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- PDB-5dlq: Crystal structure of RanGTP-Exportin 4-eIF5A complex -

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基本情報

登録情報
データベース: PDB / ID: 5dlq
タイトルCrystal structure of RanGTP-Exportin 4-eIF5A complex
要素
  • Eukaryotic translation initiation factor 5A-1
  • Exportin-4
  • GTP-binding nuclear protein Ran
キーワードPROTEIN TRANSPORT / Active transport / Nuclear transport / Nuclear export Importin-Beta family / Exportin / HEAT repeat / GTPase / Nucleotide binding / eIF5A / Translation factor / Hypusine / Unusual amino acid
機能・相同性
機能・相同性情報


Hypusine synthesis from eIF5A-lysine / positive regulation of translational termination / annulate lamellae / positive regulation of translational elongation / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / nuclear export signal receptor activity / manchette / cellular response to mineralocorticoid stimulus ...Hypusine synthesis from eIF5A-lysine / positive regulation of translational termination / annulate lamellae / positive regulation of translational elongation / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / nuclear export signal receptor activity / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MicroRNA (miRNA) biogenesis / DNA metabolic process / dynein intermediate chain binding / mitotic sister chromatid segregation / translational elongation / ribosomal large subunit export from nucleus / spermatid development / viral process / positive regulation of protein binding / U6 snRNA binding / sperm flagellum / translation elongation factor activity / nuclear pore / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / centriole / protein export from nucleus / mitotic spindle organization / tumor necrosis factor-mediated signaling pathway / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / recycling endosome / cellular response to virus / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / nuclear envelope / protein transport / mitotic cell cycle / ribosome binding / G protein activity / actin cytoskeleton organization / midbody / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / synapse / endoplasmic reticulum membrane / chromatin binding / chromatin / GTP binding / protein-containing complex binding / nucleolus / magnesium ion binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
類似検索 - 分子機能
Exportin 4/7-like / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Exportin-1, C-terminal ...Exportin 4/7-like / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Exportin-1, C-terminal / CRM1 C terminal / Ran GTPase / Small GTPase Ran-type domain profile. / SH3 type barrels. - #30 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Nucleic acid-binding proteins / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / SH3 type barrels. / Armadillo-like helical / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Small GTP-binding protein domain / Alpha Horseshoe / Translation protein SH3-like domain superfamily / Armadillo-type fold / Ribosomal protein L2, domain 2 / Roll / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
GUANOSINE-5'-TRIPHOSPHATE / GTP-binding nuclear protein Ran / Eukaryotic translation initiation factor 5A-1 / Exportin-4
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 3.2 Å
データ登録者Aksu, M. / Trakhanov, S. / Gorlich, D.
資金援助 ドイツ, 1件
組織認可番号国
ドイツ
引用ジャーナル: Nat Commun / 年: 2016
タイトル: Structure of the exportin Xpo4 in complex with RanGTP and the hypusine-containing translation factor eIF5A.
著者: Aksu, M. / Trakhanov, S. / Gorlich, D.
履歴
登録2015年9月7日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02016年6月22日Provider: repository / タイプ: Initial release
改定 1.12016年6月29日Group: Database references
改定 1.22024年10月16日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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
B: Exportin-4
C: GTP-binding nuclear protein Ran
F: Eukaryotic translation initiation factor 5A-1
A: Exportin-4
D: GTP-binding nuclear protein Ran
E: Eukaryotic translation initiation factor 5A-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)324,44410
ポリマ－323,3496
非ポリマー1,0954
水00
1
B: Exportin-4
C: GTP-binding nuclear protein Ran
F: Eukaryotic translation initiation factor 5A-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)162,2225
ポリマ－161,6743
非ポリマー5472
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-29 kcal/mol
Surface area58630 Å2
手法PISA
2
A: Exportin-4
D: GTP-binding nuclear protein Ran
E: Eukaryotic translation initiation factor 5A-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)162,2225
ポリマ－161,6743
非ポリマー5472
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-28 kcal/mol
Surface area57920 Å2
手法PISA
単位格子
Length a, b, c (Å)98.616, 98.616, 726.864
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain C and (resseq 7:75 or (resid 76 and (name...
21(chain D and (resseq 7:33 or (resid 34 and (name...
12(chain A and (resseq 9 or (resid 10 and (name...
22(chain B and (resseq 9 or (resid 10 and (name...
13(chain E and (resseq 16:67 or (resid 68 and (name...
23(chain F and (resseq 16:17 or (resid 18 and (name...

