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- PDB-6zg3: the structure of ECF PanT transporter in a complex with a nanobody -

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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: 6zg3
タイトルthe structure of ECF PanT transporter in a complex with a nanobody
要素
  • (Energy-coupling factor transporter ATP-binding protein ...) x 2
  • CA14381 nanobody
  • Conserved hypothetical membrane protein
  • Putative cobalt ABC transporter, permease protein
キーワードTRANSPORT PROTEIN / ECF transporter / vitamin transport / pantothenate / membrane protein
機能・相同性
機能・相同性情報


トランスロカーゼ / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・物質の膜輸送を触媒する / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
類似検索 - 分子機能
ECF transporter, substrate-specific component / ECF transporter transmembrane protein EcfT / ECF transporter, substrate-specific component / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / Cobalt import ATP-binding protein cbiO. / : / ABC transporter, CbiO/EcfA subunit ...ECF transporter, substrate-specific component / ECF transporter transmembrane protein EcfT / ECF transporter, substrate-specific component / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / Cobalt import ATP-binding protein cbiO. / : / ABC transporter, CbiO/EcfA subunit / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
類似検索 - ドメイン・相同性
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Conserved hypothetical membrane protein / Energy-coupling factor transporter transmembrane protein EcfT / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1
類似検索 - 構成要素
生物種Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (乳酸菌)
Lama glama (ラマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å
データ登録者Setyawati, I. / Guskov, A. / Slotboom, D.J.
資金援助 オランダ, 1件
組織認可番号国
Netherlands Organisation for Scientific Research (NWO) オランダ
引用ジャーナル: Elife / 年: 2020
タイトル: In vitro reconstitution of dynamically interacting integral membrane subunits of energy-coupling factor transporters.
著者: Setyawati, I. / Stanek, W.K. / Majsnerowska, M. / Swier, L.J.Y.M. / Pardon, E. / Steyaert, J. / Guskov, A. / Slotboom, D.J.
履歴
登録2020年6月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年3月3日Provider: repository / タイプ: Initial release
改定 1.12024年1月24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
改定 1.22024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Energy-coupling factor transporter ATP-binding protein EcfA1
B: Energy-coupling factor transporter ATP-binding protein EcfA2
C: Conserved hypothetical membrane protein
D: Putative cobalt ABC transporter, permease protein
E: CA14381 nanobody
F: Energy-coupling factor transporter ATP-binding protein EcfA1
G: Energy-coupling factor transporter ATP-binding protein EcfA2
H: Conserved hypothetical membrane protein
I: Putative cobalt ABC transporter, permease protein
J: CA14381 nanobody
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)271,25329
ポリマ－266,23310
非ポリマー5,02019
水00
1
A: Energy-coupling factor transporter ATP-binding protein EcfA1
E: CA14381 nanobody
G: Energy-coupling factor transporter ATP-binding protein EcfA2
H: Conserved hypothetical membrane protein
I: Putative cobalt ABC transporter, permease protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)135,67013
ポリマ－133,1175
非ポリマー2,5538
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18190 Å2
ΔGint-87 kcal/mol
Surface area50360 Å2
手法PISA
2
B: Energy-coupling factor transporter ATP-binding protein EcfA2
C: Conserved hypothetical membrane protein
D: Putative cobalt ABC transporter, permease protein
F: Energy-coupling factor transporter ATP-binding protein EcfA1
J: CA14381 nanobody
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)135,58416
ポリマ－133,1175
非ポリマー2,46711
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17550 Å2
ΔGint-91 kcal/mol
Surface area49790 Å2
手法PISA
単位格子
Length a, b, c (Å)97.290, 110.470, 110.500
Angle α, β, γ (deg.)88.997, 102.271, 102.244
Int Tables number1
Space group name H-MP1
Space group name HallP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and resid 2 through 280)
d_2ens_1chain "F"
d_1ens_2chain "B"
d_2ens_2(chain "G" and resid 2 through 283)
d_1ens_3(chain "C" and resid 1 through 501)
d_2ens_3(chain "H" and (resid 1 through 207 or (resid 601...
d_1ens_4(chain "D" and (resid 6 through 53 or resid 55 through 301))
d_2ens_4(chain "I" and (resid 6 through 53 or resid 55 through 301))
d_1ens_5(chain "E" and resid 2 through 126)
d_2ens_5chain "J"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERSERA2 - 280
d_21ens_1SERSERJ1 - 279
d_11ens_2ALAGLYB1 - 282
d_21ens_2ALAGLYK2 - 283
d_11ens_3METARGC1 - 207
d_12ens_3LMTLMTD
d_21ens_3METARGL1 - 207
d_22ens_3LMTLMTM
d_11ens_4ILEALAG1 - 48
d_12ens_4VALHISG51 - 261
d_13ens_4LMTLMTH
d_21ens_4ILEALAQ1 - 48
d_22ens_4VALHISQ50 - 260
d_23ens_4LMTLMTR
d_11ens_5VALSERI2 - 126
d_21ens_5VALSERS1 - 125

