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- PDB-8v4z: Crystal structure of a HLA-B*35:01-NP7 with D1 TCR -

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基本情報

登録情報
データベース: PDB / ID: 8v4z
タイトルCrystal structure of a HLA-B*35:01-NP7 with D1 TCR
要素
  • Beta-2-microglobulin
  • D1 TCR alpha chain
  • D1 TCR beta chain
  • LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET
  • MHC class I antigen
キーワードIMMUNE SYSTEM / HLA B*3501 / NP418 epitope / T cell immunity / glycoprotein / host-virus interaction / immune response
機能・相同性
機能・相同性情報


: / : / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...: / : / 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 / cellular response to iron ion / 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 / 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 / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能
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. ...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
類似検索 - ドメイン・相同性
PHOSPHATE ION / MHC class I antigen / Beta-2-microglobulin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Influenza A virus (A型インフルエンザウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.40000208775 Å
データ登録者Littler, D.R. / Rossjohn, J.
資金援助 オーストラリア, 1件
組織認可番号国
Australian Research Council (ARC) オーストラリア
引用ジャーナル: Sci Immunol / 年: 2025
タイトル: Molecular determinants of cross-strain influenza A virus recognition by alpha beta T cell receptors.
著者: Quinones-Parra, S.M. / Gras, S. / Nguyen, T.H.O. / Farenc, C. / Szeto, C. / Rowntree, L.C. / Chaurasia, P. / Sant, S. / Boon, A.C.M. / Jayasinghe, D. / Rimmelzwaan, G.F. / Petersen, J. / ...著者: Quinones-Parra, S.M. / Gras, S. / Nguyen, T.H.O. / Farenc, C. / Szeto, C. / Rowntree, L.C. / Chaurasia, P. / Sant, S. / Boon, A.C.M. / Jayasinghe, D. / Rimmelzwaan, G.F. / Petersen, J. / Doherty, P.C. / Uldrich, A.P. / Littler, D.R. / Rossjohn, J. / Kedzierska, K.
履歴
登録2023年11月29日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年12月18日Provider: repository / タイプ: Initial release
改定 1.12025年1月1日Group: Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen
改定 1.22025年2月26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_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: MHC class I antigen
B: Beta-2-microglobulin
C: LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET
D: D1 TCR alpha chain
E: D1 TCR beta chain
F: MHC class I antigen
G: Beta-2-microglobulin
H: LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET
I: D1 TCR alpha chain
J: D1 TCR beta chain
K: MHC class I antigen
L: Beta-2-microglobulin
M: LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET
N: D1 TCR alpha chain
O: D1 TCR beta chain
P: MHC class I antigen
Q: Beta-2-microglobulin
R: LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET
S: D1 TCR alpha chain
T: D1 TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)375,96424
ポリマ－375,58420
非ポリマー3804
水13,872770
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET
D: D1 TCR alpha chain
E: D1 TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,9916
ポリマ－93,8965
非ポリマー951
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
F: MHC class I antigen
G: Beta-2-microglobulin
H: LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET
I: D1 TCR alpha chain
J: D1 TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,9916
ポリマ－93,8965
非ポリマー951
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
3
K: MHC class I antigen
L: Beta-2-microglobulin
M: LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET
N: D1 TCR alpha chain
O: D1 TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,9916
ポリマ－93,8965
非ポリマー951
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
4
P: MHC class I antigen
Q: Beta-2-microglobulin
R: LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET
S: D1 TCR alpha chain
T: D1 TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,9916
ポリマ－93,8965
非ポリマー951
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)78.988, 190.209, 250.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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
11
21
31
41
12
22
32
42
13
23
33
43
14
24
34
44
15
25
35
45

