6.0902-6.96820.3021420.30145317X-RAY DIFFRACTION98
6.9682-8.76720.31881490.27675318X-RAY DIFFRACTION98
8.7672-43.17260.28411420.2715226X-RAY DIFFRACTION95
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)
14.1321-6.04391.44548.3973-2.1820.4557-0.7299-0.4773-0.11851.2530.62370.0425-0.2759-0.15380.03540.82560.1409-0.08830.8556-0.07480.8656-23.4158-34.7295143.5694
26.3092-3.1052.71044.3704-5.31586.9232-0.33840.0219-0.30390.1443-0.14930.4642-0.7727-0.43720.40810.58270.1177-0.05410.78690.01810.96721.434-72.3774147.8793
39.18241.7142-4.87121.9211-2.58015.9034-0.51120.013-0.50510.1660.24250.55930.52020.37750.31250.85530.11840.41350.84820.31381.2441-4.2298-97.6712161.0282
41.06740.8640.57692.8671-2.72475.2284-0.0157-0.0381-0.1803-0.58130.20510.32310.5234-0.4062-0.22030.7597-0.0459-0.04660.64810.04120.7094-38.429212.7927135.7421
55.5775-2.36971.93665.5711-1.38653.51980.7853-2.2016-1.1856-0.1648-0.5906-2.34960.9659-0.7202-1.01570.8455-0.3595-0.29130.70030.07920.5424-31.0825-8.3884166.8571
66.3773-2.43190.23995.5906-4.11443.66890.1607-1.0586-0.94960.27740.1912-0.2062-0.19890.3898-0.44990.8085-0.0424-0.231.06150.18241.1119-24.1196-7.1563179.4604
72.7337-4.32130.93029.2984-3.91227.5501-0.116-0.30160.096-0.06580.35580.1343-0.0075-0.6723-0.28030.6954-0.2973-0.09781.0616-0.02230.7782-41.952221.5384127.4814
84.78325.3803-4.66916.0009-5.2374.5542-0.5165-0.42070.1137-0.2012-0.4063-1.2248-1.2739-1.27080.99881.6135-0.4421-0.26041.13380.2830.93-42.105637.481999.3067
97.35515.2296-3.61814.9496-1.04093.5742-0.20090.72620.2755-0.11261.3570.02710.0302-1.0225-0.97080.8742-0.1686-0.08520.84670.0420.3964-34.781471.246183.7922
103.68543.7514-4.13294.1115-4.98157.03770.6245-0.7846-0.39730.6297-0.17410.1926-0.389-0.1787-0.44450.995-0.2216-0.08751.30420.25110.915-31.370480.211888.0857
115.9441-0.4476-0.40092.9623-2.79652.74731.04380.5063-1.44651.0524-0.76540.0494-0.63020.702-0.0451.1019-0.01460.050.85670.13911.0036-26.203574.925283.1517
122.7777-0.11113.08513.05182.70586.0224-0.89342.00220.8355-1.18641.45091.7118-1.4113-0.1501-0.67891.4822-0.1386-0.43192.06220.78520.9917-37.029196.938375.2458
132.8731-4.2282-0.79396.18821.0172.10840.28041.0253-1.04380.55270.13920.2126-1.2848-1.3472-0.6361.18110.3324-0.03351.3657-0.29071.5484-47.463997.118579.0242
148.21233.28016.37582.41710.95217.59490.2298-1.4290.34360.7744-0.40421.8726-1.2542-3.3280.42271.44360.83340.38221.51920.28431.9883-44.2836101.40687.5389
157.4777-5.0316-1.29738.0343-1.46888.1648-0.0768-0.66930.56131.85820.1321-0.98120.06540.3505-0.09710.9752-0.0235-0.3490.6592-0.09850.7633-27.9567-21.3338138.0337
164.605-3.62754.82473.4309-3.98817.72190.85670.24580.6077-0.8722-1.13470.04920.2291-0.06090.33041.07940.5810.02250.93020.11681-60.68398.0129111.1227
174.1885-2.6702-3.1024.16384.09786.75890.1315-0.935-0.5488-1.3361-0.44590.7941-1.3665-1.0395-0.1351.10430.373-0.52110.81840.3050.9822-62.395410.346397.7967
