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- PDB-5d6y: Crystal structure of double tudor domain of human lysine demethyl... -

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基本情報

登録情報
データベース: PDB / ID: 5d6y
タイトルCrystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3
要素
  • Lysine-specific demethylase 4A
  • peptide H3K23me3 (19-28)
キーワードOXIDOREDUCTASE / double tudor domain / reader domain / Structural Genomics / PSI-2 / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro
機能・相同性
機能・相同性情報


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H4K20me2 reader activity / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H4K20me2 reader activity / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / Chromatin modifying enzymes / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / positive regulation of neuron differentiation / negative regulation of autophagy / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / response to nutrient levels / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / fibrillar center / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / cadherin binding / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol
類似検索 - 分子機能
Vcp-like ATPase; Chain A, domain 2 - #70 / : / : / : / Vcp-like ATPase; Chain A, domain 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 ...Vcp-like ATPase; Chain A, domain 2 - #70 / : / : / : / Vcp-like ATPase; Chain A, domain 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / SH3 type barrels. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Roll / Roll / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Lysine-specific demethylase 4A / Histone H3.1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 解像度: 2.287 Å
データ登録者Wang, F. / Su, Z. / Miller, M.D. / Denu, J.M. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM098248 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R37GM059785-15/P250VA 米国
引用ジャーナル: Nat Commun / 年: 2016
タイトル: Reader domain specificity and lysine demethylase-4 family function.
著者: Su, Z. / Wang, F. / Lee, J.H. / Stephens, K.E. / Papazyan, R. / Voronina, E. / Krautkramer, K.A. / Raman, A. / Thorpe, J.J. / Boersma, M.D. / Kuznetsov, V.I. / Miller, M.D. / Taverna, S.D. / ...著者: Su, Z. / Wang, F. / Lee, J.H. / Stephens, K.E. / Papazyan, R. / Voronina, E. / Krautkramer, K.A. / Raman, A. / Thorpe, J.J. / Boersma, M.D. / Kuznetsov, V.I. / Miller, M.D. / Taverna, S.D. / Phillips, G.N. / Denu, J.M.
履歴
登録2015年8月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年2月10日Provider: repository / タイプ: Initial release
改定 1.12016年12月7日Group: Database references
改定 1.22017年9月20日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32019年12月25日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42025年4月2日Group: Data collection / Database references ...Data collection / Database references / Refinement description / 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Lysine-specific demethylase 4A
a: peptide H3K23me3 (19-28)
B: Lysine-specific demethylase 4A
b: peptide H3K23me3 (19-28)
C: Lysine-specific demethylase 4A
c: peptide H3K23me3 (19-28)
D: Lysine-specific demethylase 4A
d: peptide H3K23me3 (19-28)
E: Lysine-specific demethylase 4A
F: Lysine-specific demethylase 4A


分子量 (理論値)分子数
合計 (水以外)86,83610
ポリマ－86,83610
非ポリマー00
水3,891216
1
A: Lysine-specific demethylase 4A
a: peptide H3K23me3 (19-28)


分子量 (理論値)分子数
合計 (水以外)14,8452
ポリマ－14,8452
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Lysine-specific demethylase 4A
b: peptide H3K23me3 (19-28)


分子量 (理論値)分子数
合計 (水以外)14,8452
ポリマ－14,8452
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Lysine-specific demethylase 4A
c: peptide H3K23me3 (19-28)


分子量 (理論値)分子数
合計 (水以外)14,8452
ポリマ－14,8452
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Lysine-specific demethylase 4A
d: peptide H3K23me3 (19-28)


分子量 (理論値)分子数
合計 (水以外)14,8452
ポリマ－14,8452
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Lysine-specific demethylase 4A


分子量 (理論値)分子数
合計 (水以外)13,7271
ポリマ－13,7271
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Lysine-specific demethylase 4A


分子量 (理論値)分子数
合計 (水以外)13,7271
ポリマ－13,7271
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)106.159, 106.159, 79.206
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
12chain a
22chain b
13chain c
23chain d

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTHRTHRchain AAA898 - 10058 - 115
21SERSERTHRTHRchain BBC898 - 10058 - 115
31SERSERVALVALchain CCE898 - 10038 - 113
41SERSERVALVALchain DDG898 - 10038 - 113
51SERSERTHRTHRchain EEI898 - 10058 - 115
61SERSERTHRTHRchain FFJ898 - 10058 - 115
12GLNGLNLYSLYSchain aaB19 - 271 - 9
22GLNGLNLYSLYSchain bbD19 - 271 - 9
13LEULEUARGARGchain ccF20 - 262 - 8
23LEULEUARGARGchain ddH20 - 262 - 8