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNGLNGLN(chain I and (resseq 2:6 or resseq 8:22 or resseq...II2 - 61 - 5
121PROPROASNASN(chain I and (resseq 2:6 or resseq 8:22 or resseq...II8 - 226 - 20
131THRTHRGLYGLY(chain I and (resseq 2:6 or resseq 8:22 or resseq...II24 - 2922 - 27
141PHEPHELEULEU(chain I and (resseq 2:6 or resseq 8:22 or resseq...II36 - 5828 - 50
151ASPASPTHRTHR(chain I and (resseq 2:6 or resseq 8:22 or resseq...II63 - 6851 - 56
161GLYGLYPHEPHE(chain I and (resseq 2:6 or resseq 8:22 or resseq...II74 - 10357 - 86
171ALAALAPHEPHE(chain I and (resseq 2:6 or resseq 8:22 or resseq...II105 - 21288 - 195
181PROPROPROPRO(chain I and (resseq 2:6 or resseq 8:22 or resseq...II214197
291GLNGLNGLNGLN(chain D and (resseq 2:6 or resseq 8:22 or resseq...DD2 - 61 - 5
2101PROPROASNASN(chain D and (resseq 2:6 or resseq 8:22 or resseq...DD8 - 226 - 20
2111THRTHRGLYGLY(chain D and (resseq 2:6 or resseq 8:22 or resseq...DD24 - 2922 - 27
2121PHEPHELEULEU(chain D and (resseq 2:6 or resseq 8:22 or resseq...DD36 - 5828 - 50
2131ASPASPTHRTHR(chain D and (resseq 2:6 or resseq 8:22 or resseq...DD63 - 6851 - 56
2141GLYGLYPHEPHE(chain D and (resseq 2:6 or resseq 8:22 or resseq...DD74 - 10357 - 86
2151ALAALAPHEPHE(chain D and (resseq 2:6 or resseq 8:22 or resseq...DD105 - 21288 - 195
2161PROPROPROPRO(chain D and (resseq 2:6 or resseq 8:22 or resseq...DD214197
3171GLNGLNGLNGLN(chain N and (resseq 2:6 or resseq 8:22 or resseq...NN2 - 61 - 5
3181PROPROASNASN(chain N and (resseq 2:6 or resseq 8:22 or resseq...NN8 - 226 - 20
3191THRTHRGLYGLY(chain N and (resseq 2:6 or resseq 8:22 or resseq...NN24 - 2922 - 27
3201PHEPHELEULEU(chain N and (resseq 2:6 or resseq 8:22 or resseq...NN36 - 5828 - 50
3211ASPASPTHRTHR(chain N and (resseq 2:6 or resseq 8:22 or resseq...NN63 - 6851 - 56
3221GLYGLYPHEPHE(chain N and (resseq 2:6 or resseq 8:22 or resseq...NN74 - 10357 - 86
3231ALAALAPHEPHE(chain N and (resseq 2:6 or resseq 8:22 or resseq...NN105 - 21288 - 195
3241PROPROPROPRO(chain N and (resseq 2:6 or resseq 8:22 or resseq...NN214197
4251GLNGLNGLNGLN(chain S and (resseq 2:6 or resseq 8:22 or resseq...SS2 - 61 - 5
4261PROPROASNASN(chain S and (resseq 2:6 or resseq 8:22 or resseq...SS8 - 226 - 20
4271THRTHRGLYGLY(chain S and (resseq 2:6 or resseq 8:22 or resseq...SS24 - 2922 - 27
4281PHEPHELEULEU(chain S and (resseq 2:6 or resseq 8:22 or resseq...SS36 - 5828 - 50
4291ASPASPTHRTHR(chain S and (resseq 2:6 or resseq 8:22 or resseq...SS63 - 6851 - 56
4301GLYGLYPHEPHE(chain S and (resseq 2:6 or resseq 8:22 or resseq...SS74 - 10357 - 86
4311ALAALAPHEPHE(chain S and (resseq 2:6 or resseq 8:22 or resseq...SS105 - 21288 - 195
4321PROPROPROPRO(chain S and (resseq 2:6 or resseq 8:22 or resseq...SS214197
1332SERSERTHRTHR(chain A and (resseq 2:6 or (resid 7 and (name...AA2 - 102 - 10
1342SERSERTRPTRP(chain A and (resseq 2:6 or (resid 7 and (name...AA13 - 6013 - 60
1352ARGARGGLNGLN(chain A and (resseq 2:6 or (resid 7 and (name...AA62 - 6562 - 65
1362PHEPHETYRTYR(chain A and (resseq 2:6 or (resid 7 and (name...AA67 - 7467 - 74
1372GLUGLUARGARG(chain A and (resseq 2:6 or (resid 7 and (name...AA76 - 9776 - 97
1382TYRTYRGLNGLN(chain A and (resseq 2:6 or (resid 7 and (name...AA99 - 14499 - 144
1392LYSLYSTHRTHR(chain A and (resseq 2:6 or (resid 7 and (name...AA146 - 190146 - 190
1402PROPROGLNGLN(chain A and (resseq 2:6 or (resid 7 and (name...AA193 - 218193 - 218
1412ASPASPGLNGLN(chain A and (resseq 2:6 or (resid 7 and (name...AA220 - 255220 - 255
1422TYRTYRLEULEU(chain A and (resseq 2:6 or (resid 7 and (name...AA257 - 272257 - 272
2432SERSERTHRTHR(chain F and (resseq 2:6 or (resid 7 and (name...FF2 - 102 - 10
2442SERSERTRPTRP(chain F and (resseq 2:6 or (resid 7 and (name...FF13 - 6013 - 60
2452ARGARGGLNGLN(chain F and (resseq 2:6 or (resid 7 and (name...FF62 - 6562 - 65
2462PHEPHETYRTYR(chain F and (resseq 2:6 or (resid 7 and (name...FF67 - 7467 - 74
2472GLUGLUARGARG(chain F and (resseq 2:6 or (resid 7 and (name...FF76 - 9776 - 97
2482TYRTYRGLNGLN(chain F and (resseq 2:6 or (resid 7 and (name...FF99 - 14499 - 144
2492LYSLYSTHRTHR(chain F and (resseq 2:6 or (resid 7 and (name...FF146 - 190146 - 190
2502PROPROGLNGLN(chain F and (resseq 2:6 or (resid 7 and (name...FF193 - 218193 - 218
2512ASPASPGLNGLN(chain F and (resseq 2:6 or (resid 7 and (name...FF220 - 255220 - 255
2522TYRTYRLEULEU(chain F and (resseq 2:6 or (resid 7 and (name...FF257 - 272257 - 272
3532SERSERTHRTHR(chain K and (resseq 2:6 or (resid 7 and (name...KK2 - 102 - 10
3542SERSERTRPTRP(chain K and (resseq 2:6 or (resid 7 and (name...KK13 - 6013 - 60
3552ARGARGGLNGLN(chain K and (resseq 2:6 or (resid 7 and (name...KK62 - 6562 - 65
3562PHEPHETYRTYR(chain K and (resseq 2:6 or (resid 7 and (name...KK67 - 7467 - 74
3572GLUGLUARGARG(chain K and (resseq 2:6 or (resid 7 and (name...KK76 - 9776 - 97
3582TYRTYRGLNGLN(chain K and (resseq 2:6 or (resid 7 and (name...KK99 - 14499 - 144
3592LYSLYSTHRTHR(chain K and (resseq 2:6 or (resid 7 and (name...KK146 - 190146 - 190
3602PROPROGLNGLN(chain K and (resseq 2:6 or (resid 7 and (name...KK193 - 218193 - 218
3612ASPASPGLNGLN(chain K and (resseq 2:6 or (resid 7 and (name...KK220 - 255220 - 255
