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

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基本情報

登録情報
データベース: PDB / ID: 4pko
タイトルCrystal structure of the Football-shaped GroEL-GroES2-(ADPBeFx)14 complex
要素
  • 10 kDa chaperonin
  • 60 kDa chaperonin
キーワードPROTEIN BINDING / chaperonin / protein encapsulation / GroEL-GroES2 complex
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: 3.84 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 Maryland College ParkAnn.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: Advisory / Data collection ...Advisory / 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 / pdbx_validate_symm_contact / refine_hist / struct_conn / struct_conn_type
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 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_conn.conn_type_id / _struct_conn.id / _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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
改定 1.42024年10月9日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: 60 kDa chaperonin
B: 60 kDa chaperonin
C: 60 kDa chaperonin
D: 60 kDa chaperonin
E: 60 kDa chaperonin
F: 60 kDa chaperonin
G: 60 kDa chaperonin
H: 60 kDa chaperonin
I: 60 kDa chaperonin
J: 60 kDa chaperonin
K: 60 kDa chaperonin
L: 60 kDa chaperonin
M: 60 kDa chaperonin
N: 60 kDa chaperonin
O: 10 kDa chaperonin
P: 10 kDa chaperonin
Q: 10 kDa chaperonin
R: 10 kDa chaperonin
S: 10 kDa chaperonin
T: 10 kDa chaperonin
U: 10 kDa chaperonin
V: 10 kDa chaperonin
W: 10 kDa chaperonin
X: 10 kDa chaperonin
Y: 10 kDa chaperonin
Z: 10 kDa chaperonin
1: 10 kDa chaperonin
2: 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 area106780 Å2
ΔGint-677 kcal/mol
Surface area349820 Å2
手法PISA
単位格子
Length a, b, c (Å)169.790, 174.490, 410.160
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 ABCDEFGHIJKLMNOPQRSTUVWXYZ12

#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
発現宿主: Escherichia coli (大腸菌) / 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
プラスミド: pKK233-2 / 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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詳細

Has protein modificationY

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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: 3.2 Å3/Da / 溶媒含有率: 61.57 %
結晶化温度: 293 K / 手法: 蒸気拡散法
詳細: 8.5 % 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-E / 波長: 0.9792 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2013年11月23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: 3.84→90.9 Å / Num. obs: 124259 / % possible obs: 100 % / 冗長度: 7.2 % / Net I/σ(I): 9.2
反射 シェル解像度: 3.84→3.91 Å / 冗長度: 7.3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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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: 3.84→90.898 Å / SU ML: 0.44 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 24.68 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2485 1358 1.09 %
