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- PDB-4pkn: Crystal structure of the football-shaped GroEL-GroES2-(ADPBeFx)14... -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 4pkn
タイトルCrystal structure of the football-shaped GroEL-GroES2-(ADPBeFx)14 complex containing substrate Rubisco
要素
  • 10 kDa chaperonin
  • 60 kDa chaperonin
キーワードPROTEIN BINDING / chaperonin / protein encapsulation / GroEL-GroES2 "football" complex / Rubisco
機能・相同性
機能・相同性情報


chaperonin ATPase / : / isomerase activity / protein folding chaperone / ATP-dependent protein folding chaperone / unfolded protein binding / protein-folding chaperone binding / protein refolding / ATP binding / metal ion binding / cytoplasm
類似検索 - 分子機能
10 Kd Chaperonin, Protein Cpn10; Chain O / GroES chaperonin / GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroEL ...10 Kd Chaperonin, Protein Cpn10; Chain O / GroES chaperonin / GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroEL / GroEL / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / GroES-like superfamily / 3-Layer(bba) Sandwich / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / : / Chaperonin GroEL / Co-chaperonin GroES
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.66 Å
データ登録者Fei, X. / Ye, X. / Laronde-Leblanc, N. / Lorimer, G.H.
資金援助 米国, 2件
組織認可番号国
University of MarylandAnn.Wylie dissertation fellowship 米国
University of MarylandBailey fellowship 米国
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2014
タイトル: Formation and structures of GroEL:GroES2 chaperonin footballs, the protein-folding functional form.
著者: Fei, X. / Ye, X. / LaRonde, N.A. / Lorimer, G.H.
履歴
登録2014年5月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年8月20日Provider: repository / タイプ: Initial release
改定 1.12014年9月3日Group: Database references
改定 1.22014年10月1日Group: Database references
改定 1.32023年12月27日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
G: 60 kDa chaperonin
A: 60 kDa chaperonin
B: 60 kDa chaperonin
F: 60 kDa chaperonin
E: 60 kDa chaperonin
C: 60 kDa chaperonin
D: 60 kDa chaperonin
O: 10 kDa chaperonin
P: 10 kDa chaperonin
Q: 10 kDa chaperonin
U: 10 kDa chaperonin
T: 10 kDa chaperonin
R: 10 kDa chaperonin
S: 10 kDa chaperonin
K: 60 kDa chaperonin
J: 60 kDa chaperonin
I: 60 kDa chaperonin
L: 60 kDa chaperonin
M: 60 kDa chaperonin
H: 60 kDa chaperonin
N: 60 kDa chaperonin
X: 10 kDa chaperonin
W: 10 kDa chaperonin
V: 10 kDa chaperonin
Y: 10 kDa chaperonin
Z: 10 kDa chaperonin
2: 10 kDa chaperonin
1: 10 kDa chaperonin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)956,89084
ポリマ－949,09728
非ポリマー7,79356
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area106810 Å2
ΔGint-649 kcal/mol
Surface area346410 Å2
手法PISA
単位格子
Length a, b, c (Å)171.952, 173.653, 411.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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タンパク質 , 2種, 28分子 GABFECDKJILMHNOPQUTRSXWVYZ21

#1: タンパク質
60 kDa chaperonin / GroEL protein / Protein Cpn60