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質
Lysine-specific demethylase 4A / JmjC domain-containing histone demethylation protein 3A / Jumonji domain-containing protein 2A


分子量: 13727.131 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)
参照: UniProt: O75164, 酸化還元酵素; 電子対供与作用を持つ; 分子酸素を取り込むないしは分子酸素を還元する; 2- ...参照: UniProt: O75164, 酸化還元酵素; 電子対供与作用を持つ; 分子酸素を取り込むないしは分子酸素を還元する; 2-オキソグルタル酸類を片方の電子供与体とする; 酸素分をそれぞれの電子供与体に取り込む
#2: タンパク質・ペプチド
peptide H3K23me3 (19-28)


分子量: 1118.350 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P68431*PLUS
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 216 / 由来タイプ: 天然 / 式: H2O
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: 2.97 Å3/Da / 溶媒含有率: 58.55 %
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: Protein-peptide Solution (30mg/ml KDM4A DTD and 3.5mg/ml peptide in 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.2M sodium phosphate monobasic, ...詳細: Protein-peptide Solution (30mg/ml KDM4A DTD and 3.5mg/ml peptide in 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.2M sodium phosphate monobasic, 0.8M potassium phosphate dibasic, 0.1M CAPS/sodium hydroxide pH10.5, 0.2M lithium sulfate) Cryoprotected with additional 20% glycerol

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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: APS / ビームライン: 21-ID-F / 波長: 0.979 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2014年10月23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: 0.979 Å / 相対比: 1
反射解像度: 2.287→50 Å / Num. obs: 82623 / % possible obs: 91.5 % / Observed criterion σ(I): -3 / 冗長度: 5.68 % / Biso Wilson estimate: 35.63 Å2 / Rmerge F obs: 0.993 / Rmerge(I) obs: 0.217 / Rrim(I) all: 0.239 / Χ2: 0.959 / Net I/σ(I): 9.15 / Num. measured all: 466605
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)最高解像度 (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.29-2.420.3351.7521.127002914476144231.9799.6
2.42-2.590.5921.3621.828056113754137531.496100
2.59-2.80.8160.7913.12493581270086990.87168.5
2.8-3.060.9220.4925.136890911720117190.54100
3.06-3.420.980.2589.155967510574102320.28396.8
3.42-3.940.9910.13415.2534507935661380.14765.6
3.94-4.80.9970.06924.246435788678850.076100
4.8-6.690.9970.0723.4236634622862280.077100
6.690.9990.04429.1520497359035460.04998.8

