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- PDB-6pte: Crystal Structure of ILNAMITKI peptide bound to HLA-A2 -

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基本情報

登録情報
データベース: PDB / ID: 6pte
タイトルCrystal Structure of ILNAMITKI peptide bound to HLA-A2
要素
  • Beta-2-microglobulin
  • HAUS augmin-like complex subunit 3
  • HLA class I histocompatibility antigen, A-2 alpha chain
キーワードIMMUNE SYSTEM / MHC class I / HLA A2 / immune system complex / neoantigen
機能・相同性
機能・相同性情報


HAUS complex / regulation of microtubule nucleation / microtubule organizing center organization / mitotic spindle microtubule / centrosome cycle / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation ...HAUS complex / regulation of microtubule nucleation / microtubule organizing center organization / mitotic spindle microtubule / centrosome cycle / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / microtubule organizing center / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / intercellular bridge / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / AURKA Activation by TPX2 / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / mitotic spindle / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / Regulation of PLK1 Activity at G2/M Transition / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / microtubule cytoskeleton / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory
類似検索 - 分子機能
HAUS augmin-like complex subunit 3 / HAUS augmin-like complex subunit 3, N-terminal / HAUS augmin-like complex subunit 3 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin ...HAUS augmin-like complex subunit 3 / HAUS augmin-like complex subunit 3, N-terminal / HAUS augmin-like complex subunit 3 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / HAUS augmin-like complex subunit 3
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: 1.901 Å
データ登録者Smith, A.R. / Arbuiso, A. / Keller, G.L.J. / Baker, B.M.
引用ジャーナル: Front Immunol / 年: 2019
タイトル: Structure Based Prediction of Neoantigen Immunogenicity.
著者: Riley, T.P. / Keller, G.L.J. / Smith, A.R. / Davancaze, L.M. / Arbuiso, A.G. / Devlin, J.R. / Baker, B.M.
履歴
登録2019年7月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年9月4日Provider: repository / タイプ: Initial release
改定 1.12019年9月18日Group: Data collection / Derived calculations
カテゴリ: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
改定 1.22019年10月9日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.32023年10月11日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_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
改定 1.42024年11月6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: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: HAUS augmin-like complex subunit 3
E: HLA class I histocompatibility antigen, A-2 alpha chain
F: Beta-2-microglobulin
D: HAUS augmin-like complex subunit 3
H: HLA class I histocompatibility antigen, A-2 alpha chain
I: Beta-2-microglobulin
G: HAUS augmin-like complex subunit 3
K: HLA class I histocompatibility antigen, A-2 alpha chain
L: Beta-2-microglobulin
J: HAUS augmin-like complex subunit 3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)180,20128
ポリマ－179,00312
非ポリマー1,19716
水27,3111516
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: HAUS augmin-like complex subunit 3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,0507
ポリマ－44,7513
非ポリマー2994
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-35 kcal/mol
Surface area18840 Å2
手法PISA
2
E: HLA class I histocompatibility antigen, A-2 alpha chain
F: Beta-2-microglobulin
D: HAUS augmin-like complex subunit 3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,0507
ポリマ－44,7513
非ポリマー2994
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-35 kcal/mol
Surface area18790 Å2
手法PISA
3
H: HLA class I histocompatibility antigen, A-2 alpha chain
I: Beta-2-microglobulin
G: HAUS augmin-like complex subunit 3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,0507
ポリマ－44,7513
非ポリマー2994
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-37 kcal/mol
Surface area18720 Å2
手法PISA
4
K: HLA class I histocompatibility antigen, A-2 alpha chain
L: Beta-2-microglobulin
J: HAUS augmin-like complex subunit 3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,0507
ポリマ－44,7513
非ポリマー2994
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-36 kcal/mol
Surface area18730 Å2
手法PISA
単位格子
Length a, b, c (Å)58.429, 84.106, 85.363
Angle α, β, γ (deg.)90.010, 90.060, 90.020
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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要素

