[日本語] English
万見
- PDB-5w1v: Structure of the HLA-E-VMAPRTLIL/GF4 TCR complex -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 5w1v
タイトルStructure of the HLA-E-VMAPRTLIL/GF4 TCR complex
要素
  • Beta-2-microglobulin
  • GF4 T cell receptor alpha chain
  • GF4 T cell receptor beta chain
  • HLA class I histocompatibility antigen, alpha chain E
  • VMAPRTLIL peptide from CMV gpUL40
キーワードIMMUNE SYSTEM / T-cell receptor / TCR / HLA-E / CMV / pMHC-TCR complex
機能・相同性
機能・相同性情報


symbiont-mediated suppression of host natural killer cell activation / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction ...symbiont-mediated suppression of host natural killer cell activation / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell proliferation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of immunoglobulin production / 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 / positive regulation of interleukin-4 production / beta-2-microglobulin binding / MHC class I protein 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 / T cell receptor binding / negative regulation of T cell proliferation / : / : / 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 / 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 / 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 / positive regulation of tumor necrosis factor production / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / 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 / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / receptor ligand activity / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding
類似検索 - 分子機能
Herpesvirus UL40 / Glycoprotein of human cytomegalovirus HHV-5 / 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 / : ...Herpesvirus UL40 / Glycoprotein of human cytomegalovirus HHV-5 / 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, alpha chain E / Protein UL40 / Beta-2-microglobulin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Human herpesvirus 5 strain AD169 (ヘルペスウイルス)
手法X線回折 / シンクロトロン / 解像度: 3.31 Å
データ登録者Gras, S. / Walpole, N. / Farenc, C. / Rossjohn, J.
資金援助 オーストラリア, 2件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia) オーストラリア
Australian Research Council (ARC) オーストラリア
引用ジャーナル: J. Biol. Chem. / 年: 2017
タイトル: A conserved energetic footprint underpins recognition of human leukocyte antigen-E by two distinct alpha beta T cell receptors.
著者: Sullivan, L.C. / Walpole, N.G. / Farenc, C. / Pietra, G. / Sum, M.J.W. / Clements, C.S. / Lee, E.J. / Beddoe, T. / Falco, M. / Mingari, M.C. / Moretta, L. / Gras, S. / Rossjohn, J. / Brooks, A.G.
履歴
登録2017年6月4日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年10月4日Provider: repository / タイプ: Initial release
改定 1.12017年10月18日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22018年1月3日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
改定 1.32018年1月17日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52024年11月6日Group: Data collection / Database references / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

-
集合体

登録構造単位
A: HLA class I histocompatibility antigen, alpha chain E
B: Beta-2-microglobulin
C: VMAPRTLIL peptide from CMV gpUL40
D: GF4 T cell receptor alpha chain
E: GF4 T cell receptor beta chain
F: HLA class I histocompatibility antigen, alpha chain E
G: Beta-2-microglobulin
H: VMAPRTLIL peptide from CMV gpUL40
I: GF4 T cell receptor alpha chain
J: GF4 T cell receptor beta chain
K: HLA class I histocompatibility antigen, alpha chain E
L: Beta-2-microglobulin
M: VMAPRTLIL peptide from CMV gpUL40
N: GF4 T cell receptor alpha chain
O: GF4 T cell receptor beta chain
P: HLA class I histocompatibility antigen, alpha chain E
Q: Beta-2-microglobulin
R: VMAPRTLIL peptide from CMV gpUL40
S: GF4 T cell receptor alpha chain
T: GF4 T cell receptor beta chain


分子量 (理論値)分子数
合計 (水以外)381,09420
ポリマ－381,09420
非ポリマー00
水00
1
A: HLA class I histocompatibility antigen, alpha chain E
B: Beta-2-microglobulin
C: VMAPRTLIL peptide from CMV gpUL40
D: GF4 T cell receptor alpha chain
E: GF4 T cell receptor beta chain


分子量 (理論値)分子数
合計 (水以外)95,2745
ポリマ－95,2745
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, alpha chain E
G: Beta-2-microglobulin
H: VMAPRTLIL peptide from CMV gpUL40
I: GF4 T cell receptor alpha chain
J: GF4 T cell receptor beta chain


分子量 (理論値)分子数
合計 (水以外)95,2745
ポリマ－95,2745
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
K: HLA class I histocompatibility antigen, alpha chain E
L: Beta-2-microglobulin
M: VMAPRTLIL peptide from CMV gpUL40
N: GF4 T cell receptor alpha chain
O: GF4 T cell receptor beta chain


