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- PDB-5tbk: Crystal structure of human importin a3 bound to RCC1 -

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基本情報

登録情報
データベース: PDB / ID: 5tbk
タイトルCrystal structure of human importin a3 bound to RCC1
要素
  • Importin subunit alpha-3
  • Regulator of chromosome condensation
キーワードPROTEIN TRANSPORT / NUCLEAR PROTEIN / Nuclear Import (核局在化シグナル) / Importin alpha / RCC1 like Domain (RLD) / NLS / PROTEIN TRANSPORT - NUCLEAR PROTEIN complex
機能・相同性
機能・相同性情報


mitotic nuclear membrane reassembly / dopamine secretion / sulfate binding / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / nucleosomal DNA binding / nuclear import signal receptor activity ...mitotic nuclear membrane reassembly / dopamine secretion / sulfate binding / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / nucleosomal DNA binding / nuclear import signal receptor activity / nuclear localization sequence binding / regulation of mitotic nuclear division / NLS-bearing protein import into nucleus / nucleosome binding / spindle assembly / 核膜孔 / viral process / mitotic spindle organization / guanyl-nucleotide exchange factor activity / condensed nuclear chromosome / chromosome segregation / G1/S transition of mitotic cell cycle / ISG15 antiviral mechanism / small GTPase binding / protein import into nucleus / 染色体 / 遺伝子発現 / histone binding / 核膜 / protein heterodimerization activity / 細胞分裂 / chromatin binding / クロマチン / protein-containing complex / 核質 / 細胞核 / 細胞質基質 / 細胞質
類似検索 - 分子機能
Regulator of chromosome condensation (RCC1) signature 1. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily ...Regulator of chromosome condensation (RCC1) signature 1. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Αソレノイド / Armadillo-type fold / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
Importin subunit alpha-3 / Regulator of chromosome condensation
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 / 分子置換 / 解像度: 3.45 Å
データ登録者Sankhala, R.S. / Lokareddy, R.K. / Pumroy, R.A. / Cingolani, G.
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)GM074846 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100888 米国
引用ジャーナル: Nat Commun / 年: 2017
タイトル: Three-dimensional context rather than NLS amino acid sequence determines importin alpha subtype specificity for RCC1.
著者: Sankhala, R.S. / Lokareddy, R.K. / Begum, S. / Pumroy, R.A. / Gillilan, R.E. / Cingolani, G.
履歴
登録2016年9月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年9月13日Provider: repository / タイプ: Initial release
改定 1.12017年10月4日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22017年11月1日Group: Author supporting evidence / Database references
カテゴリ: citation / citation_author / pdbx_struct_assembly_auth_evidence
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 1.32019年12月25日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42023年10月4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: Importin subunit alpha-3
B: Importin subunit alpha-3
C: Importin subunit alpha-3
D: Importin subunit alpha-3
E: Importin subunit alpha-3
F: Importin subunit alpha-3
G: Importin subunit alpha-3
H: Importin subunit alpha-3
I: Regulator of chromosome condensation
K: Regulator of chromosome condensation
L: Regulator of chromosome condensation
M: Regulator of chromosome condensation
N: Regulator of chromosome condensation
O: Regulator of chromosome condensation
P: Regulator of chromosome condensation
J: Regulator of chromosome condensation


分子量 (理論値)分子数
合計 (水以外)823,73116
ポリマ－823,73116
非ポリマー00
水0
1
A: Importin subunit alpha-3
K: Regulator of chromosome condensation


分子量 (理論値)分子数
合計 (水以外)102,9662
ポリマ－102,9662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-1 kcal/mol
Surface area35190 Å2
手法PISA
2
B: Importin subunit alpha-3
I: Regulator of chromosome condensation


分子量 (理論値)分子数
合計 (水以外)102,9662
ポリマ－102,9662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-2 kcal/mol
Surface area34850 Å2
手法PISA
3
C: Importin subunit alpha-3
J: Regulator of chromosome condensation


分子量 (理論値)分子数
合計 (水以外)102,9662
ポリマ－102,9662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-1 kcal/mol
Surface area34890 Å2
手法PISA
4
D: Importin subunit alpha-3
P: Regulator of chromosome condensation


分子量 (理論値)分子数
合計 (水以外)102,9662
ポリマ－102,9662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-2 kcal/mol
Surface area35020 Å2
手法PISA
5
E: Importin subunit alpha-3
L: Regulator of chromosome condensation


