[日本語] English
万見
- PDB-8vdu: Crystal structure of hybrid insulin peptide (InsC8-15-IAPP74-80) ... -

+
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: 8vdu
タイトルCrystal structure of hybrid insulin peptide (InsC8-15-IAPP74-80) bound to HLA-DQ8
要素
  • (MHC class II HLA-DQ- ...) x 2
  • Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80)
キーワードIMMUNE SYSTEM / pMHC II complex
機能・相同性
機能・相同性情報


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal membrane
類似検索 - 分子機能
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / MHC class II HLA-DQ-beta-1 / MHC class II HLA-DQ-alpha chain
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.5 Å
データ登録者Tran, T.M. / Lim, J.J. / Loh, T.Y. / Mannering, I.S. / Rossjohn, J. / Reid, H.H.
資金援助 オーストラリア, 2件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)APP1123586. オーストラリア
National Health and Medical Research Council (NHMRC, Australia)APP1123586 オーストラリア
引用ジャーナル: J.Biol.Chem. / 年: 2024
タイトル: A structural basis of T cell cross-reactivity to native and spliced self-antigens presented by HLA-DQ8.
著者: Tran, M.T. / Lim, J.J. / Loh, T.J. / Mannering, S.I. / Rossjohn, J. / Reid, H.H.
履歴
登録2023年12月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年8月7日Provider: repository / タイプ: Initial release
改定 1.12024年8月14日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
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: MHC class II HLA-DQ-alpha chain
B: MHC class II HLA-DQ-beta-1
C: Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80)
D: MHC class II HLA-DQ-alpha chain
E: MHC class II HLA-DQ-beta-1
F: Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80)
G: MHC class II HLA-DQ-alpha chain
H: MHC class II HLA-DQ-beta-1
I: Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80)
J: MHC class II HLA-DQ-alpha chain
K: MHC class II HLA-DQ-beta-1
L: Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)182,22518
ポリマ－180,76212
非ポリマー1,4626
水181
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)72.319, 138.116, 101.832
Angle α, β, γ (deg.)90.000, 102.498, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
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 0 through 36 or (resid 37...
d_2ens_1(chain "D" and (resid 0 through 36 or (resid 37...
d_3ens_1(chain "G" and (resid 0 through 48 or (resid 49...
d_4ens_1(chain "J" and (resid 0 through 36 or (resid 37...
d_1ens_2(chain "B" and (resid 3 through 21 or (resid 22...
d_2ens_2(chain "E" and (resid 3 through 21 or (resid 22...
d_3ens_2(chain "H" and (resid 3 through 47 or (resid 48...
d_4ens_2(chain "K" and (resid 3 through 21 or (resid 22...
d_1ens_3(chain "C" and (resid 1 through 2 or (resid 3...
d_2ens_3(chain "F" and ((resid 1 and (name N or name...
d_3ens_3(chain "I" and ((resid 1 and (name N or name...
d_4ens_3chain "L"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASPASPALAALAAA0 - 1572 - 160
d_12ens_1GLUGLUGLUGLUAA159 - 181162 - 184
d_21ens_1ASPASPALAALADD0 - 1572 - 160
d_22ens_1GLUGLUGLUGLUDD159 - 181162 - 184
d_31ens_1ASPASPGLUGLUGG0 - 1812 - 184
d_41ens_1ASPASPALAALAJJ0 - 1572 - 160
d_42ens_1GLUGLUGLUGLUJJ159 - 181162 - 184
d_11ens_2SERSERALAALABB3 - 1903 - 190
d_21ens_2SERSERSERSEREE3 - 1043 - 104
d_22ens_2HISHISGLUGLUEE111 - 162111 - 162
d_23ens_2ARGARGALAALAEE167 - 190167 - 190
d_31ens_2SERSERSERSERHH3 - 1043 - 104
d_32ens_2HISHISGLUGLUHH111 - 162111 - 162
d_33ens_2ARGARGALAALAHH167 - 190167 - 190
d_41ens_2SERSERSERSERKK3 - 1043 - 104
d_42ens_2HISHISGLUGLUKK111 - 162111 - 162
d_43ens_2ARGARGALAALAKK167 - 190167 - 190
d_11ens_3GLNGLNCYSCYSCC1 - 132 - 14
d_21ens_3GLNGLNCYSCYSFF1 - 132 - 14
d_31ens_3GLNGLNCYSCYSII1 - 132 - 14
d_41ens_3GLNGLNCYSCYSLL1 - 132 - 14