分子量 (理論値)分子数
合計 (水以外)95,2745
ポリマ－95,2745
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
P: HLA class I histocompatibility antigen, alpha chain E
Q: Beta-2-microglobulin
R: VMAPRTLIL peptide from CMV gpUL40
S: GF4 T cell receptor alpha chain
T: GF4 T cell receptor beta chain


分子量 (理論値)分子数
合計 (水以外)95,2745
ポリマ－95,2745
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)71.646, 228.246, 276.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
要素

#1: タンパク質
HLA class I histocompatibility antigen, alpha chain E / MHC class I antigen E


分子量: 32082.305 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-E, HLA-6.2, HLAE / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21-Gold(DE3)pLysS AG / 参照: UniProt: P13747
#2: タンパク質
Beta-2-microglobulin


分子量: 11879.356 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: B2M, CDABP0092, HDCMA22P / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21-Gold(DE3)pLysS AG / 参照: UniProt: P61769
#3: タンパク質・ペプチド
VMAPRTLIL peptide from CMV gpUL40


分子量: 1014.305 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Human herpesvirus 5 strain AD169 (ヘルペスウイルス)
遺伝子: UL40 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21-Gold(DE3)pLysS AG / 参照: UniProt: P16780*PLUS
#4: タンパク質
GF4 T cell receptor alpha chain


分子量: 22688.107 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: TRAC TCRA / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21-Gold(DE3)pLysS AG
#5: タンパク質
GF4 T cell receptor beta chain


分子量: 27609.461 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: TRBC1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21-Gold(DE3)pLysS AG
Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.97 Å3/Da / 溶媒含有率: 58.59 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 / 詳細: 0.2M K, Na tartrate, 20% PEG 3350

-
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: Australian Synchrotron / ビームライン: MX2 / 波長: 1 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2010年2月18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: 1 Å / 相対比: 1
反射解像度: 3.312→54.93 Å / Num. obs: 68257 / % possible obs: 99 % / 冗長度: 2 % / Biso Wilson estimate: 71.44 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.05642 / Net I/σ(I): 13.35
反射 シェル解像度: 3.312→3.431 Å / 冗長度: 2 % / Rmerge(I) obs: 0.2775 / Mean I/σ(I) obs: 2.75 / Num. unique obs: 6341 / CC1/2: 0.859 / % possible all: 94