分子量 (理論値)分子数
合計 (水以外)102,9662
ポリマ－102,9662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-3 kcal/mol
Surface area34580 Å2
手法PISA
6
F: Importin subunit alpha-3
M: Regulator of chromosome condensation


分子量 (理論値)分子数
合計 (水以外)102,9662
ポリマ－102,9662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-3 kcal/mol
Surface area34970 Å2
手法PISA
7
G: Importin subunit alpha-3
N: Regulator of chromosome condensation


分子量 (理論値)分子数
合計 (水以外)102,9662
ポリマ－102,9662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-3 kcal/mol
Surface area35420 Å2
手法PISA
8
H: Importin subunit alpha-3
O: Regulator of chromosome condensation


分子量 (理論値)分子数
合計 (水以外)102,9662
ポリマ－102,9662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-4 kcal/mol
Surface area35020 Å2
手法PISA
単位格子
Length a, b, c (Å)127.403, 162.494, 161.592
Angle α, β, γ (deg.)75.65, 85.63, 72.17
Int Tables number1
Space group name H-MP1
詳細Determined by size exclusion chromatography and small angle x-ray scattering

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要素

#1: タンパク質
Importin subunit alpha-3 / / Importin alpha Q1 / Qip1 / Karyopherin subunit alpha-4


分子量: 57941.387 Da / 分子数: 8 / 由来タイプ: 組換発現
詳細: Functions in nuclear protein import as an adapter protein
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KPNA4, QIP1 / プラスミド: pET28a / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: O00629
#2: タンパク質
Regulator of chromosome condensation / Cell cycle regulatory protein / Chromosome condensation protein 1


分子量: 45024.949 Da / 分子数: 8 / 由来タイプ: 組換発現
詳細: Guanine-nucleotide releasing factor that promotes the exchange of Ran-bound GDP by GTP.
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RCC1, CHC1 / プラスミド: pGEX-6P-1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P18754

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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: 3.94 Å3/Da / 溶媒含有率: 68.82 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5
詳細: 0.1 M sodium cacodylate buffer (pH 6.5), 0.2M Calcium acetate, 8% PEG 8000 and galactose 3%

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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: 0.97 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2015年10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: 0.97 Å / 相対比: 1
反射解像度: 3.45→50 Å / Num. obs: 935054 / % possible obs: 90.4 % / Observed criterion σ(F): 2.5 / 冗長度: 2 % / Biso Wilson estimate: 85.62 Å2 / Rsym value: 0.13 / Net I/σ(I): 12.2
反射 シェル解像度: 3.45→3.53 Å / 冗長度: 1.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.8 / % possible all: 71.5

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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
HKL-2000データ削減
HKL-2000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: 4UAE and 1A12