分子量: 57391.711 Da / 分子数: 14 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌)
遺伝子: groEL, groL, mopA, BN17_41231, BU34_16740, ECs5124, LF82_0923
プラスミド: pKK233-2 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: Q548M1
#2: タンパク質
10 kDa chaperonin / GroES protein / Protein Cpn10


分子量: 10400.938 Da / 分子数: 14 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌)
遺伝子: groS, groES, mopB, BN17_41221, BU34_16745, ECs5123, LF82_0924
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q7BGE6

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非ポリマー , 4種, 56分子

#3: 化合物
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP


分子量: 427.201 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / コメント: ADP, エネルギー貯蔵分子*YM
#4: 化合物
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


分子量: 66.007 Da / 分子数: 14 / 由来タイプ: 合成 / 式: BeF3
#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: 14 / 由来タイプ: 合成 / 式: Mg
#6: 化合物
ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 14 / 由来タイプ: 合成 / 式: K

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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: 3.23 Å3/Da / 溶媒含有率: 61.98 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 10 % PEG 550 mme (v/v), 0.1 M acetic acid-KCl buffer
PH範囲: 4.8-5.2

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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: APS / ビームライン: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2013年11月6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: 0.9792 Å / 相対比: 1
反射解像度: 3.66→122.185 Å / Num. obs: 135754 / % possible obs: 99.7 % / 冗長度: 6.1 % / Net I/σ(I): 6.9
反射 シェル解像度: 3.66→3.86 Å / 冗長度: 6.4 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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解析

ソフトウェア名称: PHENIX / バージョン: (phenix.refine: 1.8.4_1496) / 分類: 精密化
精密化構造決定の手法: 分子置換 / 解像度: 3.66→122.185 Å / SU ML: 0.44 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.47 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.241 1999 1.48 %
Rwork0.1881 --
obs0.1889 135496 99.53 %
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: 3.66→122.185 Å
タンパク質核酸リガンド溶媒全体
原子数64117 0 462 0 64579
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00665013
X-RAY DIFFRACTIONf_angle_d1.20787795
X-RAY DIFFRACTIONf_dihedral_angle_d13.13824559
X-RAY DIFFRACTIONf_chiral_restr0.04710677
X-RAY DIFFRACTIONf_plane_restr0.00511405
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.66-3.75160.31691410.26389456X-RAY DIFFRACTION100
3.7516-3.8530.28251420.24079443X-RAY DIFFRACTION100
3.853-3.96640.30911420.24259415X-RAY DIFFRACTION100
3.9664-4.09440.28921420.22449503X-RAY DIFFRACTION100
4.0944-4.24080.28311390.20519462X-RAY DIFFRACTION100
4.2408-4.41060.2471380.20059422X-RAY DIFFRACTION99
4.4106-4.61130.23191450.18559509X-RAY DIFFRACTION100
4.6113-4.85440.24191440.18099491X-RAY DIFFRACTION100
4.8544-5.15860.221430.18379496X-RAY DIFFRACTION100
5.1586-5.55690.26571440.19899563X-RAY DIFFRACTION100
5.5569-6.11610.28031420.20439537X-RAY DIFFRACTION99