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
111PROPROLEULEU(chain C and (resseq 7:75 or (resid 76 and (name...CB7 - 753 - 71
121ARGARGARGARG(chain C and (resseq 7:75 or (resid 76 and (name...CB7672
131PROPROMETMET(chain C and (resseq 7:75 or (resid 76 and (name...CB7 - 1793 - 175
141PROPROMETMET(chain C and (resseq 7:75 or (resid 76 and (name...CB7 - 1793 - 175
151PROPROMETMET(chain C and (resseq 7:75 or (resid 76 and (name...CB7 - 1793 - 175
161PROPROMETMET(chain C and (resseq 7:75 or (resid 76 and (name...CB7 - 1793 - 175
211PROPROGLYGLY(chain D and (resseq 7:33 or (resid 34 and (name...DE7 - 333 - 29
221GLUGLUGLUGLU(chain D and (resseq 7:33 or (resid 34 and (name...DE3430
231PROPROALAALA(chain D and (resseq 7:33 or (resid 34 and (name...DE7 - 1783 - 174
241PROPROALAALA(chain D and (resseq 7:33 or (resid 34 and (name...DE7 - 1783 - 174
251PROPROALAALA(chain D and (resseq 7:33 or (resid 34 and (name...DE7 - 1783 - 174
261PROPROALAALA(chain D and (resseq 7:33 or (resid 34 and (name...DE7 - 1783 - 174
112PROPROPROPRO(chain A and (resseq 9 or (resid 10 and (name...AD99
122GLUGLUGLUGLU(chain A and (resseq 9 or (resid 10 and (name...AD1010
132PROPROGLYGLY(chain A and (resseq 9 or (resid 10 and (name...AD9 - 11459 - 1107
142PROPROGLYGLY(chain A and (resseq 9 or (resid 10 and (name...AD9 - 11459 - 1107
152PROPROGLYGLY(chain A and (resseq 9 or (resid 10 and (name...AD9 - 11459 - 1107
212PROPROPROPRO(chain B and (resseq 9 or (resid 10 and (name...BA99
222GLUGLUGLUGLU(chain B and (resseq 9 or (resid 10 and (name...BA1010
232ALAALALEULEU(chain B and (resseq 9 or (resid 10 and (name...BA4 - 11484 - 1110
242ALAALALEULEU(chain B and (resseq 9 or (resid 10 and (name...BA4 - 11484 - 1110
252ALAALALEULEU(chain B and (resseq 9 or (resid 10 and (name...BA4 - 11484 - 1110
113ALAALALYSLYS(chain E and (resseq 16:67 or (resid 68 and (name...EF16 - 673 - 54
123LYSLYSLYSLYS(chain E and (resseq 16:67 or (resid 68 and (name...EF6855
133ALAALAMETMET(chain E and (resseq 16:67 or (resid 68 and (name...EF16 - 1523 - 139
143ALAALAMETMET(chain E and (resseq 16:67 or (resid 68 and (name...EF16 - 1523 - 139
153ALAALAMETMET(chain E and (resseq 16:67 or (resid 68 and (name...EF16 - 1523 - 139
163ALAALAMETMET(chain E and (resseq 16:67 or (resid 68 and (name...EF16 - 1523 - 139
173ALAALAMETMET(chain E and (resseq 16:67 or (resid 68 and (name...EF16 - 1523 - 139
213ALAALATHRTHR(chain F and (resseq 16:17 or (resid 18 and (name...FC16 - 173 - 4
223PHEPHEPHEPHE(chain F and (resseq 16:17 or (resid 18 and (name...FC185
233SERSERMETMET(chain F and (resseq 16:17 or (resid 18 and (name...FC15 - 1522 - 139
243SERSERMETMET(chain F and (resseq 16:17 or (resid 18 and (name...FC15 - 1522 - 139
253SERSERMETMET(chain F and (resseq 16:17 or (resid 18 and (name...FC15 - 1522 - 139
263SERSERMETMET(chain F and (resseq 16:17 or (resid 18 and (name...FC15 - 1522 - 139