3622TYRTYRLEULEU(chain K and (resseq 2:6 or (resid 7 and (name...KK257 - 272257 - 272
4632SERSERTHRTHR(chain P and (resseq 2:6 or (resid 7 and (name...PP2 - 102 - 10
4642SERSERTRPTRP(chain P and (resseq 2:6 or (resid 7 and (name...PP13 - 6013 - 60
4652ARGARGGLNGLN(chain P and (resseq 2:6 or (resid 7 and (name...PP62 - 6562 - 65
4662PHEPHETYRTYR(chain P and (resseq 2:6 or (resid 7 and (name...PP67 - 7467 - 74
4672GLUGLUARGARG(chain P and (resseq 2:6 or (resid 7 and (name...PP76 - 9776 - 97
4682TYRTYRGLNGLN(chain P and (resseq 2:6 or (resid 7 and (name...PP99 - 14499 - 144
4692LYSLYSTHRTHR(chain P and (resseq 2:6 or (resid 7 and (name...PP146 - 190146 - 190
4702PROPROGLNGLN(chain P and (resseq 2:6 or (resid 7 and (name...PP193 - 218193 - 218
4712ASPASPGLNGLN(chain P and (resseq 2:6 or (resid 7 and (name...PP220 - 255220 - 255
4722TYRTYRLEULEU(chain P and (resseq 2:6 or (resid 7 and (name...PP257 - 272257 - 272
1733ILEILEGLNGLN(chain B and (resseq 1:2 or resseq 4:15 or resseq...BB1 - 22 - 3
1743THRTHRPROPRO(chain B and (resseq 1:2 or resseq 4:15 or resseq...BB4 - 145 - 15
1753ASNASNTHRTHR(chain B and (resseq 1:2 or resseq 4:15 or resseq...BB17 - 7318 - 74
1763ASPASPASPASP(chain B and (resseq 1:2 or resseq 4:15 or resseq...BB76 - 9677 - 97
1773ASPASPMETMET(chain B and (resseq 1:2 or resseq 4:15 or resseq...BB98 - 9999 - 100
2783ILEILEGLNGLN(chain G and (resseq 1:2 or resseq 4:15 or resseq...GG1 - 22 - 3
2793THRTHRPROPRO(chain G and (resseq 1:2 or resseq 4:15 or resseq...GG4 - 145 - 15
2803ASNASNTHRTHR(chain G and (resseq 1:2 or resseq 4:15 or resseq...GG17 - 7318 - 74
2813ASPASPASPASP(chain G and (resseq 1:2 or resseq 4:15 or resseq...GG76 - 9677 - 97
2823ASPASPMETMET(chain G and (resseq 1:2 or resseq 4:15 or resseq...GG98 - 9999 - 100
3833ILEILEGLNGLN(chain L and (resseq 1:2 or resseq 4:15 or resseq...LL1 - 22 - 3
3843THRTHRPROPRO(chain L and (resseq 1:2 or resseq 4:15 or resseq...LL4 - 145 - 15
3853ASNASNTHRTHR(chain L and (resseq 1:2 or resseq 4:15 or resseq...LL17 - 7318 - 74
3863ASPASPASPASP(chain L and (resseq 1:2 or resseq 4:15 or resseq...LL76 - 9677 - 97
3873ASPASPMETMET(chain L and (resseq 1:2 or resseq 4:15 or resseq...LL98 - 9999 - 100
4883ILEILEGLNGLN(chain Q and (resseq 1:2 or resseq 4:15 or resseq...QQ1 - 22 - 3
4893THRTHRPROPRO(chain Q and (resseq 1:2 or resseq 4:15 or resseq...QQ4 - 145 - 15
4903ASNASNTHRTHR(chain Q and (resseq 1:2 or resseq 4:15 or resseq...QQ17 - 7318 - 74
4913ASPASPASPASP(chain Q and (resseq 1:2 or resseq 4:15 or resseq...QQ76 - 9677 - 97
4923ASPASPMETMET(chain Q and (resseq 1:2 or resseq 4:15 or resseq...QQ98 - 9999 - 100
1934GLYGLYHISHIS(chain J and (resseq 3:9 or (resid 10 and (name...JJ3 - 291 - 27
1944VALVALPROPRO(chain J and (resseq 3:9 or (resid 10 and (name...JJ37 - 5028 - 41
1954PHEPHEASNASN(chain J and (resseq 3:9 or (resid 10 and (name...JJ52 - 5843 - 49
1964GLUGLUPROPRO(chain J and (resseq 3:9 or (resid 10 and (name...JJ63 - 8150 - 68
1974GLUGLULEULEU(chain J and (resseq 3:9 or (resid 10 and (name...JJ83 - 10369 - 89
1984ALAALAVALVAL(chain J and (resseq 3:9 or (resid 10 and (name...JJ105 - 18291 - 168
1994THRTHRASPASP(chain J and (resseq 3:9 or (resid 10 and (name...JJ184 - 256170 - 242
21004GLYGLYHISHIS(chain E and (resseq 3:9 or (resid 10 and (name...EE3 - 291 - 27
21014VALVALPROPRO(chain E and (resseq 3:9 or (resid 10 and (name...EE37 - 5028 - 41
21024PHEPHEASNASN(chain E and (resseq 3:9 or (resid 10 and (name...EE52 - 5843 - 49
21034GLUGLUPROPRO(chain E and (resseq 3:9 or (resid 10 and (name...EE63 - 8150 - 68
21044GLUGLULEULEU(chain E and (resseq 3:9 or (resid 10 and (name...EE83 - 10369 - 89
21054ALAALAVALVAL(chain E and (resseq 3:9 or (resid 10 and (name...EE105 - 18291 - 168
21064THRTHRASPASP(chain E and (resseq 3:9 or (resid 10 and (name...EE184 - 256170 - 242
31074GLYGLYHISHIS(chain O and (resseq 3:9 or (resid 10 and (name...OO3 - 291 - 27
31084VALVALPROPRO(chain O and (resseq 3:9 or (resid 10 and (name...OO37 - 5028 - 41
31094PHEPHEASNASN(chain O and (resseq 3:9 or (resid 10 and (name...OO52 - 5843 - 49
31104GLUGLUPROPRO(chain O and (resseq 3:9 or (resid 10 and (name...OO63 - 8150 - 68
31114GLUGLULEULEU(chain O and (resseq 3:9 or (resid 10 and (name...OO83 - 10369 - 89
31124ALAALAVALVAL(chain O and (resseq 3:9 or (resid 10 and (name...OO105 - 18291 - 168
31134THRTHRASPASP(chain O and (resseq 3:9 or (resid 10 and (name...OO184 - 256170 - 242
41144GLYGLYHISHIS(chain T and (resseq 3:9 or (resid 10 and (name...TT3 - 291 - 27
41154VALVALPROPRO(chain T and (resseq 3:9 or (resid 10 and (name...TT37 - 5028 - 41
41164PHEPHEASNASN(chain T and (resseq 3:9 or (resid 10 and (name...TT52 - 5843 - 49
41174GLUGLUPROPRO(chain T and (resseq 3:9 or (resid 10 and (name...TT63 - 8150 - 68
41184GLUGLULEULEU(chain T and (resseq 3:9 or (resid 10 and (name...TT83 - 10369 - 89
41194ALAALAVALVAL(chain T and (resseq 3:9 or (resid 10 and (name...TT105 - 18291 - 168
41204THRTHRASPASP(chain T and (resseq 3:9 or (resid 10 and (name...TT184 - 256170 - 242
11215LEULEUMETMETchain CCC1 - 91 - 9
21225LEULEUMETMETchain HHH1 - 91 - 9
31235LEULEUMETMETchain MMM1 - 91 - 9
41245LEULEUMETMETchain RRR1 - 91 - 9