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解析

ソフトウェア
名称バージョン分類
XSCALEデータスケーリング
PHENIX精密化
PDB_EXTRACT3.15データ抽出
XDSデータ削減
PHENIX位相決定
精密化解像度: 2.287→28.581 Å / SU ML: 0.33 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 30.44 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2947 3668 4.45 %
Rwork0.2636 78808 -
obs0.265 82476 91.4 %
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 max: 177.26 Å2 / Biso mean: 59.3756 Å2 / Biso min: 20.83 Å2
精密化ステップサイクル: final / 解像度: 2.287→28.581 Å
タンパク質核酸リガンド溶媒全体
原子数5317 0 0 216 5533
Biso mean---48.3 -
残基数----671
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0115428
X-RAY DIFFRACTIONf_angle_d1.3917357
X-RAY DIFFRACTIONf_chiral_restr0.066796
X-RAY DIFFRACTIONf_plane_restr0.008964
X-RAY DIFFRACTIONf_dihedral_angle_d14.8911937
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3037X-RAY DIFFRACTION12.379TORSIONAL
12B3037X-RAY DIFFRACTION12.379TORSIONAL
13C3037X-RAY DIFFRACTION12.379TORSIONAL
14D3037X-RAY DIFFRACTION12.379TORSIONAL
15E3037X-RAY DIFFRACTION12.379TORSIONAL
16F3037X-RAY DIFFRACTION12.379TORSIONAL
21a64X-RAY DIFFRACTION12.379TORSIONAL
22b64X-RAY DIFFRACTION12.379TORSIONAL
31c38X-RAY DIFFRACTION12.379TORSIONAL
32d38X-RAY DIFFRACTION12.379TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2867-2.31680.32561520.33713183333596
2.3168-2.34850.33961430.3253237338099
2.3485-2.38210.37121600.337233613521100
2.3821-2.41760.36971440.34233143458100
2.4176-2.45540.34691620.328933343496100
2.4554-2.49560.31051520.333532943446100
2.4956-2.53860.36351560.320633453501100
2.5386-2.58470.34261560.313932943450100
2.5847-2.63440.3631560.31813277343398
2.6344-2.68820.277820.2661192113
2.6882-2.74660.42391390.31592821296098
2.7466-2.81040.35231400.301533163456100
2.8104-2.88060.28941560.293833503506100
2.8806-2.95840.3121520.28433413493100
2.9584-3.04540.29231640.276832663430100
3.0454-3.14360.29231600.278332883448100
3.1436-3.25580.2871600.246532863446100
3.2558-3.38590.26111480.245133693517100
3.3859-3.53980.2661880.24041915200358
3.5398-3.7260.2996920.23822199229167
3.726-3.95890.31461120.24052425253773
3.9589-4.26360.2631600.217133703530100
4.2636-4.6910.22521480.216132793427100
4.691-5.36590.28631600.219132903450100
5.3659-6.74580.34841400.266533283468100
6.7458-28.5830.22261660.26433073473100
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)
13.29360.91632.28260.49710.18382.52171.1332-0.4754-0.6245-0.05950.34821.26210.6675-1.34260.05310.43-0.2854-0.13871.20310.15540.411134.1245-40.21869.5639
23.98360.90432.71344.44840.12772.51130.34790.2563-0.10310.3746-0.7389-0.42340.48020.0983-0.10140.5554-0.0216-0.1020.26970.11140.283745.0675-39.77027.5191
31.82831.71911.01164.8143-1.05083.244-0.3123-0.30421.02530.27990.03530.3175-0.3922-0.05380.07260.40790.01450.08470.52970.28580.650353.6832-35.82192.5093
42.01041.44322.52511.30650.01852.4584-0.0668-0.233-0.127-0.00290.072-0.1671-0.3266-0.36420.03340.18430.028-0.0050.37770.03970.280337.551-38.9596-3.8973
51.44771.01470.66732.3251.00110.8486-0.26090.426-0.3965-0.41270.2836-0.3017-0.12360.1371-0.0280.364-0.07180.10370.3101-0.03950.427235.27-40.6092-20.824
62.94641.13471.43452.86180.51832.74590.0895-0.0399-0.0942-0.6503-0.4728-0.31450.1316-0.86890.06390.3146-0.06730.16870.1590.00620.322724.4461-39.9983-20.7876
70.5310.26111.2541.93350.12452.0176-0.50910.18730.078-1.12180.4119-0.1239-0.48770.56180.06250.4997-0.19550.13780.4512-0.10910.354938.7244-37.8885-25.7889
82.69781.1931.39840.86030.06032.43760.12350.59350.1527-0.70940.75721.079-0.33130.3973-0.16940.4304-0.14330.19180.3386-0.07540.287634.8174-44.3839-25.3345
91.97921.90281.36370.88140.02482.50870.2819-0.7183-0.4819-0.0464-0.1064-0.23980.2492-0.63440.06850.15370.0021-0.03820.36530.05320.328835.9427-38.6504-1.9319
103.16380.35651.30252.3043-0.59753.22130.0106-0.1026-0.23280.20780.1286-0.09720.2665-0.52230.00690.3416-0.0292-0.05210.45150.08790.335743.0978-38.28613.097
114.8032-1.47260.07894.5854-0.11075.2705-0.20990.2611-0.44360.70670.0373-0.08760.69330.22290.18090.4071-0.00360.08470.3761-0.05490.605643.3555-45.8439-17.4646
122.27032.03771.11532.42032.17812.97930.23810.7370.2591-0.17211.2196-0.8181-0.99221.23960.10770.9748-0.7101-0.19120.7318-0.9019-1.639117.7424-49.6644-34.244