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質 Exportin-4 / Exp4


分子量: 125894.023 Da / 分子数: 2 / 変異: H1085Y / 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: Xpo4, Kiaa1721 / 発現宿主: Escherichia coli K-12 (大腸菌) / Variant (発現宿主): Top10 F' / 参照: UniProt: Q9ESJ0
#2: タンパク質 GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


分子量: 20192.484 Da / 分子数: 2 / 変異: Q69L / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RAN, ARA24, OK/SW-cl.81 / 発現宿主: Escherichia coli K-12 (大腸菌) / Variant (発現宿主): Top10 F' / 参照: UniProt: P62826
#3: タンパク質 Eukaryotic translation initiation factor 5A-1 / eIF-5A1 / Eukaryotic initiation factor 5A isoform 1 / eIF-5A / Rev-binding factor / eIF-4D


分子量: 15587.991 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: EIF5A / 発現宿主: Escherichia coli BL21 (大腸菌) / Variant (発現宿主): NEB express / 参照: UniProt: P63241
#4: 化合物 ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP


分子量: 523.180 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / コメント: GTP, エネルギー貯蔵分子*YM
#5: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg
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: 2

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試料調製

結晶
IDマシュー密度 (Å3/Da)溶媒含有率 (%)
13.1661.08
23.1661.1
結晶化
温度 (K)Crystal-ID手法pH詳細
2931蒸気拡散法, ハンギングドロップ法6.26Peg 400, MES
2932蒸気拡散法, ハンギングドロップ法6.26Peg 400, MES, DTT

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データ収集

回折
ID平均測定温度 (K)Crystal-ID
11001
21002
放射光源
由来サイトビームラインID波長 (Å)
シンクロトロンSLS X10SA11
シンクロトロンSLS X10SA20.9786
検出器
タイプID検出器日付
DECTRIS PILATUS 6M-F1PIXEL2014年6月13日
DECTRIS PILATUS 6M-F2PIXEL2014年7月10日
放射
IDプロトコル単色(M)・ラウエ(L)散乱光タイプWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
放射波長
ID波長 (Å)相対比
111
20.97861
反射解像度: 3→49.407 Å / Num. obs: 157964 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / 冗長度: 9.9 % / Biso Wilson estimate: 106.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.097 / Χ2: 1.008 / Net I/σ(I): 14.55 / Num. measured all: 828210
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)最高解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.0810.21.6120.995847411673115580.4551.899
3.08-3.161.1291.476189211428114260.6591.251100
3.16-3.250.8671.895916311019110180.7730.962100
3.25-3.350.6162.625696210795107940.8340.685100
3.35-3.460.4473.555276110386103770.9020.49999.9
3.46-3.590.3414.735264610113101120.940.379100
3.59-3.720.266.2252827977197710.9650.288100
3.72-3.870.1818.6750739939993990.9830.2100
3.87-4.050.1410.9847266897489740.9880.155100
4.05-4.240.10613.7442961860786000.9920.11999.9
4.24-4.470.08317.2841815824882440.9950.092100
4.47-4.740.06721.3241014773477330.9970.075100
4.74-5.070.0623.738047717871750.9970.067100
5.07-5.480.06223.0235508687868760.9970.069100
5.48-60.05824.9131723612561250.9970.064100
6-6.710.0529.131212566456640.9980.056100
6.71-7.750.03439.9526220493849340.9990.03899.9
7.75-9.490.02157.39209114188418510.02499.9
9.49-13.420.01676.6172853240324010.018100
13.420.01479.0387841790175910.01598.3