NCSアンサンブル:
ID
1
2
3
4
5

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要素

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タンパク質 , 4種, 16分子 AFKPBGLQDINSEJOT

#1: タンパク質
MHC class I antigen


分子量: 31940.246 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 株: B*35:01 / 遺伝子: HLA-B / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: F4NBT2
#2: タンパク質
Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 4 / Mutation: M1 / 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 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P61769
#4: タンパク質
D1 TCR alpha chain


分子量: 21807.949 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: TRAV1*01 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#5: タンパク質
D1 TCR beta chain


分子量: 27202.172 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: TRBV7-8*01 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)

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タンパク質・ペプチド , 1種, 4分子 CHMR

#3: タンパク質・ペプチド
LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET


分子量: 1066.291 Da / 分子数: 4 / 由来タイプ: 合成
由来: (合成) Influenza A virus (A型インフルエンザウイルス)

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非ポリマー , 2種, 774分子

#6: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 4 / 由来タイプ: 天然 / 式: PO4
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 770 / 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: 2.48 Å3/Da / 溶媒含有率: 50.31 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: PEG

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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: 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1月1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: 2.4→50 Å / Num. obs: 147969 / % possible obs: 100 % / 冗長度: 2 % / Biso Wilson estimate: 36.3548140718 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.6
反射 シェル解像度: 2.4→2.49 Å / Rmerge(I) obs: 0.3912 / Num. unique obs: 14575 / CC1/2: 0.784