135.33950.71921.18543.32462.6122.0985-0.26140.4713-0.14460.65690.09550.1306-0.08130.0189-0.05770.34530.08530.01610.401-0.14330.318211.8997-58.9316-32.1602
144.5631-0.4296-0.16342.34771.52692.94170.03340.59191.1011-0.5533-0.32380.19110.0124-0.03360.08990.525-0.02330.16710.4363-0.13650.53834.1665-64.3966-27.1806
152.16521.54591.10911.18181.71452.0577-0.1090.0244-0.2851-0.18740.16260.0746-0.38370.19540.0650.3096-0.07160.02130.2551-00.300814.945-52.0041-20.7456
163.31240.18341.11011.37150.48870.93940.4383-0.5246-0.6563-0.1229-0.4138-0.4820.39080.1923-0.09530.2294-0.0595-0.00780.340.13280.476619.1235-56.237-5.1868
171.69170.60871.38970.78051.04492.50030.1192-0.5543-0.14190.495-0.12320.35980.07640.02370.17650.26170.0040.04470.3780.07820.322115.5458-44.0065-2.0809
183.5090.89091.07612.09391.04032.8666-0.230.1363-0.1450.1244-0.0458-0.1369-0.17240.09940.10720.2295-0.02980.0350.35210.13080.261322.4111-41.1682-3.8334
191.4012-0.38670.60420.47780.79011.5439-0.5157-1.1534-0.4377-0.05780.1986-0.02590.5128-0.38290.09740.2787-0.0516-0.01890.68360.16370.42113.4385-52.49551.1426
203.09041.65471.12980.77611.26011.8498-0.1369-0.1783-0.3554-0.16610.092-0.1179-0.20350.23530.04030.2713-0.04880.04790.2339-0.00520.29617.4142-51.1195-14.6162
212.66561.1416-0.01512.6391.62413.2389-0.19640.3836-0.4302-0.18010.2134-0.1894-0.43770.56550.03290.3896-0.05050.06150.3741-0.12760.301811.5587-56.4349-27.7217
224.0391-1.15191.24885.7931-0.20886.32560.17980.4196-0.29030.3007-0.6032-0.13160.50240.28160.37720.3494-0.016-0.04190.30490.06150.678318.0334-60.4604-7.1831
233.2910.8656-1.20824.0476-0.91724.5560.573-0.27060.21460.611-0.26930.1887-0.9270.62170.23320.6777-0.22980.15440.48790.00670.28671.9668-47.585912.7971
240.4343-0.186-2.03522.1986-2.29322.86170.0971-0.32090.04870.1679-0.37220.012-0.21720.4720.19550.29-0.0695-0.01350.27940.00570.33141.9671-44.8893-2.3007
252.26210.7747-0.46522.1202-0.67751.8459-0.0563-0.03250.1342-0.1982-0.1338-0.0075-0.22860.10280.1720.2564-0.0317-0.02230.16520.020.30894.4031-42.0918-13.0162
261.64412.5288-2.04614.0793-1.29675.39790.7646-0.46310.00780.044-0.49380.4754-0.22960.24910.27450.382-0.0570.07270.44670.00830.27343.5397-47.55518.6072
274.53360.6024-3.34175.46622.30836.5295-0.5381-0.69980.5929-0.32920.66860.3712-0.48250.1388-0.44050.3124-0.0294-0.07610.1740.07820.3499-4.3239-49.5621-9.7409
284.4390.037-1.66612.6378-1.17824.60030.13760.90570.58280.30720.2553-0.02840.0625-1.19780.26440.2668-0.06730.13130.89080.21570.293640.2353-25.5075-37.4452
291.8052-1.8704-3.11470.435-0.09882.9061-0.25590.6618-0.0225-0.102-0.06560.00920.4851-0.63420.25540.2821-0.12170.01110.4265-0.00460.374836.1667-25.657-26.9605
304.2434-0.0018-1.68411.5226-0.78234.5098-0.4919-0.48961.18840.2494-0.93720.45230.5224-0.55150.13610.27150.0892-0.01590.2439-0.0290.239941.4064-20.8965-12.7211
316.50790.1848-1.97131.993-2.69134.27210.2151-0.82080.09160.0566-0.1638-0.0824-0.10090.05630.31530.27170.02510.05970.3434-0.02250.292432.1256-28.189-6.7379
323.53350.9948-0.57471.08890.19462.4102-0.2128-0.08360.28450.31380.45580.47180.0416-0.00910.10530.23790.0733-0.00380.3254-0.09280.340830.491-23.2053-6.1178
332.36370.7882-1.63141.48650.34053.7914-0.2630.18150.0718-0.3263-0.0254-0.0301-0.0136-0.32920.21560.1687-0.01640.00950.2391-0.02330.267237.4011-24.8091-16.8195
345.2996-0.0537-2.32580.3042-0.97875.8214-0.02060.69360.2528-0.12670.01980.42650.0389-0.49230.3040.3733-0.03550.09190.39680.03760.287739.408-26.8366-33.2573
354.36240.68371.08580.94-1.8224.9770.4984-0.48050.6185-0.39280.05160.08190.2224-0.8757-0.36240.1104-0.01960.00080.3667-0.10970.425745.0578-21.0254-14.9349
363.8503-1.6325-2.29222.69463.02773.5469-0.41690.1069-1.15190.52180.1693-0.49932.75160.63610.16561.4650.1486-0.03751.2140.18350.868414.349-8.7734.9311
371.4019-0.838-2.00292.14823.1164.9914-0.4186-0.4908-0.45550.3492-0.34060.00340.87971.41670.33570.95190.16880.05260.94380.29770.734512.6058-7.902-6.4865
382.7225-1.3406-1.31732.25373.02554.38181.0412-0.54790.7612-0.53722.6412-3.278-0.15730.8324-0.04130.83081.2714-0.57350.39923.15-1.994718.6583-7.1141-23.1177
390.4403-0.3748-0.56680.2290.47430.93820.20830.1829-0.55510.74630.55920.80530.0933-0.88490.34920.99680.14920.17841.23840.16680.508314.4439-19.1564-26.6918