Rwork0.1832 --
obs0.1839 124259 99.9 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 3.84→90.898 Å
タンパク質核酸リガンド溶媒全体
原子数64097 0 462 0 64559
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00464989
X-RAY DIFFRACTIONf_angle_d0.90787765
X-RAY DIFFRACTIONf_dihedral_angle_d13.54324545
X-RAY DIFFRACTIONf_chiral_restr0.03310675
X-RAY DIFFRACTIONf_plane_restr0.00311401
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.84-3.89440.31571390.260212148X-RAY DIFFRACTION100
3.8944-4.05030.28351380.239512187X-RAY DIFFRACTION100
4.0503-4.23470.24761250.207112151X-RAY DIFFRACTION100
4.2347-4.45790.24841350.190112214X-RAY DIFFRACTION100
4.4579-4.73720.22491310.177612213X-RAY DIFFRACTION100
4.7372-5.10290.22051400.179312235X-RAY DIFFRACTION100
5.1029-5.61640.29891330.195512302X-RAY DIFFRACTION100
5.6164-6.42890.31231390.204912299X-RAY DIFFRACTION100
6.4289-8.0990.22991350.178112440X-RAY DIFFRACTION100
8.099-90.92440.20931430.136612712X-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)
12.4986-0.68670.24951.58890.27571.48020.18720.448-0.4078-0.0191-0.1944-0.52280.43410.29670.00610.7281-0.0175-0.12740.65270.03370.7051-6.067372.9075-92.1776
28.6635-1.0230.78453.42232.7816.1441-0.4731-0.8735-0.6132-0.09440.062-0.0138-0.1993-0.54960.53471.78280.3364-0.48340.96080.09991.55720.790454.7009-92.6448
34.77092.0559-2.30162.7125-0.33250.0365-0.10340.4893-0.3512-0.36030.1298-0.37370.1104-0.3313-0.04220.66380.0078-0.03020.9084-0.05910.4128-17.224878.8202-101.57
43.79580.8235-0.24492.23210.32064.31690.07990.4104-0.56350.0183-0.07970.10690.39220.30420.04930.584-0.1826-0.12380.6384-0.02450.6412-45.039452.9182-84.1159
57.7533-2.74091.61568.1003-0.25173.4388-0.1884-2.6577-0.46090.94960.55560.2253-0.118-0.3837-0.14881.23560.31470.15692.01190.12981.0721-7.796829.0323-90.4402
61.90510.5139-0.63652.2339-0.12683.4833-0.2540.6065-0.2812-0.46460.05780.00230.0172-0.15740.19810.7186-0.2205-0.12610.876-0.15210.6798-48.890849.4866-90.2863
73.17021.2280.83864.77852.45883.9208-0.14440.0128-0.61160.35420.21890.23250.26090.1339-0.03950.6168-0.23410.03560.73260.10070.5822-56.715744.1561-47.8665
88.6694-6.0294-0.80764.40530.33610.05260.92451.5334-0.5096-1.4733-2.2606-0.76820.30531.09241.13451.22420.55660.36922.43870.38611.8533-34.515216.7474-69.4205
94.0553-3.6713-1.60484.27360.6061.27460.95141.40650.1182-1.4192-2.5451-2.65020.00860.60771.36411.03740.4120.08973.10830.91713.1522-14.14418.6552-66.8987
107.70422.63092.17481.6382-1.62926.31240.0076-0.9191-0.35130.0745-0.7799-0.2669-0.3443-0.58790.76810.79840.14480.18842.19080.31412.5129-27.33349.6939-57.4573
118.5672-2.20773.52713.4866-3.44023.7139-1.6093-2.1705-1.3970.37950.3984-0.9516-2.1685-0.24341.63261.7551-0.0004-0.12841.986-0.21311.5796-40.401324.2659-55.7566
120.36481.16141.58764.56781.97455.4271-0.1050.0419-0.17570.03050.05540.93310.5864-0.31270.00330.4304-0.19830.04770.71780.02821.1122-65.026539.4101-47.7206