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4
ens_5

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要素

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Energy-coupling factor transporter ATP-binding protein ... , 2種, 4分子 AFBG

#1: タンパク質 Energy-coupling factor transporter ATP-binding protein EcfA1 / ECF transporter A component EcfA1


分子量: 33166.418 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: His-tag with TEV cleavage site an N-terminus
由来: (組換発現) Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (乳酸菌)
遺伝子: ecfA1, cbiO1, Ldb0424 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q1GBJ0, トランスロカーゼ
#2: タンパク質 Energy-coupling factor transporter ATP-binding protein EcfA2 / ECF transporter A component EcfA2


分子量: 31672.156 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (乳酸菌)
遺伝子: ecfA2, cbiO2, Ldb0425 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q1GBI9, 加水分解酵素; 酸無水物に作用; 酸無水物に作用・物質の膜輸送を触媒する

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タンパク質 , 2種, 4分子 CHDI

#3: タンパク質 Conserved hypothetical membrane protein


分子量: 23008.416 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: StrepII tag at C-terminus
由来: (組換発現) Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (乳酸菌)
遺伝子: Ldb0463 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q1GBG0
#4: タンパク質 Putative cobalt ABC transporter, permease protein


分子量: 30290.283 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (乳酸菌)
遺伝子: cbiQ, Ldb0426 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q1GBI8

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抗体 / 糖 , 2種, 9分子 EJ

#5: 抗体 CA14381 nanobody


分子量: 14979.450 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Lama glama (ラマ)
#7: 糖
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE / ドデシルβ-D-マルトシド


タイプ: D-saccharide / 分子量: 510.615 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C24H46O11 / コメント: 可溶化剤*YM

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非ポリマー , 2種, 12分子

#6: 化合物
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 10 / 由来タイプ: 合成 / 式: C4H10O3
#8: 化合物 ChemComp-CIT / CITRIC ACID / クエン酸


分子量: 192.124 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C6H8O7

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詳細

研究の焦点であるリガンドがあるかN
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 / 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: 4.26 Å3/Da / 溶媒含有率: 71.11 %
結晶化温度: 277.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.5 / 詳細: 70mM citrate, 22% PEG 300

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I04-1 / 波長: 0.91587 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2019年3月19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: 0.91587 Å / 相対比: 1
反射解像度: 2.8→48.83 Å / Num. obs: 104704 / % possible obs: 96.7 % / 冗長度: 1.72 % / Biso Wilson estimate: 85.15 Å2 / CC1/2: 0.997 / Net I/σ(I): 4.7
反射 シェル解像度: 2.8→2.87 Å / Num. unique obs: 7625 / CC1/2: 0.195 / % possible all: 95

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2_3874精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5JSZ