184.4829-3.06992.24178.315-5.86084.1410.81770.8519-0.2647-0.495-0.44730.3092-0.2511-0.274-0.15191.24420.5099-0.04121.38230.08410.8197-68.62113.282688.6487
199.17641.3865-4.64137.3638-0.56312.36060.61872.53461.6671-0.76531.0065-0.7269-0.1993-0.6618-0.6472.1621.31180.08662.27190.12430.8931-69.768534.570172.2756
206.5717-0.04180.96443.40390.61833.297-0.06520.05961.16820.0140.1124-0.157-0.65880.2243-0.03960.6634-0.0044-0.13520.5719-0.08820.8746-13.361138.7693168.6574
210.89290.87990.26131.97780.53422.1182-0.14190.0414-0.09380.04760.113-0.3099-0.1518-0.17040.04490.4997-0.0428-0.17520.64270.00270.6421-24.467819.2342151.1844
222.16710.00420.39131.707-0.23692.1191-0.02820.038-0.3897-0.04360.0427-0.37740.06980.1714-0.020.4503-0.0877-0.07730.7389-0.06870.7541-5.95410.4468153.9407
232.4668-0.51540.14694.14353.07486.84280.1860.2247-0.3475-0.0945-0.23570.27810.9242-0.57030.16430.8281-0.1061-0.09830.6922-0.08580.5482-56.2665-25.845695.8153
240.5638-0.9127-0.48362.05150.39843.5070.096-0.1946-0.0652-0.01240.1136-0.33820.09050.2973-0.31590.51610.0428-0.01270.5885-0.14030.5686-35.1366-11.7428106.5063
254.4705-0.10060.79973.46920.97523.48080.22890.70670.5009-0.78-0.19050.2179-0.2557-0.0169-0.04310.88630.0120.03110.698-0.02130.5315-40.6829-5.280785.9568
264.2492-1.97170.67311.5652-1.00868.15430.25010.5310.91-0.2462-0.4938-0.2343-0.34570.65050.27850.91210.1910.09140.74780.11951.1256-0.9553-46.6288113.723
271.3752-0.0905-0.10042.09910.32632.2532-0.1664-0.050.35380.10680.02770.1153-0.04750.03230.07850.68740.0444-0.220.6478-0.08280.7427-18.8417-44.8316130.9074
285.7168-1.30280.13442.1386-0.35792.1279-0.27640.46860.0328-0.0070.0298-0.16330.940.30020.25781.0410.1461-0.16330.7364-0.02010.79-16.8262-66.9101122.9911
295.24052.66084.09011.64522.65143.9763-0.09280.1838-0.24880.5499-0.2207-0.8986-0.02920.28020.31581.3134-0.2789-0.151.09630.46731.564-16.280948.9825104.1811
303.79570.40750.74284.4516-0.06721.7002-0.3543-0.3778-0.02940.71120.03930.5263-0.33150.50870.35611.4697-0.2252-0.05080.93890.03430.6755-35.038952.3877123.7526
319.031-1.2555-0.68885.91092.446.05721.2252-0.09830.62742.0816-1.3163-1.5790.0283-0.69730.25581.8685-0.7151-0.70961.12110.53421.5436-17.233874.2874110.0498
326.2717-2.28644.26313.0947-1.34063.5564-0.7342-0.41330.77820.67010.8158-0.0641-0.3203-0.86710.23660.96140.40990.1561.50170.43730.6438-64.976812.462459.5592
332.6317-3.00120.66514.04120.87554.5641-0.9238-0.78140.1805-0.31720.90011.14773.017-0.5188-0.10111.5146-0.1259-0.65891.56270.33931.1204-67.63535.568759.6912
347.114-0.5533-1.85522.06320.60934.31751.13120.2904-1.8238-0.50041.96232.14192.3842-0.0355-2.38071.05790.1132-0.35281.03720.21420.821-63.1529.298558.7699
353.07282.7507-3.43093.2738-1.02799.22480.1657-0.5603-0.5880.2910.2003-1.88921.43830.927-0.2891.17740.4506-0.43611.35330.02521.3428-53.6315.43561.6522
362.9783.53563.38175.30756.75252.00440.3968-1.0860.36192.04110.57661.79990.382-4.9595-0.22931.38790.69440.26782.21520.85840.8212-61.747721.066265.9068