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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
XSCALEデータスケーリング
PDB_EXTRACT3.15データ抽出
XDSデータ削減
PHENIX位相決定
精密化構造決定の手法: 単波長異常分散 / 解像度: 3.2→49.407 Å / SU ML: 0.4 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 27.55 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2695 3494 5 %
Rwork0.2211 66335 -
obs0.2235 69829 99.91 %
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: 211.92 Å2 / Biso mean: 118.5607 Å2 / Biso min: 55 Å2
精密化ステップサイクル: final / 解像度: 3.2→49.407 Å
タンパク質核酸リガンド溶媒全体
原子数20622 0 66 0 20688
Biso mean--76.87 --
残基数----2655
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00221055
X-RAY DIFFRACTIONf_angle_d0.50428592
X-RAY DIFFRACTIONf_chiral_restr0.0373383
X-RAY DIFFRACTIONf_plane_restr0.0033624
X-RAY DIFFRACTIONf_dihedral_angle_d9.54112654
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11C1575X-RAY DIFFRACTION9.818TORSIONAL
12D1575X-RAY DIFFRACTION9.818TORSIONAL
21A8595X-RAY DIFFRACTION9.818TORSIONAL
22B8595X-RAY DIFFRACTION9.818TORSIONAL
31E1217X-RAY DIFFRACTION9.818TORSIONAL
32F1217X-RAY DIFFRACTION9.818TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2001-3.2440.33191360.30625742710100
3.244-3.29030.41681420.294826882830100
3.2903-3.33940.3371330.276525182651100
3.3394-3.39160.28581390.264826422781100
3.3916-3.44720.33571350.266425622697100
3.4472-3.50660.33531380.268726322770100
3.5066-3.57030.28511370.266426012738100
3.5703-3.6390.33091390.266426362775100
3.639-3.71320.32991360.256925872723100
3.7132-3.7940.33241400.237326632803100
3.794-3.88220.25641350.232125592694100
3.8822-3.97920.27111380.216326372775100
3.9792-4.08680.2611400.222226462786100
4.0868-4.2070.30961350.223125782713100
4.207-4.34270.2581410.218226782819100
4.3427-4.49780.26171420.193726892831100
4.4978-4.67770.23271360.188125952731100
4.6777-4.89040.25831410.19226652806100
4.8904-5.1480.26421390.20226552794100
5.148-5.47020.26381420.217226882830100
5.4702-5.89190.28271400.239326662806100
5.8919-6.48370.29351430.24827072850100
6.4837-7.41910.26721440.239427502894100
7.4191-9.3370.19671460.178327642910100
9.337-49.41290.25381570.21022955311299
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)
13.06021.0165-0.37791.632-0.5622.9374-0.10430.9269-0.1777-0.3683-0.03090.03550.0969-0.32820.00220.44660.067-0.06510.998-0.08720.653414.086750.4646797.5276
23.7031-0.67360.07162.0930.43350.22360.020.65260.78370.403-0.0219-0.1416-0.90140.0667-0.02250.9354-0.24580.03511.16270.36470.887247.520967.5291796.4257
33.2034-0.5377-0.12481.7268-0.64321.73210.11170.53240.292-0.1847-0.1552-0.0493-0.57860.5559-0.2460.6628-0.35450.02931.10920.21670.761466.283462.3473805.5216
43.4025-1.0049-0.49142.6387-1.72431.551-0.18210.3198-0.00610.1265-0.2254-0.44360.22920.4854-0.00750.5052-0.21430.03361.1640.00670.889573.064447.7387813.0182
54.70271.4444-0.74722.9514-0.54583.25080.103-0.2872-0.30090.4771-0.138-0.36890.15820.2659-0.00150.5319-0.0532-0.10680.77660.04210.767361.399729.7011830.9725
62.49581.97632.1471.53041.67731.83630.5197-0.4349-0.23820.6357-0.4569-0.46790.3967-0.46950.00010.6978-0.2082-0.09520.64740.17870.885637.878419.3439826.7505
71.89570.03650.5341.27390.97182.6333-0.20781.0786-0.1689-0.82570.06670.9796-0.1830.0783-0.56611.0263-0.2964-0.1750.9998-0.13981.390717.495216.0198813.3165