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
XDSデータ削減
Aimless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: 2.40000208775→49.0643676691 Å / SU ML: 0.321790927904 / 交差検証法: FREE R-VALUE / σ(F): 1.96715742794 / 位相誤差: 27.3036807468
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.252287726965 7336 4.96074546426 %0.05
Rwork0.218166072864 140545 --
obs0.219887878441 147881 99.9101436351 %-
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: 68.2822005343 Å2
精密化ステップサイクル: LAST / 解像度: 2.40000208775→49.0643676691 Å
タンパク質核酸リガンド溶媒全体
原子数26378 0 20 770 27168
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.010643865000927390
X-RAY DIFFRACTIONf_angle_d1.5443769275237268
X-RAY DIFFRACTIONf_chiral_restr0.07407426617363874
X-RAY DIFFRACTIONf_plane_restr0.005697491002194940
X-RAY DIFFRACTIONf_dihedral_angle_d22.984799821410132
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.401-2.42730.3611074666212530.2999363034734584X-RAY DIFFRACTION99.9380165289
2.4273-2.45580.3276394018512170.2931123431924639X-RAY DIFFRACTION100
2.4558-2.48580.3249406203092350.2847257275564647X-RAY DIFFRACTION100
2.4858-2.51720.35206153192110.2842456338584682X-RAY DIFFRACTION99.9795668165
2.5172-2.55040.3541758163292530.2936156289474681X-RAY DIFFRACTION99.9797365755
2.5504-2.58530.3259340766812280.2779946691954562X-RAY DIFFRACTION99.9374087211
2.5853-2.62220.2833985797192480.2644658547754674X-RAY DIFFRACTION99.8579833638
2.6222-2.66140.3082052740392550.2536954764644595X-RAY DIFFRACTION99.8353231783
2.6614-2.7030.2674064812032470.2513699328914643X-RAY DIFFRACTION99.8774509804
2.703-2.74730.2984888055622130.2531134290674696X-RAY DIFFRACTION99.9796334012
2.7473-2.79460.2889893615752210.2589452290914668X-RAY DIFFRACTION99.9795501022
2.7946-2.84540.3464358124992550.2509093226754634X-RAY DIFFRACTION99.9386753884
2.8454-2.90020.3009290748322250.2519932561994671X-RAY DIFFRACTION99.9795793343
2.9002-2.95940.2995485427482440.2471651893474647X-RAY DIFFRACTION99.959125281
2.9594-3.02370.2880466416782390.2466949650994687X-RAY DIFFRACTION100
3.0237-3.0940.2711353463162950.2343978904674580X-RAY DIFFRACTION99.9589911831
3.094-3.17140.2717465202992360.233307889564719X-RAY DIFFRACTION99.9798224374
3.1714-3.25710.2836767519672260.2380210662334665X-RAY DIFFRACTION99.9795584628
3.2571-3.35290.282187520682570.2332879808964633X-RAY DIFFRACTION99.9591169256
3.3529-3.46110.288241416362270.2203090825144711X-RAY DIFFRACTION100
3.4611-3.58480.2502294430042600.2174337927394699X-RAY DIFFRACTION99.9798387097
3.5848-3.72830.2296329524782570.2066968394684662X-RAY DIFFRACTION99.939049167
3.7283-3.89790.2219487014832700.201293008674677X-RAY DIFFRACTION99.9797898141
3.8979-4.10330.2336625160012530.192827789884716X-RAY DIFFRACTION99.9597666465
4.1033-4.36020.220678043932070.1788386851434747X-RAY DIFFRACTION99.9596448749
4.3602-4.69670.1830220429912680.1694323088074726X-RAY DIFFRACTION99.9399639784
4.6967-5.16880.2030529008732520.1640577597034737X-RAY DIFFRACTION99.9799599198
5.1688-5.91570.2051418057192530.1887793051774769X-RAY DIFFRACTION100
5.9157-7.44890.2480474462212620.2124191209014823X-RAY DIFFRACTION99.9410377358
7.4489-49.050.2029099729782690.1957887404564971X-RAY DIFFRACTION98.6074520135
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)
12.798324025653.176096618030.05908661963277.74941456115-0.3498302196031.44604838640.226993056989-0.2852513384430.3400115427020.205928523651-0.155400587803-0.0903747337824-0.03400032365220.261591618034-0.1180468796640.302101337260.0303141589035-0.04613023229820.280826229995-0.05086512373840.523100130535-14.4575027364-9.7094281302117.6501039235
20.2700509069520.929519504011-0.2157176186523.27072493982-0.6726668902761.97104589061-0.208440064445-0.461783067610.1158884323240.2533786523730.158842342616-0.9823903914110.3931254516520.676419702361-0.04454681977050.3762643842070.103659045021-0.114753520640.416869492481-0.03519208041210.717931179002-8.80129687251-20.037728380117.5085009126
32.13334938106-1.19481467695-0.03336863629272.60449852787-0.5027079765111.489468748410.1126319072370.2777251746230.20705383355-0.265855157952-0.356234449185-0.1110385758550.01385111023040.1197986814860.1635109821140.230233307527-0.0304582570184-0.0003546491121040.274699297606-0.02490541654440.500421260145-12.3473167436-8.756641855117.55000596773
42.509134992991.199365882160.1507658084484.881485506520.6475841440161.195102852260.0577077672213-0.2398900000450.06693184183240.2508964342540.0307113480649-0.364284966153-0.0442724030695-0.144483244792-0.03961104657220.2174673888060.00828280925151-0.04251322392850.363546221568-0.0780629784050.447525971121-24.4049925444-8.8467637398115.9658915184
51.405317139840.2421271010750.3468341699341.357250563060.1440008810621.181580485580.1826347007150.01793867903850.335578298660.272996501565-0.1091164960430.1485174577230.018404379913-0.411050631266-0.02021354597190.204005704836-0.00885612393115-0.01704549867340.306104968979-0.08095244744370.5880552003-31.3317228499-4.9245471235812.7415005569
60.4714836927740.2453538727690.04123432851141.948740054181.309238480751.678562543920.1118843957880.06959026790430.234416619732-0.0628824896392-0.2955965485540.01748290716450.0176299926449-0.2709604482660.08643595653690.1931121772660.0127851199307-0.006146376491640.267269269469-0.01500262225140.494845230279-28.697818466-8.199633393094.23738371252