131.7573-0.5202-0.45951.7436-0.11481.9530.0512-0.1505-0.08830.2821-0.039-0.71850.28880.2652-0.0450.7583-0.1644-0.08810.66860.02060.731711.998492.7685-67.0327
142.63471.75940.31957.54641.61347.15530.27550.4843-1.2917-0.2489-0.07570.31410.99110.2125-0.23891.24410.3432-0.35281.1838-0.03332.076236.338372.0892-62.4616
154.28881.38270.44451.45831.42512.92660.2964-0.18910.323-0.15680.1354-0.4278-0.25770.723-0.37470.6863-0.2110.11610.7146-0.03070.81157.674105.0915-75.1392
161.5670.16750.66763.1721-0.52924.89930.1541-0.30720.08920.21030.1028-0.61440.01820.656-0.15590.7155-0.3568-0.02411.0555-0.15090.6293.6092101.6227-34.7786
173.5042-1.77550.76981.58060.54074.2177-0.1971-0.0682-0.39710.12870.408-0.74550.73-0.2383-0.21541.4026-0.09190.07931.0338-0.13021.767128.993868.4928-21.6745
184.2077-0.4394-0.16561.03590.12124.78050.1345-0.93780.65650.2039-0.1763-0.4633-0.2940.53680.02060.8572-0.4267-0.13560.9185-0.28560.74656.847110.2644-31.8037
191.8745-0.4930.21250.45180.61621.1502-0.2545-0.0526-0.76920.39390.22510.14540.36940.45590.0240.88720.0670.18370.89160.05410.6842-36.714143.2476-19.9577
203.881-2.16813.2873.001-1.59923.203-0.219-0.8622-0.44180.55840.4198-0.2281-0.60311.0064-0.13041.192-0.01570.10581.7427-0.12581.2557-21.544520.8985-20.694
213.72031.58360.17262.9878-0.71842.38850.1065-0.8321-0.25810.4991-0.00390.370.2938-0.112-0.10380.7424-0.01060.16970.84230.09980.5342-49.07555.4614-8.3142
222.61740.9287-1.13043.9525-0.95362.5751-0.3998-0.12770.02810.21640.4925-0.19060.22110.5281-0.04830.66090.0411-0.02160.8259-0.19510.3849-16.933983.4035-10.2627
236.8652-5.69331.3717.13830.752.9673-0.0215-0.01460.5383-0.10080.1072-0.1786-0.37610.0083-0.07381.08320.1862-0.13080.91430.23820.77532.019444.2082-6.4564
242.95420.6085-1.10642.3366-1.37584.8143-0.1584-0.79380.05970.64840.1148-0.1229-0.28870.570.04840.91910.125-0.12811.1106-0.20670.439-17.122286.6599-1.265
257.10711.15955.55456.8829-0.09497.52790.6749-0.9255-0.73350.44730.3320.067-2.159-2.77-0.67111.40260.50850.06521.09440.27230.599940.395124.326-72.5805
267.1956-7.14094.2218.0175-5.0033.26940.89120.6097-1.37910.70321.61493.63411.4338-1.2007-2.49291.62260.2523-0.25132.31990.31952.834818.567625.9567-86.9265
272.2803-1.90861.91075.1987-4.10953.46570.73630.8143-0.302-0.5565-0.4452-0.1751-1.9063-0.67190.34411.85590.6717-0.07091.34670.07390.665331.585322.6943-76.0025
285.186-3.86843.46465.3912-1.30562.9685-0.1392-2.4401-0.99541.0038-0.37212.1356-1.0763-1.4440.50321.16670.2460.03071.7615-0.19660.782543.992410.777-58.2976
295.14024.0159-0.99564.19241.74067.2401-0.8203-0.75850.82220.66660.5187-0.0222-0.9235-1.9620.11151.1730.5648-0.15421.3848-0.29940.63235.341517.872-72.6387
303.6318-1.7382.10541.6866-0.48141.9324-0.37571.00960.8137-0.9165-0.0333-1.4252-1.4151-1.92060.22561.36220.4764-0.02641.35530.12510.906134.256825.3479-75.5198
310.7567-1.77812.284.3453-5.47587.00950.25370.215-0.2339-0.6843-0.46360.4065-0.7918-1.44540.39970.70690.0027-0.23971.4911-0.07850.801624.81218.7207-76.172