6.1161-7.0010.28961470.19639630X-RAY DIFFRACTION100
7.001-8.82020.18891440.14529620X-RAY DIFFRACTION99
8.8202-122.25350.16731460.13919950X-RAY DIFFRACTION99
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0067-1.2084-0.28181.9454-0.35792.33470.19240.032-0.2498-0.0559-0.30870.19970.1244-0.11170.07820.42520.0069-0.08130.4964-0.06110.488320.352878.3091505.2573
26.38946.4567-1.65276.85380.0027-0.3323-0.36640.4799-0.226-0.13970.28190.02050.7804-0.12190.0561.5127-0.1021-0.16560.94420.11.1685-18.92158.7003501.7874
32.1992-0.5866-0.91042.59490.20731.3127-0.0106-0.3071-0.0230.2623-0.03210.1266-0.05730.09290.02330.47630.0247-0.0430.61910.00360.398222.153581.6158514.1428
42.061-0.3732-0.2721.45820.10471.46490.1068-0.2049-0.3183-0.0965-0.20460.03980.248-0.2172-0.00040.6080.1516-0.00790.67120.05030.632740.093251.1617497.0691
53.59830.9411-1.63155.4973-0.21381.8761-0.82411.9717-0.7904-0.04980.33280.01970.37310.07420.61261.3355-0.26530.18441.647-0.14431.20936.229226.3025501.66
61.7284-0.4761-0.3062.3438-0.20423.525-0.1865-0.0911-0.33590.14780.01920.01580.32740.15850.12940.51190.169-0.02420.62810.12690.638148.226348.2334501.0432
71.350.33540.02820.77860.36611.7685-0.0639-0.012-0.5398-0.0885-0.1256-0.07850.1514-0.40690.15580.66680.22480.12620.78210.01660.765352.657138.7157464.1916
83.84113.3227-0.66797.7992-1.69656.97840.1104-0.21610.64410.1893-0.39410.5680.0333-0.22680.17660.86670.01790.04261.3438-0.29871.383823.44869.3959472.3339
9-0.1388-0.30850.25752.4542-0.61223.3899-0.13270.0619-0.20550.0730.0584-0.42330.44160.17820.07280.62060.2070.13380.6290.02940.863861.402236.6943460.9275
102.5143-0.76520.9711.2721-0.53433.09710.1691-0.0609-0.07-0.0925-0.05070.41060.0132-0.2385-0.06850.52630.1215-0.01230.6308-0.02550.5992-1.49999.7146483.3345
112.91194.2514-0.19386.1678-0.9595-0.18180.0776-0.1665-0.79250.0371-0.1985-0.04510.2718-0.0413-0.10381.05430.0544-0.17761.28620.21331.6251-35.288574.8136470.2405
123.9103-1.05050.91991.82-1.14093.85230.1250.0620.2584-0.08960.03010.2879-0.4262-0.5521-0.13970.48140.17730.10990.55030.05090.7035-4.3524107.7657488.102
130.7489-0.2001-0.65291.85760.54743.8213-0.14940.08180.0816-0.18830.10030.2780.1197-0.4390.01050.55360.1757-0.08350.82150.11460.6307-2.8645101.0476445.0744
146.09414.682-0.15034.1908-2.06223.06890.2698-0.19820.07850.360.09250.76490.2747-0.2608-0.34371.1508-0.04730.04851.0710.16471.5042-28.757168.1294433.1462
153.10860.17140.05141.3096-0.58872.7114-0.04650.55480.3459-0.27140.12360.2445-0.1746-0.4111-0.04270.65780.2281-0.11940.88420.10480.6169-6.1659110.2348442.8643
161.36920.47020.54221.1978-0.34591.2099-0.0274-0.1543-0.587-0.20460.0466-0.11150.3686-0.36170.00410.81270.03590.08650.8284-0.00540.70737.085443.0645431.497
175.0834.18660.31223.1799-0.41330.8848-0.01830.1812-0.0382-0.33930.46160.32460.1338-0.8382-0.32351.10850.0779-0.09581.17720.05461.104125.611323.9913432.0744
184.1899-2.1358-0.00882.77180.34171.52960.15310.989-0.0362-0.4468-0.212-0.35340.28330.15430.05090.69930.03070.17860.7259-0.00560.464550.844658.2663416.9497