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(0.64475729747, 0.53308039822, -0.547825990979), (0.709044367871, -0.149356211451, 0.689165296929), (0.285559296379, -0.832777287835, -0.474276161236)9.53172136091, 59.0375960008, 70.1775887204
2given(-0.359885526516, 0.929022433065, 0.0860216639338), (0.932760853051, 0.360334057259, 0.010796212027), (-0.0209666120122, 0.0841230410815, -0.996234769088)-15.0490600399, 9.35395256389, -2.02767091171
3given(-0.278121397693, -0.757051765562, -0.591203105882), (-0.3500667681, 0.653042981986, -0.671556491704), (0.894484066944, 0.0201863304643, -0.446643891759)44.3078197751, -23.6935637463, 42.3178663184
4given(0.63514675913, 0.526992951732, -0.564683117502), (0.730293887353, -0.171670301723, 0.661211120295), (0.251514278843, -0.832350729159, -0.493895567106)9.72343115357, 60.0604867806, 69.9781993157
5given(-0.329518124273, 0.940654076101, 0.0811647392024), (0.942525198801, 0.332773603608, -0.0301326793734), (-0.0553539104267, 0.066570547966, -0.996245103749)-14.7214602387, 10.7185699259, -2.04022182044
6given(-0.303642622367, -0.749146428277, -0.588711123457), (-0.354152093013, 0.662355767528, -0.660197797813), (0.884521030217, 0.00802908594342, -0.46643121774)43.5625280492, -23.9239068717, 42.7319203811
7given(0.697290465711, 0.550009802707, -0.459646846345), (0.637169334635, -0.181882537918, 0.748955259947), (0.328330999801, -0.815112237257, -0.477274339603)8.37777997899, 57.6351409898, 70.9612827411
8given(-0.353240686224, 0.931121383257, 0.0907413204558), (0.93526366696, 0.349149107413, 0.0581100168433), (0.0224252282216, 0.105393882341, -0.994177669586)-15.4766059117, 8.76024669946, -1.77696702319
9given(-0.263567325418, -0.763378086399, -0.589733975771), (-0.37278189305, 0.644459703222, -0.667611676903), (0.889699907377, 0.0438815237844, -0.454432048479)44.2868966531, -24.1893736781, 42.1048462957

-
要素

-
MHC class II HLA-DQ- ... , 2種, 8分子 ADGJBEHK

#1: タンパク質
MHC class II HLA-DQ-alpha chain / DQA1*03:01 (DQ8-alpha chain)


分子量: 21124.516 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-DQA1 / プラスミド: pZip3 / 細胞株 (発現宿主): High Five (BTI-Tn-5B1-4) / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 株 (発現宿主): DH10B / 参照: UniProt: Q30069
#2: タンパク質
MHC class II HLA-DQ-beta-1 / DQB1*03:02 (DQ8-beta chain)


分子量: 22605.383 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-DQB1 / プラスミド: pZip3 / 細胞株 (発現宿主): High Five (BTI-Tn-5B1-4) / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 株 (発現宿主): DH10B / 参照: UniProt: O19707

-
タンパク質・ペプチド , 1種, 4分子 CFIL

#3: タンパク質・ペプチド
Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80)


分子量: 1460.632 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pZip3 / 細胞株 (発現宿主): High Five (BTI-Tn-5B1-4) / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 株 (発現宿主): DH10B

-
糖 , 2種, 4分子

#4: 多糖 beta-D-mannopyranose-(3-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(3-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb3-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+3)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
非ポリマー , 2種, 3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: 2 / 由来タイプ: 合成 / 式: C4H10O3
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1 / 由来タイプ: 天然 / 式: H2O

-
詳細

研究の焦点であるリガンドがあるかN

-
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: 2.75 Å3/Da / 溶媒含有率: 55.22 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 / 詳細: 0.2 M Monopotassium phosphate, 17% PEG 8K