4uae

1a12


解像度: 3.45→19.988 Å / SU ML: 0.6 / 交差検証法: FREE R-VALUE / σ(F): 2.5 / 位相誤差: 34.98
Rfactor反射数%反射
Rfree0.296 1638 1.39 %
Rwork0.2782 --
obs0.2784 118199 75.5 %
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 mean: 129.8 Å2
精密化ステップサイクル: LAST / 解像度: 3.45→19.988 Å
タンパク質核酸リガンド溶媒全体
原子数50677 0 0 0 50677
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00551624
X-RAY DIFFRACTIONf_angle_d0.68470117
X-RAY DIFFRACTIONf_dihedral_angle_d5.84931070
X-RAY DIFFRACTIONf_chiral_restr0.0468087
X-RAY DIFFRACTIONf_plane_restr0.0059187
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.5510.4327710.41045545X-RAY DIFFRACTION43
3.551-3.66490.4343970.39976991X-RAY DIFFRACTION54
3.6649-3.79510.38531160.38357726X-RAY DIFFRACTION60
3.7951-3.94590.34671190.37188359X-RAY DIFFRACTION65
3.9459-4.1240.35651300.33569222X-RAY DIFFRACTION72
4.124-4.33930.32371400.3059966X-RAY DIFFRACTION78
4.3393-4.60810.29551490.284310664X-RAY DIFFRACTION83
4.6081-4.95880.2761530.266811037X-RAY DIFFRACTION86
4.9588-5.44870.28811570.266311324X-RAY DIFFRACTION88
5.4487-6.21630.29741620.286711530X-RAY DIFFRACTION90
6.2163-7.7550.31221710.273911943X-RAY DIFFRACTION93
7.755-19.98810.22221730.199612254X-RAY DIFFRACTION95
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)
11.03-0.09280.15092.4394-0.03861.5384-0.10910.8638-0.4291-0.0562-0.1597-0.9791-0.51910.898-0.0530.0796-0.06520.02450.9587-0.19380.8244279.81744.5669187.1655
21.3920.55530.19880.6630.02780.707-0.40450.7382-0.4735-0.5358-0.02390.6470.24340.2434-0.1202-1.2103-1.2494-1.0609-0.3828-0.68710.3009245.945845.6786198.1402
35.7849-0.33530.17472.5842-0.09722.9885-0.5917-1.90290.00490.49440.33280.8656-0.0629-0.29050.03190.3522-0.1095-0.02160.57690.19690.174240.817346.3829218.6587
40.923-1.0592-0.09781.21250.17240.48030.49191.4216-0.3331-0.7529-0.22490.82320.225-0.5947-0.18290.63590.2749-0.05442.75651.06712.4604216.90388.6778179.2885
53.990.46450.44597.0876-1.81273.9002-1.0653-0.48610.20750.3110.73421.82171.1190.5075-0.14691.63420.7150.58031.50371.01271.6908221.328683.8931187.3083
68.12520.1637-3.27279.5886-6.22625.71351.2603-0.59890.5969-0.323-0.30251.80711.0580.3464-0.77791.1001-0.0553-0.0961.85030.61361.4912226.771183.1854176.4889
70.54560.5058-0.02470.69110.31851.216-0.336-0.398-0.4465-0.46080.49750.72520.3121-0.5906-0.06580.70850.4697-0.38221.64450.54881.7084230.719576.2783183.6161
83.1328-0.60550.77364.1968-0.36141.44940.01560.79730.5241-0.33330.29490.1448-0.1864-0.6667-0.26740.69820.1182-0.08431.04040.29550.6979246.888676.9064182.6156
90.74380.7505-0.02772.27310.35860.4236-0.06820.33990.5954-0.3306-0.4406-0.9202-0.570.880.1060.5255-0.326-0.19180.15650.70291.0209266.318480.7485191.4297
100.8601-0.97550.71155.15530.87671.87020.26420.31291.1687-0.63160.1519-0.5653-0.89840.722-0.55710.9329-0.5733-0.00310.9731-0.08241.3231277.467684.4571201.0681
116.0148-1.41090.22784.239-0.1951.3696-0.4448-0.39140.43470.16140.6086-1.2438-0.4780.8071-0.17680.8657-0.4392-0.23780.9881-0.08510.913275.753685.6637210.1312
129.1871-0.99794.18273.1688-0.42386.5890.83870.4541-1.3947-0.2632-0.78520.73770.9916-1.1742-0.20791.1927-0.2281-0.66760.79570.03010.7521273.520281.467217.3378
137.8244-1.92831.32155.87040.63426.2603-0.9779-1.02140.65050.52150.9009-0.39650.2487-0.8359-0.57091.499-0.5119-0.51041.43-0.04460.8422276.980185.7088225.0533