325.6432-1.6293-5.06355.3968-0.96285.7141-1.45520.50581.9463-1.39130.04362.36191.4176-3.45961.47941.4849-0.2062-0.45142.4496-0.17952.02450.39742.5381-74.6518
334.00224.2195-1.21994.24490.1469.423-2.2060.83751.98560.05971.49041.5041-0.6711-3.28250.70941.57960.0564-0.21712.2072-0.12351.275911.04735.6106-72.2569
348.5899-2.5866-5.42891.88281.94036.65610.9948-3.38350.87020.03860.73340.87580.4793-1.2144-1.1290.7868-0.3807-0.0092.10850.01743.08239.2864.5655-60.0717
355.2657-5.1505-0.30855.2874-0.72233.09940.0193-0.17571.81350.6136-0.4377-1.48061.0377-1.74540.68681.13950.0978-0.13691.2776-0.34471.288822.2263.677-68.4616
362.00342.36293.68356.026-4.67978.49140.17780.90411.5006-1.05841.24261.26770.5233-0.5399-1.25081.44591.1101-0.5722.2613-0.08071.614918.290815.5628-81.298
375.78853.8714-1.42134.7712-0.00120.86080.3951.55320.0528-0.7437-0.11320.78580.935-0.7198-0.23721.20960.0938-0.24462.0882-0.40950.849118.10294.6922-70.2113
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1257.2504-0.2006-7.21769.2614-3.32378.549-0.76562.4226-0.7727-3.4532-3.9516-0.94470.8304-0.09423.53021.4630.54560.25942.4520.33231.7982-92.8847172.5364-40.7267
1262.2373-1.6925-3.33077.48991.73615.97230.1382-1.5254-0.2692-0.07870.2943-1.4029-0.02860.557-0.33660.84750.2446-0.09192.07540.23450.7955-90.1688178.0744-44.0606
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 2 through 255 )
2X-RAY DIFFRACTION2chain 'G' and (resid 256 through 353 )
3X-RAY DIFFRACTION3chain 'G' and (resid 354 through 525 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2 through 185 )
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 361 )
6X-RAY DIFFRACTION6chain 'A' and (resid 362 through 525 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 168 )
8X-RAY DIFFRACTION8chain 'B' and (resid 169 through 222 )
9X-RAY DIFFRACTION9chain 'B' and (resid 223 through 268 )
10X-RAY DIFFRACTION10chain 'B' and (resid 269 through 353 )
11X-RAY DIFFRACTION11chain 'B' and (resid 354 through 385 )
12X-RAY DIFFRACTION12chain 'B' and (resid 386 through 525 )
13X-RAY DIFFRACTION13chain 'F' and (resid 2 through 243 )
14X-RAY DIFFRACTION14chain 'F' and (resid 244 through 361 )
15X-RAY DIFFRACTION15chain 'F' and (resid 362 through 525 )
16X-RAY DIFFRACTION16chain 'E' and (resid 2 through 179 )
17X-RAY DIFFRACTION17chain 'E' and (resid 180 through 385 )
18X-RAY DIFFRACTION18chain 'E' and (resid 386 through 525 )
19X-RAY DIFFRACTION19chain 'C' and (resid 2 through 255 )
20X-RAY DIFFRACTION20chain 'C' and (resid 256 through 385 )
21X-RAY DIFFRACTION21chain 'C' and (resid 386 through 525 )
22X-RAY DIFFRACTION22chain 'D' and (resid 2 through 168 )
23X-RAY DIFFRACTION23chain 'D' and (resid 169 through 385 )
24X-RAY DIFFRACTION24chain 'D' and (resid 386 through 525 )
25X-RAY DIFFRACTION25chain 'O' and (resid 3 through 14 )
26X-RAY DIFFRACTION26chain 'O' and (resid 15 through 29 )
27X-RAY DIFFRACTION27chain 'O' and (resid 30 through 47 )
