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- PDB-5jwe: Crystal structure of H-2Db in complex with the LCMV-derived GP92-... -

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基本情報

登録情報
データベース: PDB / ID: 5jwe
タイトルCrystal structure of H-2Db in complex with the LCMV-derived GP92-101 peptide
要素
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Pre-glycoprotein polyprotein GP complex
キーワードIMMUNE SYSTEM / Immunology / antigen presentation / MHC class I
機能・相同性
機能・相同性情報


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / 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 / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / receptor-mediated endocytosis of virus by host cell / learning or memory / host cell endoplasmic reticulum membrane / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / metal ion binding / plasma membrane / cytosol
類似検索 - 分子機能
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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 / : ...Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Pre-glycoprotein polyprotein GP complex
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Lymphocytic choriomeningitis virus (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å
データ登録者Buratto, J. / Badia-Martinez, D. / Norstrom, M. / Sandalova, T. / Achour, A.
引用ジャーナル: PLoS ONE / 年: 2017
タイトル: Crystal structures of H-2Db in complex with the LCMV-derived peptides GP92 and GP392 explain pleiotropic effects of glycosylation on antigen presentation and immunogenicity.
著者: Hafstrand, I. / Badia-Martinez, D. / Josey, B.J. / Norstrom, M. / Buratto, J. / Pellegrino, S. / Duru, A.D. / Sandalova, T. / Achour, A.
履歴
登録2016年5月12日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02017年5月24日Provider: repository / タイプ: Initial release
改定 1.12017年12月27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
改定 1.22024年1月10日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
P: Pre-glycoprotein polyprotein GP complex
Q: Pre-glycoprotein polyprotein GP complex
R: Pre-glycoprotein polyprotein GP complex
S: Pre-glycoprotein polyprotein GP complex
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)182,38740
ポリマ－179,75712
非ポリマー2,63028
水4,918273
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
P: Pre-glycoprotein polyprotein GP complex
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,59610
ポリマ－44,9393
非ポリマー6577
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-41 kcal/mol
Surface area18770 Å2
手法PISA
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
Q: Pre-glycoprotein polyprotein GP complex
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,59210
ポリマ－44,9393
非ポリマー6537
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-42 kcal/mol
Surface area18900 Å2
手法PISA
3
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
R: Pre-glycoprotein polyprotein GP complex
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,4128
ポリマ－44,9393
非ポリマー4725
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-57 kcal/mol
Surface area18520 Å2
手法PISA
4
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
S: Pre-glycoprotein polyprotein GP complex
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,78812
ポリマ－44,9393
非ポリマー8499
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-71 kcal/mol
Surface area18720 Å2
手法PISA
単位格子
Length a, b, c (Å)85.500, 176.300, 85.600
Angle α, β, γ (deg.)90.000, 119.800, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resseq 1:6 or (resid 7 and (name...
21(chain C and (resseq 1:6 or (resid 7 and (name...
31(chain E and (resseq 1:6 or (resid 7 and (name...
41(chain G and (resseq 1:6 or (resid 7 and (name...
12(chain B and (resseq 2 or (resid 3 and (name...
22(chain D and (resseq 2:18 or resseq 20:33 or resseq...
32(chain F and (resseq 2 or (resid 3 and (name...
42(chain H and (resseq 2 or (resid 3 and (name...
13(chain Q and (resseq 1:8 or (resid 9 and (name...
23(chain P and (resseq 1:8 or (resid 9 and (name...
33(chain R and (resseq 1:8 or (resid 9 and (name...
43(chain S and (resseq 1:8 or (resid 9 and (name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 1:6 or (resid 7 and (name...A0
211(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 6
221(chain C and (resseq 1:6 or (resid 7 and (name...C7
231(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
241(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
251(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
261(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
271(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
281(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
291(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
311(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 6
321(chain E and (resseq 1:6 or (resid 7 and (name...E7
331(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
341(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
351(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
361(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
371(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
381(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
391(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
411(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 6
421(chain G and (resseq 1:6 or (resid 7 and (name...G7
431(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
441(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
451(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
461(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
471(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
481(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
491(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
112(chain B and (resseq 2 or (resid 3 and (name...B2
122(chain B and (resseq 2 or (resid 3 and (name...B3
132(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
142(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
152(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
162(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
172(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
182(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
212(chain D and (resseq 2:18 or resseq 20:33 or resseq...D2 - 18
222(chain D and (resseq 2:18 or resseq 20:33 or resseq...D20 - 33
232(chain D and (resseq 2:18 or resseq 20:33 or resseq...D35
242(chain D and (resseq 2:18 or resseq 20:33 or resseq...D37 - 43
252(chain D and (resseq 2:18 or resseq 20:33 or resseq...D44
262(chain D and (resseq 2:18 or resseq 20:33 or resseq...D1 - 99
272(chain D and (resseq 2:18 or resseq 20:33 or resseq...D1 - 99
282(chain D and (resseq 2:18 or resseq 20:33 or resseq...D1 - 99
292(chain D and (resseq 2:18 or resseq 20:33 or resseq...D1 - 99
312(chain F and (resseq 2 or (resid 3 and (name...F2
322(chain F and (resseq 2 or (resid 3 and (name...F3
332(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
342(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
352(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
362(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
372(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
382(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
412(chain H and (resseq 2 or (resid 3 and (name...H2
422(chain H and (resseq 2 or (resid 3 and (name...H3
432(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
442(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
452(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
462(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
472(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
482(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
113(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 8
123(chain Q and (resseq 1:8 or (resid 9 and (name...Q9
133(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
143(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
153(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
163(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
173(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
183(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
193(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
213(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 8
223(chain P and (resseq 1:8 or (resid 9 and (name...P9
233(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
243(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
253(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
263(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
273(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
283(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
293(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
313(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 8
323(chain R and (resseq 1:8 or (resid 9 and (name...R9
333(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
343(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
353(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
363(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
373(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
383(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
393(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
413(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 8
423(chain S and (resseq 1:8 or (resid 9 and (name...S9
433(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
443(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
453(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
463(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
473(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
483(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
493(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10