143.03161.52242.3722.0456-0.36133.793-0.08271.1423-0.843-0.28440.91490.62280.287-0.3579-0.75230.39040.0008-0.03631.31130.36792.3663185.787326.2014186.9464
152.50772.88043.63114.34586.07088.7883-0.51230.2422-0.1097-0.1030.26140.24-0.28240.4690.24760.85610.0098-0.14871.18430.3191.6127190.162119.2579190.4536
163.79670.95161.00573.86711.16782.37510.07920.7599-0.1571-1.17380.02910.366-0.32890.21720.2415-0.2023-0.1016-0.12241.12640.1431.4094202.612712.917185.7594
172.8611-0.57550.35492.5535-0.38192.83210.1460.4258-0.4523-0.6708-0.16820.30520.4025-0.4471-0.24270.2082-0.13510.04360.5251-0.04890.6028223.718310.8227188.0101
181.43310.99950.15460.8942-0.17890.6714-0.29810.08790.47340.17670.185-0.1997-0.8231-0.1833-0.1404-0.3899-0.41810.1684-0.0007-0.06191.0794242.06513.3484198.0852
192.7070.9534-0.41981.7057-0.53853.3078-0.1827-0.10260.3455-0.21270.16710.19350.4882-0.2405-0.14720.267-0.0353-0.12630.3196-0.00590.5604245.893412.7144212.7434
203.8421-0.6572-3.53322.65650.58453.1977-0.9595-2.701-0.48391.03040.7218-0.4562-0.22980.65930.1520.8463-0.0059-0.06741.2576-0.16020.9157251.280914.8672224.0147
214.5314-4.19530.83727.6889-0.16474.0933-1.4713-3.0869-1.03820.84981.0550.22951.5628-1.24870.23621.0281-0.14560.06641.36670.00730.6514246.32138.4235228.4075
222.56912.79732.95935.22572.60623.49590.01030.43180.7422-0.64290.655-2.1614-0.86930.8472-0.09231.11920.41380.36061.7675-0.3482.9781318.4345127.5868181.9738
235.3982-1.90281.1696.1484-2.2031.21390.75420.1925-0.4851-1.28010.028-1.6940.76070.7853-0.91590.7361-0.06740.00191.2802-0.64081.3289302.7339136.2982181.0503
241.4039-0.8593-0.73012.42190.12860.7256-0.15610.5253-0.68310.1460.2568-0.23170.93820.087-0.12140.76850.01110.09270.0777-1.19470.7109282.9471136.5705184.8065
250.1969-0.4433-0.21761.8703-0.41661.9257-0.21630.1861-0.0862-0.07240.56181.7434-0.0262-1.1575-0.25970.993-0.77790.16370.7761-0.13631.133265.4603129.7947203.2511
268.1203-1.16440.73226.4923-1.62492.0147-1.0845-1.04220.00131.09620.76270.92180.3477-0.4266-0.0091.6394-0.43580.47391.7710.31241.0388261.4326127.9948225.5467
271.43212.1762-0.63886.7435-2.59131.0551-0.2480.22340.6495-2.22440.65030.3705-0.48830.3531-0.35932.42440.4695-0.15931-0.33672.3969226.0469110.8398105.3768
284.82962.2714.21481.0742.19637.0266-0.26991.18291.6339-2.5089-1.70891.31790.06631.32061.91893.02690.5313-0.77361.82080.10361.8761218.7985107.3791109.6104
294.82823.3791-0.37665.60742.18461.7882-1.3036-0.45021.9313-1.03260.6437-0.0870.84570.13050.43711.89960.51260.1271.14450.13441.5193214.243899.739106.827
309.01362.4972-1.35483.152.64983.9215-0.39680.58640.9481-0.42630.0763-0.1894-0.9879-0.6220.51171.50610.42790.01390.86620.16990.9889209.439187.6812106.8314
313.19221.7929-1.35773.91092.95335.28950.11120.55250.6642-0.65-0.6189-0.4124-0.4078-0.5313-0.17091.05140.1510.17480.66440.42471.0285207.659275.6254107.0787
326.50820.6838-1.94217.5221-2.15697.68550.45010.6312-0.6372-0.5242-0.6039-0.94540.7933-0.35950.20260.63460.00680.04750.69830.08220.5668208.288863.7014115.8223
336.01730.01410.94121.01681.231.71110.06210.45870.13450.1402-0.6541-0.6393-0.00250.65250.0441.34660.2924-0.35460.8340.33820.9518209.183451.9718125.5471
342.69111.7935-0.62174.8404-0.38060.9898-0.6006-0.69020.1888-0.882-0.38820.3555-0.5361-0.13460.9061.05360.2301-0.27721.21210.09370.7167208.632154.2563136.5702