191.708-0.83230.03111.9411-0.09592.5211-0.29990.12080.029-0.10220.26510.14330.2-0.29920.04360.64-0.0673-0.0170.70530.1230.479817.241581.693420.9411
205.27164.0560.50616.4003-0.63481.75690.2854-0.37250.59310.144-0.22450.2484-0.3602-0.0426-0.08390.8932-0.1729-0.01610.8843-0.21580.7192-3.388942.5338418.3692
212.2943-0.1208-0.28011.56090.92552.4603-0.13140.3933-0.0632-0.28770.05940.02870.0265-0.28030.06640.6958-0.0137-0.11430.85880.0830.391517.787584.2936412.5424
224.60942.76166.0166.4371.77659.5751-0.19150.6651.69180.14370.18750.877-2.35210.0172-0.00961.2293-0.18360.05820.9037-0.04080.6958-41.694725.0106484.9209
235.8146-0.61594.50150.0591-0.46543.89390.14921.60861.33761.4342-0.169-2.86180.19940.58540.47821.7382-0.3345-0.06991.1663-0.09012.1228-21.005325.1757498.3118
244.38572.4114.18178.35765.14745.9136-0.31021.14340.3525-0.46571.2516-1.8931-1.53592.7796-0.89541.3648-0.479-0.11221.4565-0.09291.2493-24.680625.0273492.7882
255.74610.5076-6.94612.68560.8319.28830.5414-1.04120.3891-0.2261-0.6982-0.0008-0.4718-0.5329-0.5211.1951-0.2187-0.11670.55650.01961.0952-43.479314.6703476.3806
268.28982.34522.52565.20621.81087.4381-0.63070.7859-0.5443-1.15420.90280.99520.02181.403-0.26861.1402-0.1702-0.08191.01470.23050.9123-36.504416.6703482.2504
273.01360.57561.64552.69053.22754.38680.4072-0.57150.2411-1.1469-0.17050.4854-1.25341.1811-0.07181.1995-0.1835-0.05071.1380.12230.6947-34.530425.1795487.0138
283.4999-2.8684-2.10385.82560.24412.95331.3964-1.37840.58891.2059-0.487-0.8515-1.70250.9055-0.42261.0743-0.0921-0.28751.10010.02880.9048-25.08668.5183487.3452
292.4764-1.44931.63511.58921.3987.86840.6915-2.4387-0.72741.0991-0.3333-1.36930.55512.11560.72911.552-0.1912-0.2912.22830.29041.647-0.18072.3965486.0513
304.7498-0.55913.9437.77-3.12734.4262-0.0689-2.2714-1.47881.6043-0.9954-1.7540.32690.92880.70611.574-0.2290.20173.10130.76821.48747.34432.7329484.7747
318.3961-2.4602-0.1630.73930.01270.0550.106-1.36091.22861.5744-0.9868-1.4241-0.16471.51110.34561.07-0.3483-0.131.8570.04761.3449-4.140811.1912482.4054
321.7704-3.12850.5596.50530.79636.8541-1.75561.2121-0.00021.01520.6632-0.75130.36240.4130.98670.6529-0.15180.03411.05690.03450.9284-24.41733.375482.9683
335.1029-0.01385.78498.74373.79128.6547-1.08852.25590.70031.0931-0.92740.217-0.92251.14071.60581.0038-0.1988-0.19981.273-0.24850.8066-40.11363.5108472.197
349.043-0.1468-2.51364.10261.71124.3613-0.74831.01660.3377-0.65730.39490.01660.03170.96470.11051.00030.0274-0.00620.91090.04580.959-21.28063.8033479.8966
359.2724-5.8943-6.84594.38754.99816.970.07460.20531.07240.7663-0.3801-1.01490.74370.374-0.00061.0472-0.196-0.10141.65830.23290.7466-18.34847.9283484.9554
364.46-0.3124-2.98157.8456-2.1143.2626-0.41161.3816-0.71620.34610.1533-1.1158-0.20080.74990.35380.9933-0.1844-0.10581.3834-0.11091.2985-10.3723-3.083467.8391
376.03293.9635-6.28152.6052-4.13456.5437-1.84632.0036-1.4744-0.744-1.22760.46620.2671-2.37162.77672.041-1.4119-1.50372.54150.78623.32826.03150.719448.0733