-
解析

ソフトウェア
名称バージョン分類
BUSTER2.10.2精密化
XDSデータ削減
SCALAデータスケーリング
精密化解像度: 3.31→54.93 Å / Cor.coef. Fo:Fc: 0.84 / Cor.coef. Fo:Fc free: 0.814 / Rfactor Rfree error: 0 / 交差検証法: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.538
Rfactor反射数%反射Selection details
Rfree0.268 3445 5.05 %RANDOM
Rwork0.225 ---
obs0.228 68257 99.1 %-
原子変位パラメータBiso mean: 95.07 Å2
Baniso -1Baniso -2Baniso -3
1--44.125 Å20 Å20 Å2
2--12.7065 Å20 Å2
3---31.4185 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
精密化ステップサイクル: 1 / 解像度: 3.31→54.93 Å
タンパク質核酸リガンド溶媒全体
原子数26445 0 0 0 26445
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00827181HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8236952HARMONIC3
X-RAY DIFFRACTIONt_dihedral_angle_d9214SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes777HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3906HARMONIC5
X-RAY DIFFRACTIONt_it27181HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion20.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3430SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact28537SEMIHARMONIC4
LS精密化 シェル解像度: 3.31→3.4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.295 227 5.09 %
Rwork0.257 4233 -
all0.259 4460 -
obs--88.65 %
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)
10-0.00580.00890.001-0.0070.005-0.00010.00010.00010.00010-0.0002-0.0002-0.00020.00010.00030.00020-0.00060.0002-0.0003104.95571.6753219.414
200.0023-0.001600.00390000.00010.000100-0.000100-0.0001-0.0006-0.0005-0.0003-0.00010.0002101.34576.6985219.274
30-0.0050.00170-0.00090.0011000.0001000.000100000.0004-0.0007-0.00010.0003-0.000297.923775.3858215.395
40-0.01260.02610.0225-0.0311000-0.00010.0006-0.0003-0.0002-0.0003-0.00020.00030.00030.0009-0.002-0.000700.000398.230675.4734231.296
50.00020.0051-0.00090.0005-0.00110.0012000.00010.0001-0.0001-0.0002-0.00020.00010.00010-0.0002-0.0003-0.00030.00020.0003107.85470.0414223.187
60-0.00530.01020-0.00460.0034000.000100-0.0002-0.00010.00010.00010.00010-0.0009-0.00050.00060.0002111.50468.3942225.553
70.0002-0.00270.00450-0.00220.000900-0.000200000.000100.00010-0.0008-0.00030.00040.0002111.16666.762241.696
800.00720.00780.0013-0.00120-0.00010.0002-0.000200.00010.00030.0001-0.00010-0.0001-0.00020-0.0010.00010.0007101.59759.3403221.064
900.00050.00040-0.0023000.00010.000100-0.000100.00010-0.000200.0002-0.00020.00030.0001121.3783.2445189.727
100-0.0032-0.00640.00510.004700-0.0001000.0001-0.0001-0.00010-0.0001-0.00020.00010.0008-0.0006-0.00010.0004120.27681.096194.687
110.0007-0.0020.00060.0014-0.00230000000000000-0.00010.00030.0004127.70374.4366196.863
120.0009-0.0044-0.0030.00670.00090000000-0.000100-0.00020.00010.0006-0.00050.00010.0008121.05680.9286199.2
130.0006-0.0008-0.00050.0003-0.00010.000100000000000.00020.0002-0.00010.00020.0002125.73671.3035194.296
1400.00230.0020.0002-0.00130000-0.000100000-0.00010-0.0001-0.00030.00060.0002114.11587.8886205.109
1500.00230.00490.0022-0.0006000.000100000-0.000100-0.0001-0.0003-0.00070.00020.0002108.21987.4509204.172
160.00930.02220.00330.0094-0.002200.00010-0.000300-0.0002-0.0002-0.00010-0.0001-0.0002-0.0005-0.00060.00050.0004106.72485.446210.58
170.0089-0.0020.00110.0140.01080.003-0.00010.0003-0.00010.00030.00010.00010.00010.000100.00090.00060.0013-0.0002-0.0001-0.000887.568243.5275252.507