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タンパク質 , 2種, 8分子 AEHKBFIL

#1: タンパク質
HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


分子量: 31854.203 Da / 分子数: 4 / 断片: UNP residues 25-299 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-A, HLAA / プラスミド: pHN1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): XL1-Blue / 参照: UniProt: P01892, UniProt: P04439*PLUS
#2: タンパク質
Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 4 / 断片: UNP residues 21-119 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, CDABP0092, HDCMA22P / プラスミド: pHN1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): XL1-Blue / 参照: UniProt: P61769

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タンパク質・ペプチド , 1種, 4分子 CDGJ

#3: タンパク質・ペプチド
HAUS augmin-like complex subunit 3


分子量: 1017.306 Da / 分子数: 4 / 断片: UNP residues 154-162 / 由来タイプ: 合成
詳細: Processed peptide fragment from full-length protein containing SNP, derived from 2098 MEL cell line
由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: Q68CZ6

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非ポリマー , 3種, 1532分子

#4: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C3H8O3
#5: 化合物
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Na
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1516 / 由来タイプ: 天然 / 式: H2O

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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: 2.34 Å3/Da / 溶媒含有率: 47.51 %
結晶化温度: 296 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 / 詳細: 20% v/v PEG3350, 100 mM HEPES, pH 7.5

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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: APS / ビームライン: 23-ID-D / 波長: 1.0332 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2019年6月18日
放射モノクロメーター: Double crystal cryo-cooled Si(111)
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.0332 Å / 相対比: 1
反射解像度: 1.901→41.822 Å / Num. obs: 123624 / % possible obs: 96.7 % / 冗長度: 3.2 % / Biso Wilson estimate: 15.11 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.062 / Rrim(I) all: 0.114 / Net I/σ(I): 10.8
反射 シェル解像度: 1.901→1.97 Å / 冗長度: 2.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.33 / Num. unique obs: 11774 / CC1/2: 0.902 / Rpim(I) all: 0.193 / Rrim(I) all: 0.35 / % possible all: 92.6

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15.2_3472精密化
HKL-2000データ削減
HKL-2000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: PDB entry 1TVH