352.20590.81841.07663.71352.80872.25682.0761-1.0307-0.8827-0.2379-2.83941.2907-0.1566-0.10590.36011.4882-0.3152-0.33831.54980.14811.4132208.230152.1396149.709
363.65330.6524-0.95733.95971.12082.4644-0.02220.22250.7663-0.36450.1434-0.434-0.7785-0.8895-0.19471.30810.4180.11520.7981-0.04830.6625200.05353.518263.0053
372.00920.7410.28662.7805-0.08473.67840.1592-0.054-0.67170.5188-0.1699-0.77850.47040.05860.05070.94020.1195-0.01970.63250.17780.7335199.061513.2634280.1668
385.92.31160.34194.0799-3.01433.6424-0.3528-0.0583-1.2074-0.42370.23690.24550.7026-0.28970.4991.14210.5002-0.09350.9947-0.2021.1054298.431735.8053107.5822
391.09810.5780.0272.8099-0.10262.43890.02410.0050.5005-0.7532-0.42040.54130.33320.69660.14050.98120.2366-0.3030.9897-0.24940.6377305.636863.3307107.3087
402.2366-0.0123-0.07572.5681.69292.9660.6206-0.15490.9330.8854-0.6831.243-0.535-0.6490.43551.4636-0.07890.16570.6746-0.33871.4832300.286489.5979130.7324
414.56060.1698-2.90065.1606-3.47719.29070.19441.0076-2.3023-1.1966-0.71181.12952.1117-0.18610.31021.69110.3922-0.41841.1484-0.33882.3408282.1369-7.4018261.0487
425.6976-2.05320.93662.24030.38632.80820.20160.5094-1.4102-0.4572-0.31920.44960.72490.0876-0.71310.87240.1901-0.40991.24710.05340.3233292.912318.6932263.5446
437.5111-0.5252-1.53127.97292.93932.9111-0.15621.03980.8897-0.1251-0.08990.5369-0.739-0.9330.12920.73610.1053-0.06671.00840.06330.4901291.70640.4804277.3611
444.47960.5401-1.81133.09010.57296.36030.5769-1.2150.57821.1119-0.57250.2468-0.274-0.4539-0.05320.97290.09680.13471.2868-0.23220.7166292.26543.3214298.3365
450.131-0.0336-0.4450.95-0.39550.59170.2863-0.0209-0.23060.05960.3843-0.0191-1.1199-0.3835-0.00741.48580.2711-0.20631.07350.62111.1637245.421495.4046182.0283
465.6310.0973-2.00783.9953-3.55257.3452-0.2931-0.62280.90921.5795-0.0909-0.7438-1.62041.16840.52961.77040.1539-0.58091.23970.15411.3056245.2494108.0473175.9
473.41470.1124-4.55725.0838-3.00647.7568-1.3495-2.92931.11182.18440.73860.0308-2.77221.45970.65413.55180.374-0.31722.18330.2151.7458236.9492114.4678194.1435
484.91160.1448-1.37043.60920.24011.9940.2036-0.2760.98540.2504-0.15940.7985-0.6931-0.3122-0.13991.97910.6256-0.271.48040.09361.383226.4334120.4646174.0658
498.4006-6.8951-7.49497.52964.82637.9793-1.0321-0.2718-0.28340.56460.5078-0.32741.1046-1.2220.64330.721-0.26570.00251.0164-0.23150.8164263.085546.3201201.134
505.0254-0.1008-0.87912.25870.00212.16250.897-0.0388-1.26550.52630.1765-0.55161.21510.02510.2893-0.40120.40050.56781.2227-0.54180.6494274.356915.8445182.9022
510.9657-0.2515-0.04181.0472-0.07521.0256-0.2011-0.2311-1.1627-0.12390.0342-1.27220.53040.75140.11570.68260.39930.46151.7829-0.1121.9494290.13723.6063180.48
523.51831.2062-0.08380.3845-0.04620.02930.229-1.15590.2542-0.3043-0.8169-0.3542-0.15431.09450.37611.5506-0.27730.42841.16850.06521.0474226.796482.9144106.2395
534.9084-0.3989-4.57242.5051.50796.4053-0.3559-1.4611-0.49220.08650.3724-0.59080.83381.3460.22211.39220.06290.58372.11260.19711.1655238.998780.604897.9577
545.8015.4607-2.09519.40610.81488.4737-0.4070.4817-0.66330.59490.1912-2.83931.76372.46920.29751.93320.69160.18032.88630.29411.9221247.332886.724118.0797