180.0030.00270.00330.00410.00560.000300-0.00020.00010.00020.0001-0.0001-0.0003-0.00020.00010.00050.0004-0.0003-0.00030.000190.276957.3351253.052
190-0.0248-0.0030.0126-0.0160-0.0001-0.0007-0.00020.00070.00010.0002-0.00010.0001-0.00010.00130.00210.0005-0.001-0.0004-0.000994.726748.9827252.182
200.00570.0122-0.00540.025-0.02770.00180-0.00010-0.00010-0.00010.0001-0.000200.0001-0.00020.0005-0.00030.00120.00168.795845.522275.925
210.0001-0.0088-0.00450.00150.01900-0.000100.00010.00010.0004-0.0001-0.0002-0.00010.00020.00070.0004-0.0003-0.00130.000175.351474.5872252.493
220.0071-0.00780.00210.00170.00020.008200-0.00020.0001-0.00010.00030.0001-0.00030.00010.00010.00030.000500.0001080.331164.3474244.928
230-0.0305-0.0140-0.00250-0.00010.00030.00030.00020.00040.0008-0.0001-0.0006-0.00020.00020.00160.0004-0.0007-0.00060.000377.206572.683243.387
240.0236-0.0386-0.041400.0040.00660-0.00030.0002000.00060.0002-0.000100.00010.00180.00240.00010.0013068.663357.3962273.129
250-0.0126-0.00820-0.01210.00220-0.00010.00020.0001-0.00010.00010-0.00010.00010.00010.00070.000400.0006-0.0009103.91117.6023272.148
260-0.005-0.00140-0.00490.00150-0.00010.00020-0.00010.00010-0.00010.00010.00010.0005-0.00010.00020.0006-0.0005104.16411.4975270.976
2700.0001-0.00320.0006-0.00370.00140-0.000100000000.00010.00030.000300.0006-0.000199.04539.9099271.742
2800.00180.00320-0.06290.021500.0001000.0001-0.00050.00010-0.00010.0010.00070.00070.00030.0025-0.001108.71912.995259.544
290-0.004-0.00280-0.01080.01170-0.00020.0001-0.0001-0.000100.00020.00010.00010.00030.00050.00050.00010.0007-0.0006106.98921.264270.588
300-0.01570.00150-0.00690.00540-0.000300-0.000200-0.00020.00020.00030.0006-0.000400.0008-0.0005109.98124.92270.628
3100.0005-0.00060.0006-0.00180000000-0.0001000.0003-0.0002-0.0003-0.00010.0008-0.0001118.51428.8461257.354
320-0.0086-0.00010-0.00900-0.0001-0.0001-0.000100.00050-0.000100.00090.00140.0001-0.00010.0004-0.000996.209626.3846266.245
3300.00190.00030-0.0024000-0.00010.0001-0.0001-0.0001000.00010.0002-0.00030.0001-0.00010.0003-0.0003102.77310.5551306.929
340.002-0.0004-0.00360.00070.00010.001200000-0.00020000.0001-0.00010.000100.0003-0.0003103.63812.6446301.969
350.00050.0006-0.00130.00050.000300000000000.0002-0.00010.00010.000100106.42222.602303.679
3600.00060.0020-0.0006000.00010.0001-0.00010-0.00010000.00010.00010.0001-0.00030.0003-0.0003106.58813.8677298.72
370.00010.0015-0.00040.00050.00010.00040000000000.0002-0.00030.000100.0003-0.0001102.02923.7219303.879
3800.0001-0.00010-0.00230.00040000000000.0002-0.00010.00010.00010.0011-0.0004109.1515.619291.393
390-0.0006-0.00020.0009-0.00090.001300-0.0001-0.000100.00010000.00020.00010.0006-0.00020.0008-0.0004104.5912.9815288.559
400-0.00060.00070.00380.00870.01010-0.0001-0.0004-0.00010.00010.0002-0.00020-0.00010.00050.00010.0007-0.00030.0007-0.0003106.5075.287282.355
410-0.0279-0.01770.0077-0.00470.00050-0.00020.00020.0001-0.00010.00020-0.00040.00020.00080.00090.0006-0.00070.0002-0.000297.352337.1504230.497
420-0.0162-0.00070.0023-0.0093000.0003-0.0004-0.00020.0001-0.00020.00030-0.000100.00060.0003-0.00010.0009-0.0008107.06627.7612234.25
430.0024-0.0343-0.00250.0241-0.00450000.00030.00010-0.0004-0.00030.000300.00020.0020.0018-0.00110.00170104.6536.9802235.803