376.5485-3.0613-5.39676.06815.34998.5657-0.17230.82131.27250.20090.3794-1.36680.2932-0.9111-0.29571.1978-0.0049-0.45750.99070.38420.9832-53.389818.391770.0362
389.7971-5.9128-2.91189.6291-1.5883.14110.37351.424-1.1222-1.4086-1.3671-1.76584.22022.88381.29991.36770.43910.2091.1675-0.13060.9992-45.809711.569258.1917
392.4490.3732-3.03871.1460.62485.7670.1611-0.7825-0.3818-0.1647-0.25930.1787-0.6307-0.0257-0.47741.86930.65990.05591.53270.95250.5793-64.28524.905663.4761
408.16715.5747-0.97929.44842.27181.64640.4844-0.79570.32656.35793.09742.4213-0.72660.1872-2.93452.25610.1963-0.1421.67320.62360.882-55.867929.54965.7375
412.5266-0.5824.20141.8632-1.13397.0954-1.311.01411.57040.2120.4244-0.36-1.2564-0.1290.69491.47560.051-0.06591.05660.08350.91-59.150924.279457.6793
422.03341.87642.69772.32171.58724.9431-2.08292.50640.899-0.08081.6371-0.709-4.1368-2.8624-0.05721.47720.0565-0.03051.61390.62591.636-61.772220.515848.7703
433.15122.02550.98691.9290.22859.383-0.394-1.6135-0.74290.3171.061.4589-0.0666-1.6184-0.72250.75660.3464-0.05541.26340.70081.54210.7755-6.2977195.4599
443.3844-0.66243.64392.35650.31029.8383-1.68420.76080.91580.5238-0.7722-0.19890.4140.4540.280.90480.2141-0.14531.00550.83341.2686-1.68-1.0402193.9437
455.0446-0.51624.91475.3721.05455.36540.59431.2398-1.3282-0.47870.6236-0.10220.590.1674-1.61650.63330.2094-0.05381.16650.16720.90445.0006-3.5834185.9187
467.71135.7398-7.93124.6205-5.51558.7284-1.90440.6401-1.34-0.28810.91630.5280.4617-3.03650.72020.83780.0797-0.12731.39630.4051.7273-2.4445-14.5873181.3951
471.06731.30650.32778.3190.75243.52142.38292.26242.6527-1.49750.0375-0.1141-0.21932.4603-2.45340.973-0.0201-0.07841.54710.231.861413.3995-6.8449180.2681
487.21765.6185-4.85474.4395-4.25617.4694-0.37990.8112-1.70680.91260.3903-1.1459-0.53090.12490.15190.82940.0273-0.14560.97370.4751.42140.187-17.9884191.5369
494.3344-3.3472-1.83057.4772.47391.5690.1257-0.5203-1.96680.20350.783-0.21111.0816-0.1702-0.81451.15440.1259-0.51911.0530.35181.71337.3802-18.6459191.7278
507.23434.85712.47688.50015.28865.5159-0.63631.0797-0.7898-0.58650.50830.407-0.81470.7097-0.1320.50770.23760.10991.0409-0.07891.6476.589-98.011132.02
517.01255.1346-2.56924.547-0.94822.7911.19081.24980.1154-0.4621-1.0091-1.8787-0.88011.2621-0.97220.97310.0333-0.06991.6983-0.17291.121912.9724-95.7624130.4422
520.8863-1.4387-2.07966.34432.71615.0794-1.63490.92220.25670.14520.7261.620.8917-0.32880.85570.66850.28330.23771.3571-0.08561.2015.3424-97.1732125.2517
532.98412.147-0.1983.0726-0.22421.10861.78493.08941.3354-0.8640.7521.7487-1.79460.9267-2.73781.85890.58960.15861.76980.02641.1672-0.4164-86.4107125.8182
547.6884-2.11174.29525.1498-3.47666.04240.7119-0.6386-0.6828-0.5738-0.3421.1189-0.746-0.3618-0.95090.68990.4214-0.10871.102-0.42251.4714-2.4067-96.7478132.244