385.88341.2976-2.42172.8873-1.54294.3339-0.2712-0.14041.31590.48090.2751-0.19070.7791.64080.38560.9859-0.01030.15661.5586-0.0941.4209-10.4266-0.5625461.483
393.3231-3.67292.92326.0542-1.39854.1963-0.5313-0.25790.2817-0.32060.19230.2767-1.3486-0.74980.57641.1372-0.4672-0.57912.5532-0.3461.3813-36.0652-1.0408465.9589
403.99164.5531-0.50318.0449-3.8684.01830.35831.03640.0142-0.3026-0.657-0.4772-1.02841.88040.37381.2482-0.24040.07771.3157-0.06061.1123-15.9831-1.9557460.5598
413.65811.0224.80124.38430.43717.18970.9112-0.87170.75370.0385-0.4774-0.76740.71450.8624-0.50111.0378-0.17820.28551.5223-0.01851.3765-10.0634-1.0639464.7556
429.54076.32834.59455.24923.6822.7862-0.7216-0.0031.1864-0.73280.50410.3973-0.70130.12230.34341.73320.1279-0.14070.8790.0371.1382-51.90733.7408465.6574
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1274.24630.827-2.77074.0498-2.51883.1292-0.13730.5383-0.8449-0.6906-0.70240.25671.3656-0.50470.9241.758-0.23110.14621.40310.00331.8742124.3667170.8135471.6226
1283.92712.5181-3.12713.6726-4.32656.22470.7609-0.6375-1.06140.3754-1.19810.0678-0.1363-1.2138-0.21731.4197-0.47670.09961.4367-0.46550.9238110.1772167.9054485.9661
1299.3153-0.7287-1.55459.5671-5.16056.76760.0795-0.6331-0.89810.41-0.18350.0460.7157-1.23740.20341.1598-0.44560.08931.284-0.38651.0277109.0963162.3565490.119
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 2 through 179 )
2X-RAY DIFFRACTION2chain 'G' and (resid 180 through 385 )
3X-RAY DIFFRACTION3chain 'G' and (resid 386 through 525 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2 through 212 )
5X-RAY DIFFRACTION5chain 'A' and (resid 213 through 353 )
6X-RAY DIFFRACTION6chain 'A' and (resid 354 through 525 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 212 )
8X-RAY DIFFRACTION8chain 'B' and (resid 213 through 357 )
9X-RAY DIFFRACTION9chain 'B' and (resid 358 through 525 )
10X-RAY DIFFRACTION10chain 'F' and (resid 2 through 179 )
11X-RAY DIFFRACTION11chain 'F' and (resid 180 through 385 )
12X-RAY DIFFRACTION12chain 'F' and (resid 386 through 525 )
13X-RAY DIFFRACTION13chain 'E' and (resid 2 through 185 )
14X-RAY DIFFRACTION14chain 'E' and (resid 186 through 385 )
15X-RAY DIFFRACTION15chain 'E' and (resid 386 through 525 )
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 255 )
17X-RAY DIFFRACTION17chain 'C' and (resid 256 through 409 )
18X-RAY DIFFRACTION18chain 'C' and (resid 410 through 525 )
19X-RAY DIFFRACTION19chain 'D' and (resid 2 through 179 )
20X-RAY DIFFRACTION20chain 'D' and (resid 180 through 372 )
21X-RAY DIFFRACTION21chain 'D' and (resid 373 through 525 )
22X-RAY DIFFRACTION22chain 'O' and (resid 1 through 14 )
23X-RAY DIFFRACTION23chain 'O' and (resid 15 through 24 )
24X-RAY DIFFRACTION24chain 'O' and (resid 25 through 43 )
25X-RAY DIFFRACTION25chain 'O' and (resid 44 through 49 )
26X-RAY DIFFRACTION26chain 'O' and (resid 50 through 73 )
27X-RAY DIFFRACTION27chain 'O' and (resid 74 through 97 )
28X-RAY DIFFRACTION28chain 'P' and (resid 1 through 14 )
29X-RAY DIFFRACTION29chain 'P' and (resid 15 through 24 )