556.18674.4603-0.31163.6762-1.1552.2067-0.71610.5332-0.6072-0.049-0.1706-1.9534-1.00182.65250.62751.91320.08360.04343.0867-0.60591.9408254.435398.843111.3042
560.41450.0253-0.15691.88890.4917.33070.01320.04061.02360.29070.1472-0.6206-1.06442.38660.07771.4956-0.70090.1392.31590.19341.4303252.833999.094292.1153
572.61711.8327-2.03161.2275-1.17182.6098-0.1253-1.06-0.71460.0436-0.1958-0.3574-0.04290.8380.13720.85050.06040.27221.39360.13850.6337223.277338.9236255.893
585.1910.6904-4.37398.52193.5449.151-1.3608-2.6278-0.37722.61981.0685-2.27470.6333.42760.39692.1420.263-0.28123.17640.05661.3802235.242547.0866274.1627
594.3146-0.64361.54885.2952.30435.085-0.5697-0.53861.32430.83840.5374-1.0535-1.19312.02150.03821.5204-0.5496-0.06561.7866-0.17650.9619239.874558.3561251.9022
602.52272.08091.24091.54150.7073.058-0.0644-1.13731.0561-0.2969-0.25810.80590.4452-1.34410.47471.13850.1744-0.43451.5969-0.46971.1841277.543856.993100.4547
613.37122.22361.54743.441-1.26683.3444-0.8215-1.38871.15680.66490.7771.6775-0.7285-4.07930.13042.05690.29980.02742.9025-0.22961.8659265.095148.7501117.5932
622.7322-3.20730.37894.3348-1.61783.883-0.1969-0.696-1.1490.15760.75161.28120.826-1.3124-0.44141.6641-0.6934-0.22991.8299-0.09351.5206262.659937.363495.2524
636.38522.49294.53881.19111.01014.64650.4535-1.0421-0.44810.52650.0318-0.15790.4041-0.5695-0.19480.58930.131-0.10220.8937-0.01930.723273.933915.1806261.4991
643.89870.30323.49033.16720.16653.7585-0.4258-2.66780.8760.88670.28310.3799-0.1985-1.00720.23640.9240.0721-0.20992.2315-0.36711.0492261.249717.7975256.0517
655.04184.7663-1.75955.079-0.00927.46-0.3811-1.27641.0391.60610.67270.8361-0.8368-2.5255-0.44651.82160.6861-0.37333.2896-0.33141.7667255.477510.6198275.3111
664.80580.9941-2.49410.96230.94745.56-0.8393-1.0709-0.82592.00510.34271.76820.154-2.13110.4852.5685-0.09240.29673.92090.44131.6245246.09612.0676270.4756
677.8877-0.3296-1.60535.33840.88926.3052-0.7569-0.6055-1.59230.4860.20340.93871.1948-1.820.31221.3173-0.4065-0.01171.73320.2821.1473246.82620.4965249.4939
681.0561-1.636-1.08762.60082.60283.2217-0.53380.015-0.77791.12650.2860.54461.93140.05470.81391.71460.04290.41871.1138-0.43881.6397292.358109.5403175.9978
692.95391.4993-3.49311.5266-1.11286.9902-1.90041.3095-3.7002-1.25851.2909-1.82483.4317-1.09311.01072.8563-0.40730.69952.1645-0.52872.5234295.1567100.2612196.4305
704.4022.6666-0.08594.0131-4.48268.1318-1.9778-1.6559-2.1995-1.76440.0705-0.7818-0.42960.02991.86623.11450.57960.39921.68-0.16382.2064307.156795.9072191.6209
712.9219-0.37790.67380.8935-1.48212.3071-0.041-0.7506-0.1101-0.5566-0.6784-0.03970.75350.29450.5512.01110.55870.47691.7107-0.46592.1023312.075293.795171.2155
721.0103-0.53580.46761.13430.41460.72040.10280.1953-0.0444-0.2918-0.20110.59890.1278-0.0856-0.02260.54190.0611-0.2661.24220.06710.8384212.437835.4761177.3772
732.6075-0.13410.79591.6610.01882.0641-0.0152-0.53470.4930.18390.1554-0.0926-0.0958-0.51130.14020.36130.1283-0.23281.08860.04231.036215.834743.4298189.0452
743.96090.0964-0.82181.62410.35843.06120.1077-0.31020.8842-0.2372-0.12861.3799-0.8265-1.0530.04630.66210.2329-0.38631.63150.00071.7067197.96655.4755180.9075
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 71 through 313 )
2X-RAY DIFFRACTION2chain 'A' and (resid 314 through 381 )
3X-RAY DIFFRACTION3chain 'A' and (resid 382 through 487 )