555.65145.47545.79848.9616.66596.82011.2855-1.6369-0.7035-2.1938-0.2424-2.0946-1.7708-1.1094-1.22680.6440.11570.26031.05820.05771.7289-8.2305-91.0145138.0691
568.24-1.8578-4.35924.9423-2.39474.8195-0.45051.6782-0.4493-1.0055-1.26860.9343-0.2434-1.23381.83180.6731-0.0372-0.40311.5122-0.6422.3071-8.3967-97.4759127.169
574.35322.50613.33523.0281-0.11795.1870.0645-2.4529-2.2051-0.25570.5961-0.32491.6415-1.8122-0.60540.68980.08090.02281.04980.20411.57460.647-100.8254148.0132
589.4452-2.41141.66941.5705-0.07894.1431-0.2182-0.7449-2.73660.6995-1.01062.81511.0843-1.2591.4090.99770.20130.87221.4480.09592.8625-3.3223-104.7918139.5402
591.17830.77250.80032.16520.69993.58680.2463-0.2095-1.1071.42620.8487-1.89320.95550.6403-1.01431.25260.43520.45010.88590.36343.26561.2113-111.68130.0513
606.62945.4888-5.05784.8306-4.47014.1368-1.21240.0781-1.7915-1.87650.395-2.4242-1.81020.9420.28251.4389-0.67180.17561.6076-0.13680.8769-14.2405102.701391.9664
618.90892.83432.79843.87154.07774.52041.0720.1575-0.37690.16280.76610.0942-0.3238-1.9336-1.87131.3972-0.3513-0.16651.35640.15790.6576-13.411495.779188.8257
622.51611.25883.10328.66033.41054.26410.9657-1.9471-2.87992.03650.67110.59031.3223-1.4602-1.73871.37690.0796-0.39791.190.75381.753-13.324493.153103.5725
633.0842-3.4642.37695.4575-0.64554.4580.0862-0.299-2.03432.4477-1.22460.551.72151.04390.74411.8994-0.55480.35161.65380.40361.4951-23.7904100.6942100.2635
642.660.74372.53077.35312.21292.68820.4082-1.02290.31650.2659-1.37751.8375-0.5301-1.88470.751.159-0.07940.11651.3308-0.20651.7596-27.7728104.864197.1141
655.9477-2.0231.52937.27434.55244.3105-0.1833-0.3374-0.0794-0.36040.1289-0.7273-1.1745-1.12610.39380.9045-0.0939-0.16370.87040.45541.058-20.7123112.023390.3571
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 276 )
4X-RAY DIFFRACTION4chain 'J' and (resid 4 through 97 )
5X-RAY DIFFRACTION5chain 'J' and (resid 98 through 107 )
6X-RAY DIFFRACTION6chain 'J' and (resid 108 through 166 )
7X-RAY DIFFRACTION7chain 'G' and (resid 3 through 52 )
8X-RAY DIFFRACTION8chain 'G' and (resid 53 through 73 )
9X-RAY DIFFRACTION9chain 'G' and (resid 74 through 89 )
10X-RAY DIFFRACTION10chain 'G' and (resid 90 through 141 )
11X-RAY DIFFRACTION11chain 'G' and (resid 142 through 164 )
12X-RAY DIFFRACTION12chain 'G' and (resid 165 through 188 )
13X-RAY DIFFRACTION13chain 'G' and (resid 189 through 228 )
14X-RAY DIFFRACTION14chain 'G' and (resid 229 through 247 )
15X-RAY DIFFRACTION15chain 'D' and (resid 4 through 52 )
16X-RAY DIFFRACTION16chain 'D' and (resid 53 through 98 )
17X-RAY DIFFRACTION17chain 'D' and (resid 99 through 114 )
18X-RAY DIFFRACTION18chain 'D' and (resid 115 through 164 )
19X-RAY DIFFRACTION19chain 'D' and (resid 165 through 264 )
20X-RAY DIFFRACTION20chain 'K' and (resid 3 through 243 )
21X-RAY DIFFRACTION21chain 'K' and (resid 244 through 491 )
22X-RAY DIFFRACTION22chain 'K' and (resid 492 through 722 )
23X-RAY DIFFRACTION23chain 'E' and (resid 2 through 344 )