30X-RAY DIFFRACTION30chain 'P' and (resid 25 through 29 )
31X-RAY DIFFRACTION31chain 'P' and (resid 30 through 36 )
32X-RAY DIFFRACTION32chain 'P' and (resid 37 through 48 )
33X-RAY DIFFRACTION33chain 'P' and (resid 49 through 53 )
34X-RAY DIFFRACTION34chain 'P' and (resid 54 through 73 )
35X-RAY DIFFRACTION35chain 'P' and (resid 74 through 97 )
36X-RAY DIFFRACTION36chain 'Q' and (resid 1 through 18 )
37X-RAY DIFFRACTION37chain 'Q' and (resid 19 through 28 )
38X-RAY DIFFRACTION38chain 'Q' and (resid 29 through 48 )
39X-RAY DIFFRACTION39chain 'Q' and (resid 49 through 53 )
40X-RAY DIFFRACTION40chain 'Q' and (resid 54 through 73 )
41X-RAY DIFFRACTION41chain 'Q' and (resid 74 through 97 )
42X-RAY DIFFRACTION42chain 'U' and (resid 1 through 14 )
43X-RAY DIFFRACTION43chain 'U' and (resid 15 through 24 )
44X-RAY DIFFRACTION44chain 'U' and (resid 25 through 73 )
45X-RAY DIFFRACTION45chain 'U' and (resid 74 through 80 )
46X-RAY DIFFRACTION46chain 'U' and (resid 81 through 97 )
47X-RAY DIFFRACTION47chain 'T' and (resid 1 through 14 )
48X-RAY DIFFRACTION48chain 'T' and (resid 15 through 37 )
49X-RAY DIFFRACTION49chain 'T' and (resid 38 through 53 )
50X-RAY DIFFRACTION50chain 'T' and (resid 54 through 97 )
51X-RAY DIFFRACTION51chain 'R' and (resid 1 through 14 )
52X-RAY DIFFRACTION52chain 'R' and (resid 15 through 29 )
53X-RAY DIFFRACTION53chain 'R' and (resid 30 through 49 )
54X-RAY DIFFRACTION54chain 'R' and (resid 50 through 55 )
55X-RAY DIFFRACTION55chain 'R' and (resid 56 through 73 )
56X-RAY DIFFRACTION56chain 'R' and (resid 74 through 97 )
57X-RAY DIFFRACTION57chain 'S' and (resid 1 through 14 )
58X-RAY DIFFRACTION58chain 'S' and (resid 15 through 24 )
59X-RAY DIFFRACTION59chain 'S' and (resid 25 through 36 )
60X-RAY DIFFRACTION60chain 'S' and (resid 37 through 48 )
61X-RAY DIFFRACTION61chain 'S' and (resid 49 through 58 )
62X-RAY DIFFRACTION62chain 'S' and (resid 59 through 73 )
63X-RAY DIFFRACTION63chain 'S' and (resid 74 through 97 )
64X-RAY DIFFRACTION64chain 'K' and (resid 2 through 212 )
65X-RAY DIFFRACTION65chain 'K' and (resid 213 through 353 )
66X-RAY DIFFRACTION66chain 'K' and (resid 354 through 525 )
67X-RAY DIFFRACTION67chain 'J' and (resid 2 through 195 )
68X-RAY DIFFRACTION68chain 'J' and (resid 196 through 338 )
69X-RAY DIFFRACTION69chain 'J' and (resid 339 through 525 )
70X-RAY DIFFRACTION70chain 'I' and (resid 2 through 195 )
71X-RAY DIFFRACTION71chain 'I' and (resid 196 through 385 )
72X-RAY DIFFRACTION72chain 'I' and (resid 386 through 525 )
73X-RAY DIFFRACTION73chain 'L' and (resid 2 through 179 )
74X-RAY DIFFRACTION74chain 'L' and (resid 180 through 385 )
75X-RAY DIFFRACTION75chain 'L' and (resid 386 through 525 )
76X-RAY DIFFRACTION76chain 'M' and (resid 2 through 212 )
77X-RAY DIFFRACTION77chain 'M' and (resid 213 through 372 )
78X-RAY DIFFRACTION78chain 'M' and (resid 373 through 525 )
79X-RAY DIFFRACTION79chain 'H' and (resid 2 through 212 )
80X-RAY DIFFRACTION80chain 'H' and (resid 213 through 338 )