28X-RAY DIFFRACTION28chain 'O' and (resid 48 through 52 )
29X-RAY DIFFRACTION29chain 'O' and (resid 53 through 73 )
30X-RAY DIFFRACTION30chain 'O' and (resid 74 through 97 )
31X-RAY DIFFRACTION31chain 'P' and (resid 1 through 14 )
32X-RAY DIFFRACTION32chain 'P' and (resid 15 through 24 )
33X-RAY DIFFRACTION33chain 'P' and (resid 25 through 47 )
34X-RAY DIFFRACTION34chain 'P' and (resid 48 through 52 )
35X-RAY DIFFRACTION35chain 'P' and (resid 53 through 73 )
36X-RAY DIFFRACTION36chain 'P' and (resid 74 through 80 )
37X-RAY DIFFRACTION37chain 'P' and (resid 81 through 97 )
38X-RAY DIFFRACTION38chain 'Q' and (resid 2 through 36 )
39X-RAY DIFFRACTION39chain 'Q' and (resid 37 through 47 )
40X-RAY DIFFRACTION40chain 'Q' and (resid 48 through 52 )
41X-RAY DIFFRACTION41chain 'Q' and (resid 53 through 57 )
42X-RAY DIFFRACTION42chain 'Q' and (resid 58 through 62 )
43X-RAY DIFFRACTION43chain 'Q' and (resid 63 through 67 )
44X-RAY DIFFRACTION44chain 'Q' and (resid 68 through 80 )
45X-RAY DIFFRACTION45chain 'Q' and (resid 81 through 97 )
46X-RAY DIFFRACTION46chain 'U' and (resid 1 through 19 )
47X-RAY DIFFRACTION47chain 'U' and (resid 20 through 29 )
48X-RAY DIFFRACTION48chain 'U' and (resid 30 through 73 )
49X-RAY DIFFRACTION49chain 'U' and (resid 74 through 78 )
50X-RAY DIFFRACTION50chain 'U' and (resid 79 through 97 )
51X-RAY DIFFRACTION51chain 'T' and (resid 1 through 19 )
52X-RAY DIFFRACTION52chain 'T' and (resid 20 through 24 )
53X-RAY DIFFRACTION53chain 'T' and (resid 25 through 29 )
54X-RAY DIFFRACTION54chain 'T' and (resid 30 through 42 )
55X-RAY DIFFRACTION55chain 'T' and (resid 43 through 64 )
56X-RAY DIFFRACTION56chain 'T' and (resid 65 through 97 )
57X-RAY DIFFRACTION57chain 'R' and (resid 1 through 14 )
58X-RAY DIFFRACTION58chain 'R' and (resid 15 through 24 )
59X-RAY DIFFRACTION59chain 'R' and (resid 25 through 36 )
60X-RAY DIFFRACTION60chain 'R' and (resid 37 through 42 )
61X-RAY DIFFRACTION61chain 'R' and (resid 43 through 52 )
62X-RAY DIFFRACTION62chain 'R' and (resid 53 through 62 )
63X-RAY DIFFRACTION63chain 'R' and (resid 63 through 67 )
64X-RAY DIFFRACTION64chain 'R' and (resid 68 through 81 )
65X-RAY DIFFRACTION65chain 'R' and (resid 82 through 97 )
66X-RAY DIFFRACTION66chain 'S' and (resid 2 through 24 )
67X-RAY DIFFRACTION67chain 'S' and (resid 25 through 42 )
68X-RAY DIFFRACTION68chain 'S' and (resid 43 through 63 )
69X-RAY DIFFRACTION69chain 'S' and (resid 64 through 73 )
70X-RAY DIFFRACTION70chain 'S' and (resid 74 through 97 )
71X-RAY DIFFRACTION71chain 'M' and (resid 2 through 255 )
72X-RAY DIFFRACTION72chain 'M' and (resid 256 through 353 )
73X-RAY DIFFRACTION73chain 'M' and (resid 354 through 525 )
74X-RAY DIFFRACTION74chain 'K' and (resid 2 through 255 )
75X-RAY DIFFRACTION75chain 'K' and (resid 256 through 353 )
76X-RAY DIFFRACTION76chain 'K' and (resid 354 through 525 )
77X-RAY DIFFRACTION77chain 'J' and (resid 2 through 255 )
78X-RAY DIFFRACTION78chain 'J' and (resid 256 through 353 )