24X-RAY DIFFRACTION24chain 'E' and (resid 345 through 538 )
25X-RAY DIFFRACTION25chain 'E' and (resid 539 through 722 )
26X-RAY DIFFRACTION26chain 'B' and (resid 3 through 284 )
27X-RAY DIFFRACTION27chain 'B' and (resid 285 through 538 )
28X-RAY DIFFRACTION28chain 'B' and (resid 539 through 721 )
29X-RAY DIFFRACTION29chain 'H' and (resid 189 through 361 )
30X-RAY DIFFRACTION30chain 'H' and (resid 362 through 607 )
31X-RAY DIFFRACTION31chain 'H' and (resid 608 through 721 )
32X-RAY DIFFRACTION32chain 'F' and (resid 18 through 37 )
33X-RAY DIFFRACTION33chain 'F' and (resid 38 through 56 )
34X-RAY DIFFRACTION34chain 'F' and (resid 57 through 74 )
35X-RAY DIFFRACTION35chain 'F' and (resid 75 through 86 )
36X-RAY DIFFRACTION36chain 'F' and (resid 87 through 97 )
37X-RAY DIFFRACTION37chain 'F' and (resid 98 through 110 )
38X-RAY DIFFRACTION38chain 'F' and (resid 111 through 119 )
39X-RAY DIFFRACTION39chain 'F' and (resid 120 through 135 )
40X-RAY DIFFRACTION40chain 'F' and (resid 136 through 143 )
41X-RAY DIFFRACTION41chain 'F' and (resid 144 through 165 )
42X-RAY DIFFRACTION42chain 'F' and (resid 166 through 176 )
43X-RAY DIFFRACTION43chain 'L' and (resid 18 through 38 )
44X-RAY DIFFRACTION44chain 'L' and (resid 39 through 74 )
45X-RAY DIFFRACTION45chain 'L' and (resid 75 through 93 )
46X-RAY DIFFRACTION46chain 'L' and (resid 94 through 110 )
47X-RAY DIFFRACTION47chain 'L' and (resid 111 through 119 )
48X-RAY DIFFRACTION48chain 'L' and (resid 120 through 135 )
49X-RAY DIFFRACTION49chain 'L' and (resid 136 through 176 )
50X-RAY DIFFRACTION50chain 'C' and (resid 20 through 38 )
51X-RAY DIFFRACTION51chain 'C' and (resid 39 through 56 )
52X-RAY DIFFRACTION52chain 'C' and (resid 62 through 71 )
53X-RAY DIFFRACTION53chain 'C' and (resid 72 through 81 )
54X-RAY DIFFRACTION54chain 'C' and (resid 82 through 97 )
55X-RAY DIFFRACTION55chain 'C' and (resid 98 through 107 )
56X-RAY DIFFRACTION56chain 'C' and (resid 108 through 126 )
57X-RAY DIFFRACTION57chain 'C' and (resid 127 through 135 )
58X-RAY DIFFRACTION58chain 'C' and (resid 136 through 166 )
59X-RAY DIFFRACTION59chain 'C' and (resid 167 through 174 )
60X-RAY DIFFRACTION60chain 'I' and (resid 21 through 38 )
61X-RAY DIFFRACTION61chain 'I' and (resid 39 through 73 )
62X-RAY DIFFRACTION62chain 'I' and (resid 74 through 81 )
63X-RAY DIFFRACTION63chain 'I' and (resid 82 through 108 )
64X-RAY DIFFRACTION64chain 'I' and (resid 109 through 143 )
65X-RAY DIFFRACTION65chain 'I' and (resid 144 through 169 )

+
万見について

-
お知らせ

-
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

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.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

+
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

+
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

+
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。

-
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