440.0428-0.04180.01690.0414-0.02170.028800.00020-0.00080.00010.00020.0001-0.0003-0.0001-0.00120.0022-0.00240.0009-0.0001-0.0005101.27429.3834201.291
450-0.00520.005800.0125000.0001-0.0002-0.0002-0.0001-0.00030.0002-0.00010.000100.00110.0012-0.0003-0.00070.0004106.4435.0525229.537
4600.00140.001100.00420.0026-0.00010.00030-0.0004-0.00010.0004-0.0001-0.00020.00010.00010.00060.0009-0.00080.0004-0.000399.908815.4315236.07
4700.0097-0.00050.01610.0158000.0005-0.00050.0002-0.0002-0.00010.0005-0.00090.000200.0010.0015-0.00140.00040.0003101.4666.3665237.313
480.0078-0.0359-0.00870.02720.05480.01640-0.0003-0.0013-0.00040.00070.00110-0.0004-0.0008-0.00110.0008-0.00020.0014-0.0012-0.0004105.85719.3514205.917
490-0.0063-0.000400.00740.004900-0.000100-0.000100000.00070.00020.0003-0.0005-0.000570.0818156.175256.784
500-0.00760.002700.004500000000-0.0001000.00030.00040-0.0007-0.000369.6632162.095256.574
510-0.00130.001700.000900-0.0001000000.00010-0.000100.00010-0.0008-0.000274.5514163.91257.741
520-0.0037-0.00150-0.00260.01630000-0.00010.0004-0.0002-0.00010.0001-0.00040.00050.00010.0002-0.0013-0.000365.9853161.58244.503
530-0.003-0.0020-0.00310.00290-0.000100.0002000.000100-0.0002-0.00020.00020.00040-0.000267.4645152.491254.801
540-0.0091-0.00360-0.00250.0020-0.00010.00010.0001-0.00010.00010.0001-0.00010-0.000100.00010.0003-0.0002-0.000564.9658148.531254.09
550.00070.00170.00010.00090.00320000000000-0.0002-0.00030.00030.0001-0.00050.000257.7088145.276239.729
560.00720.0037-0.012800.00290.0026-0.0001-0.00010.0002-0.00010.0001-0.00030.00030-0.0001-0.00040.00030.00060.0006-0.0005-0.000278.8062148.478250.8
570.0004-0.00090.00130-0.00040.00120000000000.0001000.00010068.1785159.325292.224
580.0003-0.00060.001100.00020.00090000.000100.000100000.00010.00020.00010-0.000167.2633157.73286.895
590.00020.00050.00010.00050.000200000000000.0001-0.00010.000100065.4953146.748286.919
600.00080.00210.002100.00090.00100-0.00010.000100.0001000000.00010.00010-0.000164.3414157.043283.004
610-0.000200.00050.00030.00010000000000.000100.000100070.1505146.039287.588
6200.0005-0.001700.00340.00030-0.000100.00010-0.000100000.00020.00030.0002-0.0004-0.000262.4261165.733276.751
630.00060.0013-0.002800.00220.0015000.000100-0.0001-0.000100-0.00010.00010.00020.0002-0.0003-0.000167.4722168.595274.863
640.0076-0.0018-0.013100.00470.003500.00010.000100.0001-0.00010-0.00020-0.0001-0.00010.00020.0003-0.0007-0.000266.1338167.16268.304
650.0138-0.0058-0.00250.0029-0.00640.00030-0.00030-0.0003-0.0001-0.00010.00010.00020.0001-0.00030.00030.00030-0.0001080.8717141.359214.151
66000.006500.0011000.00030.0003-0.00030.00010.0001-0.000200-0.00040.0001-0.00040.0003-0.0005-0.000570.1449149.649217.915
670.0076-0.0106-0.01450.0154-0.002200-0.00020.0002-0.00040.00030.00010.0002-0.0002-0.0003-0.00070.0016-0.000500.00040.000273.1608140.605218.815
680.0421-0.0314-0.02960.02110.0295000.00020.0004-0.0003-0.0001-0.0009-0.00060.00030-0.00160.00160.00220.0010.00130.00179.4243151.779186.082
690.0078-0.0137-0.00550.00510.00290.00050-0.0002-0.000100.00010.0002-0.0001-0.0002-0.0002-0.00020.0003-0.00070.0001-0.00010.000969.0743172.8215.305
700.00150.00440.00130.00470.0046000.0003000-0.00010.00010.00020-0.0008-0.0001-0.0003-0.0002-0.00060.000476.458162.266221.518
7100.02050.0070.01370.010400.00010.00010.00050.0002-0.00020.0002-0.00070.00020.0001-0.00080-0.0007-0.0004-0.00080.000773.7423171.07223.637