1tvh


解像度: 1.901→41.822 Å / SU ML: 0.17 / 交差検証法: FREE R-VALUE / σ(F): 2 / 位相誤差: 18.89
Rfactor反射数%反射Selection details
Rfree0.1855 12476 10.1 %Random
Rwork0.1593 ---
obs0.162 123541 96.71 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 74.28 Å2 / Biso mean: 20.8491 Å2 / Biso min: 6.14 Å2
精密化ステップサイクル: final / 解像度: 1.901→41.822 Å
タンパク質核酸リガンド溶媒全体
原子数12616 0 76 1516 14208
Biso mean--26.56 27.72 -
残基数----1536
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9015-1.92310.2413820.2005330588
1.9231-1.94570.23653910.1863372295
1.9457-1.96940.2144140.175355695
1.9694-1.99440.21833910.173367695
1.9944-2.02060.18964060.1618368095
2.0206-2.04830.21384160.1665365195
2.0483-2.07750.20544120.1615362396
2.0775-2.10850.20634050.1697369696
2.1085-2.14150.20294380.1731365996
2.1415-2.17660.20193930.1656367696
2.1766-2.21410.20474030.1702372596
2.2141-2.25440.24600.1673366397
2.2544-2.29770.23574250.1716368697
2.2977-2.34460.18674210.1606372297
2.3446-2.39560.20054020.169368497
2.3956-2.45130.20784290.1666370997
2.4513-2.51260.20594210.1729375797
2.5126-2.58060.2284020.1708371897
2.5806-2.65650.21244360.1704378898
2.6565-2.74220.21754240.1659367998
2.7422-2.84020.2124000.1739379498
2.8402-2.95390.17754190.164374298
2.9539-3.08830.18134180.1669376198
3.0883-3.25110.1934250.1612377298
3.2511-3.45470.18064240.1646375099
3.4547-3.72120.15364250.1473377399
3.7212-4.09540.14674310.1348379699
4.0954-4.68740.13454430.1259377399
4.6874-5.90290.15224110.1387377999
5.9029-41.820.15784090.1554375097
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)
11.52771337503-0.6447677563670.05251512641962.13166843747-0.1301262145691.085952193020.08039935922280.0916674203064-0.257596326607-0.167309407111-0.0716480104577-0.1014705362480.1490348611980.0357279265628-0.006138424202010.103331937103-0.0144529703480.006658552243070.096128019113-0.01248493119020.210561974272-15.234630161-20.5768098-19.7120074165
21.70088477024-0.685239799551-0.02211862425751.1576885207-0.1759163207990.384619307149-0.0624524293231-0.0816529322215-0.130195070150.1071775098580.05064534970410.0175745973090.00136720294299-0.05797871225130.01687097043350.0836992492886-0.00617484122629-0.008230390910840.1018684155190.009844812620790.103011933589-26.3053584007-12.5428633275-12.0468873725
32.509184238290.80709071305-0.0315498281770.8897123695730.02079207281830.024495814647-0.0100841203347-0.167062227754-0.423739991785-0.0906485052081-0.0195612653995-0.1057201598440.0303286020901-0.0198626458553-0.01385284758180.180748791063-0.00664841813405-0.005276487761170.1129618593780.0409123136620.1386443514211.00973101826-15.5180897985-8.66631126692
41.342359445430.1045214365710.05177869813411.802583045670.4418246043270.8800231698830.0137526454271-0.09651791701690.06877746646120.258736894432-0.09494014359480.1014438227830.00458683856082-0.02990423299420.06683006343620.123099368526-0.007076936145980.009943637127850.08667847902470.0005792224885130.06104121773958.71421281062-0.371992529159-9.29186985385
53.4586683874-2.77002032619-1.550729546623.92732372635-0.4199374606914.980844079110.101049408859-0.435378102296-0.08419244482580.103409040318-0.01269982886290.29130426697-0.0264115039022-0.346838994225-0.08039965215750.1559234985030.006282368322510.005261459483770.1444124217620.004949024606450.129266168516-15.02154517512.17625691981-24.4964221166
61.75179123899-0.00300285531066-0.4728050797451.57341705533-0.08131233970742.28591179374-0.06941971737570.069682413155-0.1147258492230.135453767769-0.0239538307399-0.1874325030690.0454632912190.2446479610580.05547483040080.09230585012610.0222140976701-0.003577184587820.123211460004-0.02939025805150.1603014610578.9005309519-10.9138855011-24.4620447463
75.50492339538-2.80168831788-1.15991935252.227340038970.8558287263171.635324806650.01621090552880.196045030354-0.240957521157-0.0279957165019-0.0661599735372-0.07531834192670.129937208617-0.07334998275640.04533239614420.09555332455580.0129026841778-0.01233418225640.0823624809713-0.00921256138020.1200395185420.649031106347-10.7846783268-25.1462725197
86.89925996222-3.45263912425-5.17552543911.830224277222.529822614013.919266651780.108332785810.363999507821-0.228505505055-0.187826327047-0.2087907725590.0798768489494-0.016149443898-0.04746878651360.08668158749640.1622147323160.0276678786595-0.0009748425295910.159977386401-0.004880867369680.102991588685-6.91721155737-7.36685494924-32.1364018538