81X-RAY DIFFRACTION81chain 'H' and (resid 339 through 385 )
82X-RAY DIFFRACTION82chain 'H' and (resid 386 through 525 )
83X-RAY DIFFRACTION83chain 'N' and (resid 2 through 155 )
84X-RAY DIFFRACTION84chain 'N' and (resid 156 through 385 )
85X-RAY DIFFRACTION85chain 'N' and (resid 386 through 525 )
86X-RAY DIFFRACTION86chain 'X' and (resid 2 through 8 )
87X-RAY DIFFRACTION87chain 'X' and (resid 9 through 14 )
88X-RAY DIFFRACTION88chain 'X' and (resid 15 through 24 )
89X-RAY DIFFRACTION89chain 'X' and (resid 25 through 48 )
90X-RAY DIFFRACTION90chain 'X' and (resid 49 through 53 )
91X-RAY DIFFRACTION91chain 'X' and (resid 54 through 96 )
92X-RAY DIFFRACTION92chain 'W' and (resid 2 through 14 )
93X-RAY DIFFRACTION93chain 'W' and (resid 15 through 24 )
94X-RAY DIFFRACTION94chain 'W' and (resid 25 through 36 )
95X-RAY DIFFRACTION95chain 'W' and (resid 37 through 48 )
96X-RAY DIFFRACTION96chain 'W' and (resid 49 through 53 )
97X-RAY DIFFRACTION97chain 'W' and (resid 54 through 58 )
98X-RAY DIFFRACTION98chain 'W' and (resid 59 through 73 )
99X-RAY DIFFRACTION99chain 'W' and (resid 74 through 80 )
100X-RAY DIFFRACTION100chain 'W' and (resid 81 through 97 )
101X-RAY DIFFRACTION101chain 'V' and (resid 1 through 14 )
102X-RAY DIFFRACTION102chain 'V' and (resid 15 through 24 )
103X-RAY DIFFRACTION103chain 'V' and (resid 25 through 66 )
104X-RAY DIFFRACTION104chain 'V' and (resid 67 through 96 )
105X-RAY DIFFRACTION105chain 'Y' and (resid 1 through 14 )
106X-RAY DIFFRACTION106chain 'Y' and (resid 15 through 24 )
107X-RAY DIFFRACTION107chain 'Y' and (resid 25 through 29 )
108X-RAY DIFFRACTION108chain 'Y' and (resid 30 through 48 )
109X-RAY DIFFRACTION109chain 'Y' and (resid 49 through 53 )
110X-RAY DIFFRACTION110chain 'Y' and (resid 54 through 73 )
111X-RAY DIFFRACTION111chain 'Y' and (resid 74 through 96 )
112X-RAY DIFFRACTION112chain 'Z' and (resid 1 through 24 )
113X-RAY DIFFRACTION113chain 'Z' and (resid 25 through 37 )
114X-RAY DIFFRACTION114chain 'Z' and (resid 38 through 97 )
115X-RAY DIFFRACTION115chain '2' and (resid 1 through 14 )
116X-RAY DIFFRACTION116chain '2' and (resid 15 through 29 )
117X-RAY DIFFRACTION117chain '2' and (resid 30 through 43 )
118X-RAY DIFFRACTION118chain '2' and (resid 44 through 49 )
119X-RAY DIFFRACTION119chain '2' and (resid 50 through 55 )
120X-RAY DIFFRACTION120chain '2' and (resid 56 through 73 )
121X-RAY DIFFRACTION121chain '2' and (resid 74 through 80 )
122X-RAY DIFFRACTION122chain '2' and (resid 81 through 97 )
123X-RAY DIFFRACTION123chain '1' and (resid 1 through 14 )
124X-RAY DIFFRACTION124chain '1' and (resid 15 through 24 )
125X-RAY DIFFRACTION125chain '1' and (resid 25 through 36 )
126X-RAY DIFFRACTION126chain '1' and (resid 37 through 48 )
127X-RAY DIFFRACTION127chain '1' and (resid 49 through 53 )
128X-RAY DIFFRACTION128chain '1' and (resid 54 through 73 )
129X-RAY DIFFRACTION129chain '1' and (resid 74 through 97 )

+
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://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