720.0464-0.0142-0.04180.0144-0.01540.0099-0.0002-0.00090.00070.00010.0003-0.0010.00070.0008-0.0001-0.0019-0.00110.00330.00070.00240.001373.4636160.711190.921
730.00490.0069-0.00140.00310.00130.0019-0.00010.00030000.00010-0.00010.0001-0.0001-0.0001-0.00100.0005-0.000379.0369109.228196.881
740.0010.00310.00140-0.0023000-0.00010-0.00010.00010.000100.0001-0.0002-0.0002-0.0003-0.0001-0.00010.000183.9846105.655196.22
750-0.00050.001500.001300000000.000100-0.00040.0002-0.0002-0.00010.00050.000287.3364108.857193.548
760.01830.00770.04360-0.02260.0145-0.00010.00040.00030.0004-0.00040.00030.00040.00010.0005-0.0001-0.0007-0.0002-0.00020.00120.000285.0706104.114208.644
770.00420.00770.01360.00180.00410-0.00010.0001-0.0001-0.0001-0.00010.00010.0001-0.00010.0001-0.00020-0.0006-0.0002-0.0001075.3802108.967200.089
78000.01330.00050.0024000.00020.0001-0.0001-0.00010.00010-0.00010.0001-0.00010-0.00040.0001-0.0003-0.000370.9491108.497201.985
790.00060.0006-0.00170-0.00080.00070-0.00010000.00010.0001-0.00010-0.00010.00010.00020.00030.0001068.739105.877217.612
800.0002-0.010.00350.0007-0.00670-0.000100.00030.000100-0.0001-0.000100.00010.0008-0.0017-0.00070.00030.000777.9828121.164202.179
810.001-0.00030.00020.0001-0.00040.00130000000.0001000.00010-0.00010.0001-0.00010.000171.1296101.267162.892
820.0012-0.0013-0.00050.0014-0.00330.00300-0.0001000.00010.0001000.00010-0.00030.0001-0.0002070.5086102.103168.726
830.00020-0.000300.0002000000000000-0.00010.00010060.9864105.653171.03
8400.00090.0003000.000500-0.0001000.00010.000100-0.00010-0.00030.0001-0.0001069.6635101.042173.133
850.0003-0.00010.00010.0002-0.00030.000200000000000-0.00010-0.00010.000161.9576109.812169.424
8600.0016-0.00210.00010.0015000.00010.00010000000.000100.0001-0.0001-0.0007-0.000178.100594.9688178.205
870-0.0006-0.00150.00130.00240.000200.0001000-0.000100.000100.00010.00010.0001-0.0001-0.0002083.364298.2667178.087
880.00460.01460.0060.00630.01320.0021000.00010-0.000200.000100.00020.0003-0.0001-0.0001-0.0001-0.0007083.381198.722185.041
890-0.00920.00860.0188-0.01970.00320000.00010.0002-0.00010.00010.0001-0.0002-0.00010.0007-0.0001-0.00010.00190.0003104.75103.859232.191
900-0.00610.01390-0.00730.00090-0.00010.00010.0002-0.0002-0.0002-0.00040.00050.00020.00010-0.0007-0.00060.001-0.000497.9085114.836226.836
910.0104-0.01180.00370.0047-0.00970.009800.000100.00020-0.00020.00030.000300.00010.00050.0007-0.00030.0010.0003102.355105.942221.08
920.01610.00690.04080.0112-0.00620.03150.00010.0002-0.00010.00030.0002-0.000500.0005-0.00030.0003-0.0001-0.00120.00130.0014-0.0013106.878116.25256.083
930.01250.00850.003700.00930.0001-0.0001-0.00030.00020.00090.0002-0.0001-0.00030-0.0001-0.0007-0.00050.00050.00070.0006-0.000789.0199132.543236.244
940.00330.0028-0.00480.00560.00040.00110-0.00010.00010.00030.0002-0.00010.00030.0002-0.0001-0.0001-0.0001-0.00030.00010.0005-0.000286.9841118.733234.482
950.0142-0.0142-0.00670-0.02750.00530.0001-0.00020.00010.0009-0.000200.0003-0.00020.0001-0.000100.00190.00050.0011-0.000982.1612126.996234.39
960.0008-0.00080.00620.0110.01270.01850-0.0001-0.00020.00010.0001-0.00050.00020.0002-0.00010.0002-0.0008-0.00050.00030-0.0006105.097126.876261.566
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|3 - 12}
2X-RAY DIFFRACTION2{A|21 - 28}