94.503964939012.39106224948-4.071619461671.79424931961-2.211636197833.68500165519-0.4730630986650.733360649236-0.467047868232-0.7327072034980.0883078399443-0.1614451891640.75603754206-0.4037148015210.2931256403260.264547198770.01797044103140.03588301422730.283016585755-0.0869061235230.2352350261220.689836879939-14.8930009431-36.6206604039
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575.52060909888-0.3971060122574.134279487280.6126914942970.45298927374.24908809682-0.251241743821-0.22345006506-0.0521957237038-0.01352528347840.2023537658550.256717922376-0.370407072405-0.1265510512520.06686582108470.1400553452130.01629216327270.01495754091360.1623203207980.05848628290040.183559496153-32.818350925111.3935155347-48.7217890215
587.860201268715.690697679552.437058961976.935304526912.555493291163.102454757620.05012419023290.0426112993305-0.4897308298950.1943188044020.100791679679-0.1556019469260.174576440030.316668929565-0.1178104237450.1262510757230.0008267512465710.0294895589910.12140713917-0.01203168912610.1046538172865.16998966154-4.64603468052-64.2733144078
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 197 )
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 275 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 6 )
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 20 )
7X-RAY DIFFRACTION7chain 'B' and (resid 21 through 31 )
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 42 )
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 52 )
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 72 )
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 78 )
12X-RAY DIFFRACTION12chain 'B' and (resid 79 through 91 )
13X-RAY DIFFRACTION13chain 'B' and (resid 92 through 100 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 9 )
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 174 )
16X-RAY DIFFRACTION16chain 'E' and (resid 175 through 275 )
17X-RAY DIFFRACTION17chain 'F' and (resid 1 through 6 )
18X-RAY DIFFRACTION18chain 'F' and (resid 7 through 12 )
19X-RAY DIFFRACTION19chain 'F' and (resid 13 through 20 )
20X-RAY DIFFRACTION20chain 'F' and (resid 21 through 31 )
21X-RAY DIFFRACTION21chain 'F' and (resid 32 through 42 )
22X-RAY DIFFRACTION22chain 'F' and (resid 43 through 52 )
23X-RAY DIFFRACTION23chain 'F' and (resid 53 through 72 )
24X-RAY DIFFRACTION24chain 'F' and (resid 73 through 78 )
25X-RAY DIFFRACTION25chain 'F' and (resid 79 through 91 )
26X-RAY DIFFRACTION26chain 'F' and (resid 92 through 100 )
27X-RAY DIFFRACTION27chain 'D' and (resid 1 through 9 )
28X-RAY DIFFRACTION28chain 'H' and (resid 1 through 37 )
29X-RAY DIFFRACTION29chain 'H' and (resid 38 through 56 )
30X-RAY DIFFRACTION30chain 'H' and (resid 57 through 85 )
31X-RAY DIFFRACTION31chain 'H' and (resid 86 through 103 )
32X-RAY DIFFRACTION32chain 'H' and (resid 104 through 118 )
33X-RAY DIFFRACTION33chain 'H' and (resid 119 through 174 )
34X-RAY DIFFRACTION34chain 'H' and (resid 175 through 197 )
35X-RAY DIFFRACTION35chain 'H' and (resid 198 through 275 )
36X-RAY DIFFRACTION36chain 'I' and (resid 1 through 12 )
37X-RAY DIFFRACTION37chain 'I' and (resid 13 through 20 )
38X-RAY DIFFRACTION38chain 'I' and (resid 21 through 31 )
39X-RAY DIFFRACTION39chain 'I' and (resid 32 through 42 )
40X-RAY DIFFRACTION40chain 'I' and (resid 43 through 52 )
41X-RAY DIFFRACTION41chain 'I' and (resid 53 through 62 )
42X-RAY DIFFRACTION42chain 'I' and (resid 63 through 72 )
43X-RAY DIFFRACTION43chain 'I' and (resid 73 through 78 )
44X-RAY DIFFRACTION44chain 'I' and (resid 79 through 91 )
45X-RAY DIFFRACTION45chain 'I' and (resid 92 through 100 )
46X-RAY DIFFRACTION46chain 'G' and (resid 1 through 9 )
47X-RAY DIFFRACTION47chain 'K' and (resid 1 through 174 )
48X-RAY DIFFRACTION48chain 'K' and (resid 175 through 275 )
49X-RAY DIFFRACTION49chain 'L' and (resid 1 through 12 )
50X-RAY DIFFRACTION50chain 'L' and (resid 13 through 20 )
51X-RAY DIFFRACTION51chain 'L' and (resid 21 through 31 )
52X-RAY DIFFRACTION52chain 'L' and (resid 32 through 42 )
53X-RAY DIFFRACTION53chain 'L' and (resid 43 through 52 )
54X-RAY DIFFRACTION54chain 'L' and (resid 53 through 72 )
55X-RAY DIFFRACTION55chain 'L' and (resid 73 through 78 )
56X-RAY DIFFRACTION56chain 'L' and (resid 79 through 91 )
57X-RAY DIFFRACTION57chain 'L' and (resid 92 through 100 )
58X-RAY DIFFRACTION58chain 'J' and (resid 1 through 9 )

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万見について

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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