402.794-0.04-1.06341.35631.82794.4164-0.12330.31580.1039-0.11720.10420.31710.0484-0.62090.23230.83070.1665-0.08311.32630.2460.799816.8865-16.1987-27.6014
411.4952-0.6472-2.4321.71212.14283.2607-0.5285-0.2050.50080.67820.2092-0.35371.6860.61890.21771.07880.30660.02081.01550.12460.592414.5341-9.2316-7.6131
421.4425-0.07850.95193.482-3.22383.90540.10910.38940.2402-0.2902-0.4888-0.85560.39461.0601-0.00870.9706-0.03040.14811.3078-0.25460.9321-1.3259-11.988-27.4348
431.173-0.60661.51982.5504-3.13253.00870.43650.0947-1.211-0.3125-0.55930.19691.2576-0.62870.09691.31480.33870.36460.6425-0.24060.70760.2736-18.4525-11.8473
44-0.02960.02790.02760.05030.01610.03840.42330.76331.4072-0.1013-0.3652-0.3529-1.36790.37210.221.79660.06080.11780.84160.07491.03939.6082-22.14551.9125
451.5210.83350.67031.9707-1.69543.5820.3762-0.34290.7161.3605-0.2546-0.3063-0.8862-0.01950.13671.4062-0.27060.11010.9132-0.22151.13885.7678-23.042.5944
460.5082-0.20650.56091.9633-2.69592.4282-0.06170.0782-0.0875-0.7782-0.40670.32441.07490.6190.09541.27760.15610.16080.8971-0.06730.60860.6388-17.2662-16.3081
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 898 through 903 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 904 through 908 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 909 through 913 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 914 through 932 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 933 through 950 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 951 through 961 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 962 through 971 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 972 through 978 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 979 through 990 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 991 through 1005 )A0
11X-RAY DIFFRACTION11chain 'a' and (resid 19 through 27 )a0
12X-RAY DIFFRACTION12chain 'B' and (resid 898 through 903 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 904 through 908 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 909 through 913 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 914 through 932 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 933 through 942 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 943 through 950 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 951 through 961 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 962 through 971 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 972 through 990 )B0
21X-RAY DIFFRACTION21chain 'B' and (resid 991 through 1005 )B0
22X-RAY DIFFRACTION22chain 'b' and (resid 19 through 27 )b0
23X-RAY DIFFRACTION23chain 'C' and (resid 898 through 913 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 914 through 942 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 943 through 989 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 990 through 1003 )C0
27X-RAY DIFFRACTION27chain 'c' and (resid 20 through 26 )c0
28X-RAY DIFFRACTION28chain 'D' and (resid 898 through 913 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 914 through 932 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 933 through 942 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 943 through 950 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 951 through 966 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 967 through 989 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 990 through 1003 )D0
35X-RAY DIFFRACTION35chain 'd' and (resid 20 through 26 )d0
36X-RAY DIFFRACTION36chain 'E' and (resid 898 through 908 )E0
37X-RAY DIFFRACTION37chain 'E' and (resid 909 through 932 )E0
38X-RAY DIFFRACTION38chain 'E' and (resid 933 through 942 )E0
39X-RAY DIFFRACTION39chain 'E' and (resid 943 through 950 )E0
40X-RAY DIFFRACTION40chain 'E' and (resid 951 through 972 )E0
41X-RAY DIFFRACTION41chain 'E' and (resid 973 through 1005 )E0
42X-RAY DIFFRACTION42chain 'F' and (resid 898 through 913 )F0
43X-RAY DIFFRACTION43chain 'F' and (resid 914 through 942 )F0
44X-RAY DIFFRACTION44chain 'F' and (resid 943 through 950 )F0
45X-RAY DIFFRACTION45chain 'F' and (resid 951 through 971 )F0
46X-RAY DIFFRACTION46chain 'F' and (resid 972 through 1005 )F0

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る