-
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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9537 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2018年11月26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: 0.9537 Å / 相対比: 1
反射解像度: 3.5→49.4 Å / Num. obs: 28794 / % possible obs: 97.9 % / 冗長度: 4.2 % / Biso Wilson estimate: 45.35 Å2 / CC1/2: 0.907 / Net I/σ(I): 4.6
反射 シェル解像度: 3.5→3.5 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4228 / CC1/2: 0.414

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.19_4092精密化
autoXDSデータ削減
Coot0.9.8.92モデル構築
XDS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 / 解像度: 3.5→49.04 Å / SU ML: 0.387 / 交差検証法: FREE R-VALUE / σ(F): 100 / 位相誤差: 24.1523
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2457 1216 4.93 %
Rwork0.2075 23474 -
obs0.2094 24690 99.92 %
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: 42.5 Å2
精密化ステップサイクル: LAST / 解像度: 3.5→49.04 Å
タンパク質核酸リガンド溶媒全体
原子数12100 0 95 1 12196
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002212516
X-RAY DIFFRACTIONf_angle_d0.625317103
X-RAY DIFFRACTIONf_chiral_restr0.0461933
X-RAY DIFFRACTIONf_plane_restr0.00412206
X-RAY DIFFRACTIONf_dihedral_angle_d12.74964419
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.759841712242
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.697423991026
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.797634636585
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.16255353424
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS1.13704789378
ens_2d_4BBX-RAY DIFFRACTIONTorsion NCS1.10075085038
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.973836068634
ens_3d_3CCX-RAY DIFFRACTIONTorsion NCS1.0900324725
ens_3d_4CCX-RAY DIFFRACTIONTorsion NCS0.933968022756
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.640.29191240.2552627X-RAY DIFFRACTION100
3.64-3.810.27441570.24882573X-RAY DIFFRACTION99.82
3.81-4.010.28811360.22772575X-RAY DIFFRACTION99.78
4.01-4.260.26121270.20622615X-RAY DIFFRACTION99.96
4.26-4.590.22081090.18082605X-RAY DIFFRACTION99.96
4.59-5.050.22151420.16552608X-RAY DIFFRACTION100
5.05-5.780.22081250.19572603X-RAY DIFFRACTION100
5.78-7.270.25181300.2342646X-RAY DIFFRACTION100
7.27-49.040.21831660.19522622X-RAY DIFFRACTION99.82
精密化 TLS手法: refined / Origin x: 12.07 Å / Origin y: 24.425 Å / Origin z: 18.875 Å
111213212223313233
T0.175074803142 Å20.0264361078222 Å20.00812461546138 Å2-0.303727457575 Å2-0.00942121235874 Å2--0.262574850619 Å2
L-0.00162127450911 °20.0461059039098 °20.0288188063648 °2-0.346763564696 °20.0796276612713 °2--0.191232875438 °2
S-0.0298155850557 Å °-0.0724780689361 Å °-0.00739807234 Å °-0.0247024908231 Å °0.0475136219445 Å °0.0226792817671 Å °0.0337700589958 Å °0.0799456498393 Å °-0.0120480589304 Å °
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )A0 - 181
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )A601
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )A602
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )B3 - 191
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )C1 - 14
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )D0 - 181
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )E3 - 190
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )E201
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )F1 - 14
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )G0 - 181
11X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )H3 - 190
12X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )H201
13X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )I0 - 14
14X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )J0 - 181
15X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )J201
16X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )K3 - 191
17X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )K201
18X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:181 OR RESID 601:601 OR RESID 602:602 ) ) OR ( CHAIN B AND RESID 3:191 ) OR ( CHAIN C AND RESID 1:14 ) OR ( CHAIN D AND RESID 0:181 ) OR ( CHAIN E AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN F AND RESID 1:14 ) OR ( CHAIN G AND RESID 0:181 ) OR ( CHAIN H AND ( RESID 3:190 OR RESID 201:201 ) ) OR ( CHAIN I AND RESID 0:14 ) OR ( CHAIN J AND ( RESID 0:181 OR RESID 201:201 ) ) OR ( CHAIN K AND ( RESID 3:191 OR RESID 201:201 ) ) OR ( CHAIN L AND RESID 1:13 )L1 - 13

+
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