83.98870.34760.40573.0755-0.20892.57370.20130.1316-0.2012-0.0028-0.1452-0.1642-0.1420.171300.4932-0.16550.02780.7414-0.01320.790327.588153.8965819.2743
94.33650.6473-0.85153.09540.17913.71820.0732-0.46880.29680.0016-0.3738-0.05510.1576-0.136400.99220.1364-0.03421.0637-0.02850.850547.385613.0992754.845
101.98180.5006-1.27551.9356-0.28440.7838-0.5122-0.1859-0.6283-0.6609-0.03760.09351.09691.26620.00011.56690.22430.10981.58130.16331.146977.681811.1712752.4902
111.3650.7646-0.59982.04370.38561.89580.02630.12120.1485-0.70180.01950.26960.1252-0.182-0.00011.61470.04140.22011.70560.14091.376183.526926.8083727.4372
121.48-1.74780.50292.3934-0.64592.77010.3525-0.40750.07640.2981-0.31550.6024-0.02720.25560.00011.1554-0.2455-0.04341.0630.08121.054445.194432.0034858.21
131.04870.2612-0.30961.7746-1.02982.3283-0.0341-0.06270.33420.1517-0.1173-0.3496-0.83140.54130.00020.8536-0.16340.01030.91620.0560.948351.471853.4246837.4572
141.4074-0.66630.82241.5094-0.4264.42590.0684-0.2724-0.0289-0.0131-0.29790.4249-0.0686-1.0815-0.00460.6176-0.0640.04671.4607-0.32520.897624.911718.9392766.5987
152.25021.3587-0.03660.95680.14390.1678-0.1546-0.4999-0.4177-0.171-0.17210.27850.57410.0958-0.00041.64270.2670.18711.5750.25741.032452.19466.1904788.4944
162.83930.2451-1.05970.84890.66492.8651-0.1214-1.211-0.33090.1229-0.08150.01850.55541.175-0.09021.23480.28740.08122.09040.36131.040972.813511.1771788.9303
170.63070.9039-0.08691.2636-0.28690.6963-0.0174-0.3110.40150.0212-0.0801-0.3821-0.70332.05-0.00031.23990.0503-0.12322.3633-0.05350.993383.508823.8152783.1382
182.20311.27960.82252.3795-1.15041.96980.31140.04890.3212-0.1852-0.2747-0.0589-0.25470.7648-00.8788-0.17350.13991.7196-0.12520.999182.568836.4163756.6644
191.1279-0.6676-0.41380.8289-0.40531.09440.21760.45010.1612-0.1173-0.5997-0.38960.2405-0.56620.00021.23710.19720.07710.9463-0.0191.201661.300144.9222747.9846
202.12170.96120.92151.34660.19230.4326-0.1257-0.952-0.0929-0.1641-0.00720.5076-0.7876-0.82720.00171.35390.6131-0.07591.736-0.12351.222936.308749.2687749.4132
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 4 through 364 )B4 - 364
2X-RAY DIFFRACTION2chain 'B' and (resid 365 through 460 )B365 - 460
3X-RAY DIFFRACTION3chain 'B' and (resid 461 through 646 )B461 - 646
4X-RAY DIFFRACTION4chain 'B' and (resid 647 through 744 )B647 - 744
5X-RAY DIFFRACTION5chain 'B' and (resid 745 through 924 )B745 - 924
6X-RAY DIFFRACTION6chain 'B' and (resid 949 through 1015 )B949 - 1015
7X-RAY DIFFRACTION7chain 'B' and (resid 1016 through 1148 )B0
8X-RAY DIFFRACTION8chain 'C'C7 - 179
9X-RAY DIFFRACTION9chain 'D'D7 - 178
10X-RAY DIFFRACTION10chain 'E' and (resid 16 through 83 )E16 - 83
11X-RAY DIFFRACTION11chain 'E' and (resid 84 through 152 )E84 - 152
12X-RAY DIFFRACTION12chain 'F' and (resid 84 through 152 )F84 - 152
13X-RAY DIFFRACTION13chain 'F' and (resid 15 through 83 )F15 - 83
14X-RAY DIFFRACTION14chain 'A' and (resid 9 through 364 )A9 - 364
15X-RAY DIFFRACTION15chain 'A' and (resid 365 through 451 )A365 - 451
16X-RAY DIFFRACTION16chain 'A' and (resid 460 through 646 )A460 - 646
17X-RAY DIFFRACTION17chain 'A' and (resid 647 through 744 )A647 - 744
18X-RAY DIFFRACTION18chain 'A' and (resid 745 through 922 )A745 - 922
19X-RAY DIFFRACTION19chain 'A' and (resid 952 through 1015 )A952 - 1015
20X-RAY DIFFRACTION20chain 'A' and (resid 1016 through 1145 )A0

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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