3X-RAY DIFFRACTION3{A|31 - 37}
4X-RAY DIFFRACTION4{A|59 - 85}
5X-RAY DIFFRACTION5{A|94 - 103}
6X-RAY DIFFRACTION6{A|110 - 118}
7X-RAY DIFFRACTION7{A|141 - 150}
8X-RAY DIFFRACTION8{A|152 - 173}
9X-RAY DIFFRACTION9{A|186 - 193}
10X-RAY DIFFRACTION10{A|199 - 208}
11X-RAY DIFFRACTION11{A|214 - 218}
12X-RAY DIFFRACTION12{A|241 - 248}
13X-RAY DIFFRACTION13{A|258 - 262}
14X-RAY DIFFRACTION14{B|6 - 11}
15X-RAY DIFFRACTION15{B|21 - 28}
16X-RAY DIFFRACTION16{B|60 - 70}
17X-RAY DIFFRACTION17{D|5 - 26}
18X-RAY DIFFRACTION18{D|39 - 55}
19X-RAY DIFFRACTION19{D|66 - 105}
20X-RAY DIFFRACTION20{D|133 - 202}
21X-RAY DIFFRACTION21{E|5 - 26}
22X-RAY DIFFRACTION22{E|39 - 55}
23X-RAY DIFFRACTION23{E|66 - 105}
24X-RAY DIFFRACTION24{E|133 - 202}
25X-RAY DIFFRACTION25{F|3 - 12}
26X-RAY DIFFRACTION26{F|21 - 28}
27X-RAY DIFFRACTION27{F|31 - 37}
28X-RAY DIFFRACTION28{F|59 - 85}
29X-RAY DIFFRACTION29{F|94 - 103}
30X-RAY DIFFRACTION30{F|110 - 118}
31X-RAY DIFFRACTION31{F|141 - 150}
32X-RAY DIFFRACTION32{F|152 - 173}
33X-RAY DIFFRACTION33{F|186 - 193}
34X-RAY DIFFRACTION34{F|199 - 208}
35X-RAY DIFFRACTION35{F|214 - 218}
36X-RAY DIFFRACTION36{F|241 - 248}
37X-RAY DIFFRACTION37{F|258 - 262}
38X-RAY DIFFRACTION38{G|6 - 11}
39X-RAY DIFFRACTION39{G|21 - 28}
40X-RAY DIFFRACTION40{G|60 - 70}
41X-RAY DIFFRACTION41{I|5 - 26}
42X-RAY DIFFRACTION42{I|39 - 55}
43X-RAY DIFFRACTION43{I|66 - 105}
44X-RAY DIFFRACTION44{I|133 - 202}
45X-RAY DIFFRACTION45{J|5 - 26}
46X-RAY DIFFRACTION46{J|39 - 55}
47X-RAY DIFFRACTION47{J|66 - 105}
48X-RAY DIFFRACTION48{J|133 - 202}
49X-RAY DIFFRACTION49{K|3 - 12}
50X-RAY DIFFRACTION50{K|21 - 28}
51X-RAY DIFFRACTION51{K|31 - 37}
52X-RAY DIFFRACTION52{K|59 - 85}
53X-RAY DIFFRACTION53{K|94 - 103}
54X-RAY DIFFRACTION54{K|110 - 118}
55X-RAY DIFFRACTION55{K|141 - 150}
56X-RAY DIFFRACTION56{K|152 - 173}
57X-RAY DIFFRACTION57{K|186 - 193}
58X-RAY DIFFRACTION58{K|199 - 208}
59X-RAY DIFFRACTION59{K|214 - 218}
60X-RAY DIFFRACTION60{K|241 - 248}
61X-RAY DIFFRACTION61{K|258 - 262}
62X-RAY DIFFRACTION62{L|6 - 11}
63X-RAY DIFFRACTION63{L|21 - 28}
64X-RAY DIFFRACTION64{L|60 - 70}
65X-RAY DIFFRACTION65{N|5 - 26}
66X-RAY DIFFRACTION66{N|39 - 55}
67X-RAY DIFFRACTION67{N|66 - 105}
68X-RAY DIFFRACTION68{N|133 - 202}
69X-RAY DIFFRACTION69{O|5 - 26}
70X-RAY DIFFRACTION70{O|39 - 55}
71X-RAY DIFFRACTION71{O|66 - 105}
72X-RAY DIFFRACTION72{O|133 - 202}
73X-RAY DIFFRACTION73{P|3 - 12}
74X-RAY DIFFRACTION74{P|21 - 28}
75X-RAY DIFFRACTION75{P|31 - 37}
76X-RAY DIFFRACTION76{P|59 - 85}
77X-RAY DIFFRACTION77{P|94 - 103}
78X-RAY DIFFRACTION78{P|110 - 118}
79X-RAY DIFFRACTION79{P|141 - 150}
80X-RAY DIFFRACTION80{P|152 - 173}
81X-RAY DIFFRACTION81{P|186 - 193}
82X-RAY DIFFRACTION82{P|199 - 208}
83X-RAY DIFFRACTION83{P|214 - 218}
84X-RAY DIFFRACTION84{P|241 - 248}
85X-RAY DIFFRACTION85{P|258 - 262}
86X-RAY DIFFRACTION86{Q|6 - 11}
87X-RAY DIFFRACTION87{Q|21 - 28}
88X-RAY DIFFRACTION88{Q|60 - 70}
89X-RAY DIFFRACTION89{T|5 - 26}
90X-RAY DIFFRACTION90{T|37 - 52}
91X-RAY DIFFRACTION91{T|58 - 97}
92X-RAY DIFFRACTION92{T|133 - 202}
93X-RAY DIFFRACTION93{S|5 - 26}
94X-RAY DIFFRACTION94{S|39 - 55}
95X-RAY DIFFRACTION95{S|66 - 105}
96X-RAY DIFFRACTION96{S|133 - 202}

+
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

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る