5jsz


解像度: 2.8→48.83 Å / SU ML: 0.7043 / 交差検証法: FREE R-VALUE / σ(F): 1.91 / 位相誤差: 38.0686
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2764 5211 5 %
Rwork0.2423 99073 -
obs0.244 104284 96.39 %
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
原子変位パラメータBiso mean: 110.3 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→48.83 Å
タンパク質核酸リガンド溶媒全体
原子数17885 0 338 0 18223
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0118606
X-RAY DIFFRACTIONf_angle_d1.285825218
X-RAY DIFFRACTIONf_chiral_restr0.06452953
X-RAY DIFFRACTIONf_plane_restr0.00833135
X-RAY DIFFRACTIONf_dihedral_angle_d19.45356778
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.741179805629
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.682950415462
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS1.2684072142
ens_4d_2GX-RAY DIFFRACTIONTorsion NCS3.56149900773
ens_5d_2IX-RAY DIFFRACTIONTorsion NCS0.89093080817
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.50011740.4623327X-RAY DIFFRACTION95.53
6.9-8.680.20131710.18983249X-RAY DIFFRACTION95.24
8.69-48.830.23771660.22163180X-RAY DIFFRACTION93.05
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)
13.044623695-1.935317324732.208448211133.14222730728-0.7785218684575.08044512864-0.7815936430060.9320749413450.2279399546040.2680883274-0.1691480627220.214083705784-0.7866571716421.538669750220.1521311694810.630045452447-0.112034558988-0.04563822879081.22959717450.3798276545450.5472183883940.90553981706879.269496057191.7740762564
21.63522688328-1.245503181480.6412171938594.06298626952-1.413071239813.1023464293-0.091535438036-0.0516674334445-0.114042079937-0.224587487290.1219692272550.02632269193770.175555829421-0.22180694660.08273707734210.550900493088-0.155287716068-0.04946672174440.6590156725340.06828345739290.69784264314-9.6102630135695.605417010685.5494371395
33.38325464404-1.333716559750.1347991790064.31306928357-2.660887718954.08954896278-0.132264023624-0.2253958113920.07911794599940.316072777116-0.181033861724-0.1729768151460.185691103450.2306662909230.3122776782210.63534291802-0.0982335428828-0.005000963685620.5901533118540.03390687492920.560030153076-10.372234273481.603146706199.33816493
46.07339739364-1.619428003430.7839720178438.942062515750.03757195985919.22412945267-0.8144417386570.525242478834-0.9644563440960.7358930782880.1087204705990.1307969749120.02071228537490.3850678966640.5648098090031.19363324284-0.2012485740940.1406969729121.122324485130.3623083113091.28430033141-19.962293379270.272565951115.030823295
57.370263212491.15590118366-0.3159913490965.2385308005-1.557632401646.24918223712-1.44803952251-0.1282429613511.302900818460.6917848028490.374232336726-0.135173102178-1.49974712935-0.172389124041.103712877421.28527586529-0.0663113998413-0.5162586885271.000552537110.1352041461511.29741291041-39.225865878159.599774215260.5101745693
68.94623095326-0.215902246352-4.26200433556.95475246514-0.6007883838773.02971336421-0.760142550119-0.196817466007-1.4152293298-0.633964138822-0.004773839473950.959708994931.92367799928-0.1243213666381.038378596330.97662430207-0.05624666773530.02011777554480.6430855881270.1008720822561.23849821838-41.568274572251.166919176471.2743802867
78.21508681831-1.09051874486-0.8160808953155.52046467806-4.620011705396.035425988090.0929538649174-0.4449588530690.6741759211960.395347511390.02126408122790.414896964651-1.961233968240.880125410252-0.1992091373630.742720423251-0.0848630984851-0.02377491498550.665539079654-0.008812848274010.785366376894-43.887553251959.658385321365.1992636143
88.22337585077-2.979063500135.680460616673.98890526578-2.221244247394.06260197549-0.7270492167210.626749283283-0.5749746541280.4163910680560.387458631851-0.707623825747-0.8753570550380.388181910724-0.416372358891.6688645564-0.0963359922850.01543946152180.6250614025540.01372915281511.07018936119-49.703776787549.740182983357.3806277325