79X-RAY DIFFRACTION79chain 'J' and (resid 354 through 525 )
80X-RAY DIFFRACTION80chain 'I' and (resid 2 through 255 )
81X-RAY DIFFRACTION81chain 'I' and (resid 256 through 353 )
82X-RAY DIFFRACTION82chain 'I' and (resid 354 through 525 )
83X-RAY DIFFRACTION83chain 'N' and (resid 2 through 255 )
84X-RAY DIFFRACTION84chain 'N' and (resid 256 through 353 )
85X-RAY DIFFRACTION85chain 'N' and (resid 354 through 525 )
86X-RAY DIFFRACTION86chain 'H' and (resid 2 through 255 )
87X-RAY DIFFRACTION87chain 'H' and (resid 256 through 353 )
88X-RAY DIFFRACTION88chain 'H' and (resid 354 through 525 )
89X-RAY DIFFRACTION89chain 'L' and (resid 2 through 255 )
90X-RAY DIFFRACTION90chain 'L' and (resid 256 through 353 )
91X-RAY DIFFRACTION91chain 'L' and (resid 354 through 525 )
92X-RAY DIFFRACTION92chain '1' and (resid 1 through 24 )
93X-RAY DIFFRACTION93chain '1' and (resid 25 through 42 )
94X-RAY DIFFRACTION94chain '1' and (resid 43 through 63 )
95X-RAY DIFFRACTION95chain '1' and (resid 64 through 73 )
96X-RAY DIFFRACTION96chain '1' and (resid 74 through 97 )
97X-RAY DIFFRACTION97chain 'Y' and (resid 1 through 24 )
98X-RAY DIFFRACTION98chain 'Y' and (resid 25 through 42 )
99X-RAY DIFFRACTION99chain 'Y' and (resid 43 through 63 )
100X-RAY DIFFRACTION100chain 'Y' and (resid 64 through 73 )
101X-RAY DIFFRACTION101chain 'Y' and (resid 74 through 96 )
102X-RAY DIFFRACTION102chain 'X' and (resid 1 through 24 )
103X-RAY DIFFRACTION103chain 'X' and (resid 25 through 42 )
104X-RAY DIFFRACTION104chain 'X' and (resid 43 through 63 )
105X-RAY DIFFRACTION105chain 'X' and (resid 64 through 73 )
106X-RAY DIFFRACTION106chain 'X' and (resid 74 through 97 )
107X-RAY DIFFRACTION107chain 'W' and (resid 1 through 24 )
108X-RAY DIFFRACTION108chain 'W' and (resid 25 through 42 )
109X-RAY DIFFRACTION109chain 'W' and (resid 43 through 63 )
110X-RAY DIFFRACTION110chain 'W' and (resid 64 through 73 )
111X-RAY DIFFRACTION111chain 'W' and (resid 74 through 97 )
112X-RAY DIFFRACTION112chain '2' and (resid 1 through 24 )
113X-RAY DIFFRACTION113chain '2' and (resid 25 through 42 )
114X-RAY DIFFRACTION114chain '2' and (resid 43 through 63 )
115X-RAY DIFFRACTION115chain '2' and (resid 64 through 73 )
116X-RAY DIFFRACTION116chain '2' and (resid 74 through 97 )
117X-RAY DIFFRACTION117chain 'V' and (resid 1 through 24 )
118X-RAY DIFFRACTION118chain 'V' and (resid 25 through 42 )
119X-RAY DIFFRACTION119chain 'V' and (resid 43 through 63 )
120X-RAY DIFFRACTION120chain 'V' and (resid 64 through 73 )
121X-RAY DIFFRACTION121chain 'V' and (resid 74 through 97 )
122X-RAY DIFFRACTION122chain 'Z' and (resid 1 through 24 )
123X-RAY DIFFRACTION123chain 'Z' and (resid 25 through 42 )
124X-RAY DIFFRACTION124chain 'Z' and (resid 43 through 63 )
125X-RAY DIFFRACTION125chain 'Z' and (resid 64 through 73 )
126X-RAY DIFFRACTION126chain 'Z' and (resid 74 through 95 )

+
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