NCSアンサンブル:
ID
1
2
3

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要素

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タンパク質 , 2種, 8分子 ACEGBDFH

#1: タンパク質
H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


分子量: 32087.703 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: H2-D1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01899
#2: タンパク質
Beta-2-microglobulin


分子量: 11704.359 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: B2m / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01887

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タンパク質・ペプチド , 1種, 4分子 PQRS

#3: タンパク質・ペプチド
Pre-glycoprotein polyprotein GP complex


分子量: 1147.222 Da / 分子数: 4 / 由来タイプ: 合成
由来: (合成) Lymphocytic choriomeningitis virus (ウイルス)
参照: UniProt: P09991

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非ポリマー , 3種, 301分子

#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 13 / 由来タイプ: 合成 / 式: SO4
#5: 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: 15 / 由来タイプ: 合成 / 式: C3H8O3
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 273 / 由来タイプ: 天然 / 式: H2O

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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: 3.11 Å3/Da / 溶媒含有率: 60.51 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: 100 mM Ammonium Sulfate, 100 mM Tris-HCl, 25% PEG 6000

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: ID14-1 / 波長: 0.934 Å
検出器タイプ: ADSC QUANTUM 210 / 検出器: CCD / 日付: 2007年6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: 0.934 Å / 相対比: 1
反射解像度: 2.4→19.61 Å / Num. obs: 84550 / % possible obs: 94.2 % / 冗長度: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7
反射 シェル解像度: 2.4→2.43 Å / 冗長度: 3.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.8 / % possible all: 91

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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
PDB_EXTRACT3.2データ抽出
MOSFLMデータ削減
SCALA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: 1N5A