94.77236146285-3.1530449491-1.150088332665.24297429333-2.423142690535.69606729789-0.130897346342-0.333120142636-0.9383882597040.180098360947-0.2746438417550.4039849255720.1309723192440.2538001996970.05746829196390.761173774298-0.203262803032-0.03314729941690.7754245570460.2445571873620.874322993943-59.821178781261.649606826168.7623425835
103.48104116894-0.759072755595-1.564786339123.589673839840.08542047463676.50647741788-0.3793506160430.0187239304181-0.762573637334-1.622517213121.486777640752.316909610790.545991414653-1.10012901951-0.986702802261.50266726696-0.505980405329-0.2361969910031.401072070960.4915417903191.65497721868-70.498651256557.561608468873.3382637341
112.94339867226-3.672092976951.418437534664.31532409746-2.069834156284.34690698521-0.258338507695-0.62681112102-0.5489173556260.17107790030.299581886836-0.09157539774610.28420975939-0.106639665476-0.1805847461110.870925117542-0.2786042979040.05774620980640.7856150757730.1345720525651.06539958241-62.276246200864.248623640679.3572077602
123.534567527483.561024771360.8276218315066.007010161515.293942039518.4564648138-0.251699772833-0.883520218968-1.176405953710.746178043271-0.645155659603-0.5364526312440.7776622419520.2731123522510.9471259868361.66080628794-0.410113773287-0.431738516830.7704035721250.1685327167641.85030806426-54.832145110356.81201964386.0962898209
136.95967720465-1.148819722262.881547244540.3104525323690.4093323543855.34396397975-0.05334869249650.379071929111-0.237255481812-0.2326006079570.1164825031590.3544503934120.08031612217320.806580534834-0.09796406682580.92793587437-0.0834719410591-0.01645763265360.5599049581690.03266002229671.07733433902-36.750270803656.236300466780.1493303921
147.197740643226.39906869676-1.030724950898.185356558510.1888423184352.234319892480.1061346833990.6745899404711.467194302361.31604760542-0.455692930548-0.199292126902-0.3890378248691.09644283626-0.2241362543371.07452374070.132057590877-0.1958404673861.013322677480.2743117976641.42982250749-32.834825584854.789774924299.3432385551
152.298175014231.204605399042.604593151821.44417179231.054926398149.48510230317-0.0532131664618-0.7811122668410.164129802115-0.497216993333-1.037257063770.940192667145-1.44943174703-2.72244949510.9200444021760.694931574908-0.0654167170947-0.02589059150331.30811321074-0.02460909722541.09180824884-60.269398157992.133380189270.2635969596
163.09655580365.172148340183.322294118338.987758361855.032828730384.276677591571.68067750020.3803527538390.3509857787130.54991992785-2.01456577953-1.514899919930.285664697103-0.7909134928150.05028097861870.8418435785630.2623804340480.1589560531751.992634848390.02768224850841.29096831411-62.076825384475.242725275749.1013252065
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654.053388312831.147736444071.118894613531.463707931911.527160543122.49238490189-0.509909827090.3300520164711.62906914408-0.5200601434610.408498324522-0.00718826470678-1.296848294451.0466232855-0.01724107518560.871797002093-0.0296091653032-0.02905418014770.524083793968-0.07280327409390.99218424464-35.5737975682116.0494032191.1224580706
664.763057389251.491405031752.121540879773.957377973993.138945588383.86485571666-0.315223374202-0.007228519722850.461374102296-0.230163011760.2453058263890.205490521725-0.3277845226530.3165748728640.008070726944050.659398346654-0.0103727474225-0.04083620322490.586064442127-0.03902788360470.826588121789-38.6969588238115.10520475999.175395152
674.437665521950.8432994442760.1263343566965.174458252081.917757636721.48654873627-0.18846372746-0.00558443427793-0.007350148017210.164110321680.602401828281-0.4280574600420.441937085538-0.41507345953-0.04171037110140.689207240604-0.02265964111-0.08226105241790.7014300882960.1137634947710.744752734795-35.2861301533110.13631618794.3140350142
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 45 )AA1 - 451 - 45
22chain 'A' and (resid 46 through 160 )AA46 - 16046 - 160
33chain 'A' and (resid 161 through 245 )AA161 - 245161 - 245