72.2400062677-1.814825758370.8142883506414.12480444072-3.268339661663.977132342370.009719347134660.141750790292-0.301707335606-0.2720685465830.229466477698-0.3314174726630.57754919663-0.099610320576-0.07399135576670.448998862878-0.0496588141425-0.02802993464750.225174963926-0.05822101801240.409027748848-20.8132448967-29.068411878113.277627898
81.241047945970.02766866900630.1694319717490.357070908371-0.6554136529451.261594982370.152908639039-0.5753721810760.03471571427970.249824122045-0.332277663301-0.1071488425780.1211233593270.533760809314-0.2250984211820.6946973032-0.171813294871-0.1692583216940.6184703970320.08692261576010.726378531477-20.160491996-24.867521486144.5471139057
92.17167730825-0.560034291521-1.576684174511.103637811730.2089299458912.315770351750.606420161006-0.753145189074-0.02141787888070.176520132551-0.8839051719220.160748091205-0.443699318354-0.09824205451450.1302497881240.704067613033-0.25742587052-0.04305835890830.732408215336-0.1842118922420.831471924934-28.2647851709-19.101078754247.5680975472
101.644742925540.696710259029-0.3801061253651.45180576774-0.7183498673151.852658413520.139464631766-0.753123407470.3821314842030.318445124825-0.358899365683-0.03160501059250.068227290681-0.07135487384460.1840945385520.623094649075-0.152624225939-0.0864019724140.726276195966-0.03878052425870.673143550474-25.5844773816-21.676062115547.0988691206
112.19092959453-2.259536158141.794396131325.09523247744-3.891967059544.294327347290.122381556109-0.419103278162-0.5894015552310.299186946708-0.292315567122-0.323979861258-0.148332797204-0.222301568526-0.01981027696160.602610909113-0.00217127018364-0.324008499790.524188631747-0.07096039578270.74222313399-17.1219226474-4.6514975183436.3887204971
120.682772421149-0.0700035194968-0.03316846275441.851456591090.9241177666090.486104005569-0.0109312161207-0.289710164618-0.08860105913080.3968181133910.00625136106153-0.183296388484-0.06043912662950.1258028859950.06232218279230.868411983448-0.0420189058755-0.3801363633960.8720872310490.4906385403941.73465120084-5.64116490015-21.77969143746.69815037
131.80578637805-1.168292198211.734500448511.03965626584-0.4432984058083.31815411205-0.107197104436-0.108037352033-0.3642221942820.540684700618-0.535549369953-0.78000363079-0.6792410800110.1606153225890.3342146971190.462816971271-0.10483339008-0.3409148181550.4698804819440.1179062178821.00202872454-10.1744638076-5.4018782647134.7969105646
143.042146630010.4489895259182.510095184221.339172744090.6255846929612.644253334230.179696789807-0.0293410822566-0.1002699050160.2595977864550.0066580110485-0.3337929455340.0139406775270.561905181168-0.1019650857470.824242804504-0.101786768776-0.4304024319721.172831545050.2744347135691.946793783281.06591592533-8.2923468890438.4807994366
150.655620375695-0.1063709688110.3680211898180.868053182851-0.4691967687492.19899214812-0.023879994918-0.379193749719-0.3445953487540.629644948314-0.524132900029-1.268816488740.2343877756-0.003408909923310.2781923411720.663487604076-0.15709785706-0.2912824066680.4555660002960.1552433747741.03163754648-10.1567222528-7.523484817236.540323507
161.5502547124-0.6705521838450.9350560659663.18127418878-1.5492855743.787418754920.00892665108514-0.4172890246830.0135354884730.211530189936-0.0378463932703-0.05221703261980.3719784055740.137021317298-0.2873701632271.29859555911-0.144831743902-0.4712133107140.8701171083080.006966387954130.580448036888-11.7369302893-9.1727453854248.9755481052
172.32446960542-0.5447788937190.2160539522851.23098434885-0.008027335934332.93318184885-0.1189534964120.2122016907990.47739913-0.00997312457863-0.151213505344-0.2327855699150.295035167946-0.2616556702530.08570489122280.226877007301-0.0548014342619-0.00486343945190.23788058983-0.03519232904120.377778899786-19.6659585979-11.56588909425.70941847955
184.4538931039-1.450095515282.691402800471.57085640635-1.123237469012.72297664499-0.09670800644230.2575735564150.324289208275-0.119168516902-0.0708726983521-0.117827125320.26485014278-0.0394005288928-0.008969217436820.319246137368-0.01528116348090.001140766981440.264064919550.08987789054050.370754562243-26.9982955291-23.1917610608-23.6451158575
191.277882626730.2861218288470.24050592961.496804494810.4468344563981.130740308940.08290280164920.05523750660160.123771905694-0.0548120150657-0.179956206751-0.1158791638740.2557659224170.22960290880.08567840078630.1776201645720.00362998029316-0.009157026398340.2367529007320.08389300122820.32384321656-25.0654012217-18.0782967454-13.3942531123
201.89161411236-1.090194053920.8683674203032.59877278086-1.429258010043.12173286992-0.07717099977250.1374353157050.2461355440030.0151535756324-0.038337461303-0.2161313280050.04283658672430.0969263490698-0.04076546967050.251095877319-0.0357023316197-0.02394391153240.2210262575290.02139134697570.379212375454-33.550239944-20.1685642473-12.8326974599
211.18765316152-0.7328526002090.653924118871.15057722451-0.2056231000511.655126850960.01855589385560.1289696311020.405912529451-0.1071573450640.16321278872-0.153337275337-0.140938773221-0.4718464719890.09779482270680.273164598036-0.0355228375575-0.02715400009270.2984986150780.1796633917430.321459687127-28.2071340636-15.335482961-22.4322226308
220.5959679721110.185860662471-0.1398047595851.307806047060.9997964399362.46335332157-0.2871578796810.0441220546410.05743180840050.07862540769420.0470239711985-0.202185258982-0.121997389090.0309266654982-0.01141800274190.171877888381-0.000923087842322-0.0396289851630.2953261939490.0708330964360.303361987792-16.7472595757-18.3635051731-10.1870179616