1n5a


解像度: 2.4→19.45 Å / SU ML: 0.42 / 交差検証法: FREE R-VALUE / σ(F): 1.38 / 位相誤差: 29.81
Rfactor反射数%反射Selection details
Rfree0.2589 4220 4.99 %Random
Rwork0.1994 ---
obs0.2024 84550 98.84 %-
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: 205.33 Å2 / Biso mean: 67.8522 Å2 / Biso min: 29.04 Å2
精密化ステップサイクル: final / 解像度: 2.4→19.45 Å
タンパク質核酸リガンド溶媒全体
原子数12264 0 155 273 12692
Biso mean--95.71 56.38 -
残基数----1529
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0112826
X-RAY DIFFRACTIONf_angle_d1.24117459
X-RAY DIFFRACTIONf_chiral_restr0.0641768
X-RAY DIFFRACTIONf_plane_restr0.0092260
X-RAY DIFFRACTIONf_dihedral_angle_d18.4737536
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A4082X-RAY DIFFRACTION9.74TORSIONAL
12C4082X-RAY DIFFRACTION9.74TORSIONAL
13E4082X-RAY DIFFRACTION9.74TORSIONAL
14G4082X-RAY DIFFRACTION9.74TORSIONAL
21B1732X-RAY DIFFRACTION9.74TORSIONAL
22D1732X-RAY DIFFRACTION9.74TORSIONAL
23F1732X-RAY DIFFRACTION9.74TORSIONAL
24H1732X-RAY DIFFRACTION9.74TORSIONAL
31Q168X-RAY DIFFRACTION9.74TORSIONAL
32P168X-RAY DIFFRACTION9.74TORSIONAL
33R168X-RAY DIFFRACTION9.74TORSIONAL
34S168X-RAY DIFFRACTION9.74TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.42720.39971350.34762463259891
2.4272-2.45570.40351240.33632589271394
2.4557-2.48560.38221230.30342633275699
2.4856-2.5170.33141490.29127762925100
2.517-2.55010.35511420.299926232765100
2.5501-2.58490.35371580.283727172875100
2.5849-2.62180.36161300.293826532783100
2.6218-2.66080.33851350.283827462881100
2.6608-2.70230.35021450.272726872832100
2.7023-2.74650.3671200.272627132833100
2.7465-2.79370.35211550.271827092864100
2.7937-2.84440.32291530.265126992852100
2.8444-2.89890.32171410.244726542795100
2.8989-2.95790.28851520.24327492901100
2.9579-3.02190.32951290.245926862815100
3.0219-3.0920.31751430.242626912834100
3.092-3.1690.33131110.240127512862100
3.169-3.25430.33731180.230226972815100
3.2543-3.34960.28011660.224426942860100
3.3496-3.45710.30761520.21327072859100
3.4571-3.57990.23481330.198227162849100
3.5799-3.72230.23681310.183927672898100
3.7223-3.89040.2831660.180526622828100
3.8904-4.09380.23661510.172827062857100
4.0938-4.34760.19871330.149227022835100
4.3476-4.67890.20091580.137726642822100
4.6789-5.14190.18221430.131327342877100
5.1419-5.8680.18661620.154726832845100
5.868-7.32670.2481370.18727402877100
7.3267-19.45050.22071250.19062319244484
精密化 TLS手法: refined / Origin x: -1.7349 Å / Origin y: -13.288 Å / Origin z: 0.0355 Å
111213212223313233
T0.3911 Å20.0009 Å2-0.0017 Å2-0.3813 Å2-0.0423 Å2--0.2943 Å2
L0.5678 °2-0.0031 °2-0.0154 °2-0.3661 °2-0.172 °2---0.0368 °2
S0.0249 Å °0.0049 Å °-0.0028 Å °-0.0012 Å °-0.0202 Å °0.0033 Å °0.0061 Å °-0.0009 Å °-0.0042 Å °
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 276
2X-RAY DIFFRACTION1allB1 - 99
3X-RAY DIFFRACTION1allC1 - 276
4X-RAY DIFFRACTION1allD1 - 99
5X-RAY DIFFRACTION1allE1 - 276
6X-RAY DIFFRACTION1allF1 - 99
7X-RAY DIFFRACTION1allG1 - 276
8X-RAY DIFFRACTION1allH1 - 99
9X-RAY DIFFRACTION1allP1 - 10
10X-RAY DIFFRACTION1allQ1 - 10
11X-RAY DIFFRACTION1allR1 - 10
12X-RAY DIFFRACTION1allS1 - 10
13X-RAY DIFFRACTION1allI1 - 5
14X-RAY DIFFRACTION1allI6 - 15
15X-RAY DIFFRACTION1allI16
16X-RAY DIFFRACTION1allI17 - 19
17X-RAY DIFFRACTION1allX1 - 17
18X-RAY DIFFRACTION1allY1 - 299

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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://pdbjlc1.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