44chain 'A' and (resid 246 through 280 )AA246 - 280246 - 280
55chain 'B' and (resid 2 through 21 )BB2 - 211 - 20
66chain 'B' and (resid 22 through 39 )BB22 - 3921 - 38
77chain 'B' and (resid 40 through 62 )BB40 - 6239 - 61
88chain 'B' and (resid 63 through 78 )BB63 - 7862 - 77
99chain 'B' and (resid 79 through 102 )BB79 - 10278 - 101
1010chain 'B' and (resid 103 through 132 )BB103 - 132102 - 131
1111chain 'B' and (resid 133 through 177 )BB133 - 177132 - 176
1212chain 'B' and (resid 178 through 194 )BB178 - 194177 - 193
1313chain 'B' and (resid 195 through 247 )BB195 - 247194 - 246
1414chain 'B' and (resid 248 through 283 )BB248 - 283247 - 282
1515chain 'C' and (resid 1 through 28 )CC1 - 281 - 28
1616chain 'C' and (resid 29 through 38 )CC29 - 3829 - 38
1717chain 'C' and (resid 39 through 46 )CC39 - 4639 - 46
1818chain 'C' and (resid 47 through 80 )CC47 - 8047 - 80
1919chain 'C' and (resid 81 through 93 )CC81 - 9381 - 93
2020chain 'C' and (resid 94 through 124 )CC94 - 12494 - 124
2121chain 'C' and (resid 125 through 165 )CC125 - 165125 - 165
2222chain 'C' and (resid 166 through 207 )CC166 - 207166 - 207
2323chain 'D' and (resid 8 through 20 )DG8 - 203 - 15
2424chain 'D' and (resid 21 through 84 )DG21 - 8416 - 80
2525chain 'D' and (resid 85 through 94 )DG85 - 9481 - 90
2626chain 'D' and (resid 95 through 107 )DG95 - 10791 - 103
2727chain 'D' and (resid 108 through 183 )DG108 - 183104 - 179
2828chain 'D' and (resid 184 through 197 )DG184 - 197180 - 193
2929chain 'D' and (resid 198 through 264 )DG198 - 264194 - 260
3030chain 'E' and (resid 1 through 17 )EI1 - 171 - 17
3131chain 'E' and (resid 18 through 32 )EI18 - 3218 - 32
3232chain 'E' and (resid 33 through 39 )EI33 - 3933 - 39
3333chain 'E' and (resid 40 through 60 )EI40 - 6040 - 60
3434chain 'E' and (resid 61 through 83 )EI61 - 8361 - 83
3535chain 'E' and (resid 84 through 99 )EI84 - 9984 - 99
3636chain 'E' and (resid 100 through 109 )EI100 - 109100 - 109
3737chain 'E' and (resid 110 through 126 )EI110 - 126110 - 126
3838chain 'F' and (resid 2 through 21 )FJ2 - 211 - 20
3939chain 'F' and (resid 22 through 45 )FJ22 - 4521 - 44
4040chain 'F' and (resid 46 through 116 )FJ46 - 11645 - 115
4141chain 'F' and (resid 117 through 147 )FJ117 - 147116 - 146
4242chain 'F' and (resid 148 through 245 )FJ148 - 245147 - 244
4343chain 'F' and (resid 246 through 280 )FJ246 - 280245 - 279
4444chain 'G' and (resid 1 through 16 )GK1 - 161 - 16
4545chain 'G' and (resid 17 through 39 )GK17 - 3917 - 39
4646chain 'G' and (resid 40 through 131 )GK40 - 13140 - 131
4747chain 'G' and (resid 132 through 177 )GK132 - 177132 - 177
4848chain 'G' and (resid 178 through 193 )GK178 - 193178 - 193
4949chain 'G' and (resid 194 through 234 )GK194 - 234194 - 234
5050chain 'G' and (resid 235 through 282 )GK235 - 282235 - 282
5151chain 'H' and (resid 1 through 28 )HL1 - 281 - 28
5252chain 'H' and (resid 29 through 38 )HL29 - 3829 - 38
5353chain 'H' and (resid 39 through 46 )HL39 - 4639 - 46
5454chain 'H' and (resid 47 through 117 )HL47 - 11747 - 117
5555chain 'H' and (resid 118 through 124 )HL118 - 124118 - 124
5656chain 'H' and (resid 125 through 163 )HL125 - 163125 - 163
5757chain 'H' and (resid 164 through 207 )HL164 - 207164 - 207
5858chain 'I' and (resid 6 through 20 )IQ6 - 201 - 15
5959chain 'I' and (resid 21 through 84 )IQ21 - 8416 - 79
6060chain 'I' and (resid 85 through 104 )IQ85 - 10480 - 99
6161chain 'I' and (resid 105 through 224 )IQ105 - 224100 - 219
6262chain 'I' and (resid 225 through 244 )IQ225 - 244220 - 239
6363chain 'I' and (resid 245 through 264 )IQ245 - 264240 - 259
6464chain 'J' and (resid 2 through 17 )JS2 - 171 - 16
6565chain 'J' and (resid 18 through 39 )JS18 - 3917 - 38
6666chain 'J' and (resid 40 through 99 )JS40 - 9939 - 98
6767chain 'J' and (resid 100 through 126 )JS100 - 12699 - 125

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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

他の情報も見る