230.503226546614-0.008790604881481.581406896660.659332156919-0.3925944499265.20373498388-0.3226909807160.832843023241-0.265439342861-0.3533412268850.260152859686-0.191307920159-0.329598902083-0.1292661061620.1383987872130.617621620768-0.05191561634720.003795565568310.8103027107690.2019729053610.403911124873-33.0581428261-16.7002205025-39.9982780221
240.7292889921190.3405641000790.3629585719741.13632590457-0.03752677078730.635766283956-0.07778625283070.3377759545050.22074950914-0.446942795680.0614574115041-0.271367552708-0.4466619553820.3197844668470.02471138890221.18628197443-0.09653330483570.1096971939871.85229870153-0.1134646191521.16072892226-19.7314022342-8.50937952204-55.4802212104
251.47031029671-0.7332578878250.7501180380141.962086214370.5002547332160.8577087683690.1229335688930.336150901737-0.233513021888-0.06370872430110.37721973189-0.2862569828410.2662048867110.519577168421-0.02595179863610.9877366145490.04741876519170.2663030735641.36018765995-0.003830363009521.31339634284-18.5388319891-21.8688281634-48.6958634885
266.1547956811-3.62079239658-2.240665064555.295368681091.503060151973.11190116906-0.3816624623050.120337395925-0.0732393199963-0.3284404267730.2219892370350.287327612858-0.0253721017287-0.03082502113580.03052263957850.709834867044-0.08680201993350.05872191658861.148064169530.2982176819580.685083501939-29.0582572569-8.72504472441-41.8500860601
272.836297681720.148921639541-0.103788949560.0570372286337-0.02272126508310.0265777079884-0.2643788649190.383798485809-0.0453858629109-0.03867830455110.134061958058-0.00990495889544-0.1892435618740.575564137460.04815183549260.9254775500670.06323494218470.08308770393631.134017571580.04738041782150.530392884045-24.0399985445-11.8582082686-47.3911586007
282.083492651241.2756022936-0.4991803634530.833124591321-0.2110291433520.261337099064-0.01520299859360.143253216049-0.225099354656-0.161513307897-0.11951840395-0.1016434124850.1732865165910.2787451339770.06169870442991.18535729296-0.01957095440730.1262633965621.7166831212-0.5214444680421.45191093468-22.1799069317-18.6210354017-58.2666931042
291.369743006460.194312077655-0.309931369740.756759052733-0.239636796691.466960905470.009612875960340.1591506145860.335822807659-0.126924021483-0.0549690165266-0.325327637250.03710122116060.1925698842110.03827138240910.25003502874-0.02266146546280.04416308989610.3201837158950.1296412359740.64418443929-5.84751320214-7.63735588226-15.9925926911
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1221.673302100230.07245071648140.4078671403580.687741938956-0.03451753331510.8974292657170.051492691539-0.631682144565-0.194299456144-0.0180963880653-0.4028510617480.192364019296-0.1909922928270.100429197610.2414285667240.5592899795460.00887908362635-0.05725484508830.96654478449-0.1938636133660.5405399731-15.965786489443.063669777950.8453863541
1232.475019875451.15226544751-0.1732304833062.71645718649-0.1226938629511.56568857842-0.228514874720.113369485507-0.00247689913080.1018065342070.2810257289590.326642968283-0.252106241359-0.176982011241-0.02265759466360.5618819852540.143024026549-0.07391519134820.689865053578-0.1434181050070.639297834171-21.806489729937.277681909544.5396143494
1241.028298033050.177200378026-0.04705925629120.7878472200820.07917857710940.209884731290.228265350573-0.04837157422310.06876480737920.381387382536-0.01610683767670.159766136039-0.2063327662460.220287829842-0.02178590516880.726891456670.0312764533498-0.08272219158460.817543198897-0.2307679597720.655832016855-12.29455142649.399576446850.2357656258
1253.386426433311.1267121881-0.01481571257862.149326005680.48510580821.479280050260.0658311366936-0.2662881778790.08830493602380.1666706293060.02715297558020.732201779631-0.541783554651-0.173442812775-0.1903982966350.6124531733890.207893009787-0.02620176883650.806316806499-0.2692845304450.845780681757-32.325270272648.464609922946.2478030434
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 137 )
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 162 )
7X-RAY DIFFRACTION7chain 'A' and (resid 163 through 174 )
8X-RAY DIFFRACTION8chain 'A' and (resid 175 through 197 )
9X-RAY DIFFRACTION9chain 'A' and (resid 198 through 227 )
10X-RAY DIFFRACTION10chain 'A' and (resid 228 through 274 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 11 )
12X-RAY DIFFRACTION12chain 'B' and (resid 12 through 22 )
13X-RAY DIFFRACTION13chain 'B' and (resid 23 through 41 )
14X-RAY DIFFRACTION14chain 'B' and (resid 42 through 51 )
15X-RAY DIFFRACTION15chain 'B' and (resid 52 through 90 )
16X-RAY DIFFRACTION16chain 'B' and (resid 91 through 99 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 9 )
18X-RAY DIFFRACTION18chain 'D' and (resid 2 through 18 )
19X-RAY DIFFRACTION19chain 'D' and (resid 19 through 63 )
20X-RAY DIFFRACTION20chain 'D' and (resid 64 through 91 )
21X-RAY DIFFRACTION21chain 'D' and (resid 92 through 107 )
22X-RAY DIFFRACTION22chain 'D' and (resid 108 through 119 )
23X-RAY DIFFRACTION23chain 'D' and (resid 120 through 132 )
24X-RAY DIFFRACTION24chain 'D' and (resid 133 through 153 )
25X-RAY DIFFRACTION25chain 'D' and (resid 154 through 168 )
26X-RAY DIFFRACTION26chain 'D' and (resid 169 through 181 )
27X-RAY DIFFRACTION27chain 'D' and (resid 182 through 191 )
28X-RAY DIFFRACTION28chain 'D' and (resid 192 through 214 )
29X-RAY DIFFRACTION29chain 'E' and (resid 3 through 135 )
30X-RAY DIFFRACTION30chain 'E' and (resid 136 through 256 )
31X-RAY DIFFRACTION31chain 'F' and (resid 2 through 28 )
32X-RAY DIFFRACTION32chain 'F' and (resid 29 through 56 )
33X-RAY DIFFRACTION33chain 'F' and (resid 57 through 84 )
34X-RAY DIFFRACTION34chain 'F' and (resid 85 through 137 )
35X-RAY DIFFRACTION35chain 'F' and (resid 138 through 162 )
36X-RAY DIFFRACTION36chain 'F' and (resid 163 through 174 )
37X-RAY DIFFRACTION37chain 'F' and (resid 175 through 219 )
38X-RAY DIFFRACTION38chain 'F' and (resid 220 through 274 )
39X-RAY DIFFRACTION39chain 'G' and (resid 1 through 11 )
40X-RAY DIFFRACTION40chain 'G' and (resid 12 through 21 )
41X-RAY DIFFRACTION41chain 'G' and (resid 22 through 41 )
42X-RAY DIFFRACTION42chain 'G' and (resid 42 through 51 )
43X-RAY DIFFRACTION43chain 'G' and (resid 52 through 90 )
44X-RAY DIFFRACTION44chain 'G' and (resid 91 through 99 )
45X-RAY DIFFRACTION45chain 'H' and (resid 1 through 9 )
46X-RAY DIFFRACTION46chain 'I' and (resid 2 through 18 )
47X-RAY DIFFRACTION47chain 'I' and (resid 19 through 63 )
48X-RAY DIFFRACTION48chain 'I' and (resid 64 through 91 )
49X-RAY DIFFRACTION49chain 'I' and (resid 92 through 107 )
50X-RAY DIFFRACTION50chain 'I' and (resid 108 through 119 )
51X-RAY DIFFRACTION51chain 'I' and (resid 120 through 132 )
52X-RAY DIFFRACTION52chain 'I' and (resid 133 through 145 )
53X-RAY DIFFRACTION53chain 'I' and (resid 146 through 163 )
54X-RAY DIFFRACTION54chain 'I' and (resid 164 through 191 )
55X-RAY DIFFRACTION55chain 'I' and (resid 192 through 214 )
56X-RAY DIFFRACTION56chain 'J' and (resid 3 through 135 )
57X-RAY DIFFRACTION57chain 'J' and (resid 136 through 173 )
58X-RAY DIFFRACTION58chain 'J' and (resid 174 through 201 )
59X-RAY DIFFRACTION59chain 'J' and (resid 202 through 256 )
60X-RAY DIFFRACTION60chain 'K' and (resid 2 through 28 )
61X-RAY DIFFRACTION61chain 'K' and (resid 29 through 56 )
62X-RAY DIFFRACTION62chain 'K' and (resid 57 through 84 )
63X-RAY DIFFRACTION63chain 'K' and (resid 85 through 137 )
64X-RAY DIFFRACTION64chain 'K' and (resid 138 through 162 )
65X-RAY DIFFRACTION65chain 'K' and (resid 163 through 174 )
66X-RAY DIFFRACTION66chain 'K' and (resid 175 through 219 )
67X-RAY DIFFRACTION67chain 'K' and (resid 220 through 262 )
68X-RAY DIFFRACTION68chain 'K' and (resid 263 through 275 )
69X-RAY DIFFRACTION69chain 'L' and (resid 1 through 11 )
70X-RAY DIFFRACTION70chain 'L' and (resid 12 through 19 )
71X-RAY DIFFRACTION71chain 'L' and (resid 20 through 30 )
72X-RAY DIFFRACTION72chain 'L' and (resid 31 through 41 )
73X-RAY DIFFRACTION73chain 'L' and (resid 42 through 51 )
74X-RAY DIFFRACTION74chain 'L' and (resid 52 through 71 )
75X-RAY DIFFRACTION75chain 'L' and (resid 72 through 90 )
76X-RAY DIFFRACTION76chain 'L' and (resid 91 through 99 )
77X-RAY DIFFRACTION77chain 'M' and (resid 1 through 9 )
78X-RAY DIFFRACTION78chain 'N' and (resid 2 through 18 )
79X-RAY DIFFRACTION79chain 'N' and (resid 19 through 63 )
80X-RAY DIFFRACTION80chain 'N' and (resid 64 through 91 )
81X-RAY DIFFRACTION81chain 'N' and (resid 92 through 119 )
82X-RAY DIFFRACTION82chain 'N' and (resid 120 through 132 )
83X-RAY DIFFRACTION83chain 'N' and (resid 133 through 153 )
84X-RAY DIFFRACTION84chain 'N' and (resid 154 through 168 )
85X-RAY DIFFRACTION85chain 'N' and (resid 169 through 191 )
86X-RAY DIFFRACTION86chain 'N' and (resid 192 through 214 )
87X-RAY DIFFRACTION87chain 'O' and (resid 3 through 135 )
88X-RAY DIFFRACTION88chain 'O' and (resid 136 through 256 )
89X-RAY DIFFRACTION89chain 'P' and (resid 2 through 28 )
90X-RAY DIFFRACTION90chain 'P' and (resid 29 through 56 )
91X-RAY DIFFRACTION91chain 'P' and (resid 57 through 84 )
92X-RAY DIFFRACTION92chain 'P' and (resid 85 through 118 )
93X-RAY DIFFRACTION93chain 'P' and (resid 119 through 137 )
94X-RAY DIFFRACTION94chain 'P' and (resid 138 through 162 )
95X-RAY DIFFRACTION95chain 'P' and (resid 163 through 174 )
96X-RAY DIFFRACTION96chain 'P' and (resid 175 through 257 )
97X-RAY DIFFRACTION97chain 'P' and (resid 258 through 275 )
98X-RAY DIFFRACTION98chain 'Q' and (resid 1 through 11 )
99X-RAY DIFFRACTION99chain 'Q' and (resid 12 through 19 )
100X-RAY DIFFRACTION100chain 'Q' and (resid 20 through 30 )
101X-RAY DIFFRACTION101chain 'Q' and (resid 31 through 41 )
102X-RAY DIFFRACTION102chain 'Q' and (resid 42 through 46 )
103X-RAY DIFFRACTION103chain 'Q' and (resid 47 through 51 )
104X-RAY DIFFRACTION104chain 'Q' and (resid 52 through 61 )
105X-RAY DIFFRACTION105chain 'Q' and (resid 62 through 71 )
106X-RAY DIFFRACTION106chain 'Q' and (resid 72 through 77 )
107X-RAY DIFFRACTION107chain 'Q' and (resid 78 through 90 )
108X-RAY DIFFRACTION108chain 'Q' and (resid 91 through 99 )
109X-RAY DIFFRACTION109chain 'R' and (resid 1 through 9 )
110X-RAY DIFFRACTION110chain 'S' and (resid 2 through 18 )
111X-RAY DIFFRACTION111chain 'S' and (resid 19 through 63 )
112X-RAY DIFFRACTION112chain 'S' and (resid 64 through 91 )
113X-RAY DIFFRACTION113chain 'S' and (resid 92 through 107 )
114X-RAY DIFFRACTION114chain 'S' and (resid 108 through 119 )
115X-RAY DIFFRACTION115chain 'S' and (resid 120 through 132 )
116X-RAY DIFFRACTION116chain 'S' and (resid 133 through 145 )
117X-RAY DIFFRACTION117chain 'S' and (resid 146 through 161 )
118X-RAY DIFFRACTION118chain 'S' and (resid 162 through 191 )
119X-RAY DIFFRACTION119chain 'S' and (resid 192 through 214 )
120X-RAY DIFFRACTION120chain 'T' and (resid 3 through 24 )
121X-RAY DIFFRACTION121chain 'T' and (resid 25 through 135 )
122X-RAY DIFFRACTION122chain 'T' and (resid 136 through 173 )
123X-RAY DIFFRACTION123chain 'T' and (resid 174 through 201 )
124X-RAY DIFFRACTION124chain 'T' and (resid 202 through 226 )
125X-RAY DIFFRACTION125chain 'T' and (resid 227 through 256 )

+
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

+
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