4X-RAY DIFFRACTION4chain 'B' and (resid 72 through 100 )
5X-RAY DIFFRACTION5chain 'B' and (resid 101 through 124 )
6X-RAY DIFFRACTION6chain 'B' and (resid 125 through 143 )
7X-RAY DIFFRACTION7chain 'B' and (resid 144 through 170 )
8X-RAY DIFFRACTION8chain 'B' and (resid 171 through 272 )
9X-RAY DIFFRACTION9chain 'B' and (resid 273 through 353 )
10X-RAY DIFFRACTION10chain 'B' and (resid 354 through 381 )
11X-RAY DIFFRACTION11chain 'B' and (resid 382 through 424 )
12X-RAY DIFFRACTION12chain 'B' and (resid 425 through 441 )
13X-RAY DIFFRACTION13chain 'B' and (resid 442 through 486 )
14X-RAY DIFFRACTION14chain 'C' and (resid 71 through 100 )
15X-RAY DIFFRACTION15chain 'C' and (resid 101 through 128 )
16X-RAY DIFFRACTION16chain 'C' and (resid 129 through 213 )
17X-RAY DIFFRACTION17chain 'C' and (resid 214 through 313 )
18X-RAY DIFFRACTION18chain 'C' and (resid 314 through 381 )
19X-RAY DIFFRACTION19chain 'C' and (resid 382 through 441 )
20X-RAY DIFFRACTION20chain 'C' and (resid 442 through 470 )
21X-RAY DIFFRACTION21chain 'C' and (resid 471 through 487 )
22X-RAY DIFFRACTION22chain 'D' and (resid 72 through 128 )
23X-RAY DIFFRACTION23chain 'D' and (resid 129 through 213 )
24X-RAY DIFFRACTION24chain 'D' and (resid 214 through 297 )
25X-RAY DIFFRACTION25chain 'D' and (resid 298 through 441 )
26X-RAY DIFFRACTION26chain 'D' and (resid 442 through 486 )
27X-RAY DIFFRACTION27chain 'E' and (resid 71 through 100 )
28X-RAY DIFFRACTION28chain 'E' and (resid 101 through 128 )
29X-RAY DIFFRACTION29chain 'E' and (resid 129 through 170 )
30X-RAY DIFFRACTION30chain 'E' and (resid 171 through 236 )
31X-RAY DIFFRACTION31chain 'E' and (resid 237 through 271 )
32X-RAY DIFFRACTION32chain 'E' and (resid 272 through 353 )
33X-RAY DIFFRACTION33chain 'E' and (resid 354 through 381 )
34X-RAY DIFFRACTION34chain 'E' and (resid 382 through 441 )
35X-RAY DIFFRACTION35chain 'E' and (resid 442 through 486 )
36X-RAY DIFFRACTION36chain 'F' and (resid 71 through 236 )
37X-RAY DIFFRACTION37chain 'F' and (resid 237 through 486 )
38X-RAY DIFFRACTION38chain 'G' and (resid 71 through 170 )
39X-RAY DIFFRACTION39chain 'G' and (resid 171 through 313 )
40X-RAY DIFFRACTION40chain 'G' and (resid 314 through 487 )
41X-RAY DIFFRACTION41chain 'H' and (resid 71 through 170 )
42X-RAY DIFFRACTION42chain 'H' and (resid 171 through 313 )
43X-RAY DIFFRACTION43chain 'H' and (resid 314 through 381 )
44X-RAY DIFFRACTION44chain 'H' and (resid 382 through 487 )
45X-RAY DIFFRACTION45chain 'I' and (resid 3 through 51 )
46X-RAY DIFFRACTION46chain 'I' and (resid 52 through 208 )
47X-RAY DIFFRACTION47chain 'I' and (resid 209 through 270 )
48X-RAY DIFFRACTION48chain 'I' and (resid 271 through 421 )
49X-RAY DIFFRACTION49chain 'K' and (resid 4 through 23 )
50X-RAY DIFFRACTION50chain 'K' and (resid 24 through 250 )
51X-RAY DIFFRACTION51chain 'K' and (resid 251 through 421 )
52X-RAY DIFFRACTION52chain 'L' and (resid 4 through 51 )
53X-RAY DIFFRACTION53chain 'L' and (resid 52 through 188 )
54X-RAY DIFFRACTION54chain 'L' and (resid 189 through 269 )
55X-RAY DIFFRACTION55chain 'L' and (resid 270 through 319 )
56X-RAY DIFFRACTION56chain 'L' and (resid 320 through 421 )
57X-RAY DIFFRACTION57chain 'M' and (resid 3 through 188 )
58X-RAY DIFFRACTION58chain 'M' and (resid 189 through 289 )
59X-RAY DIFFRACTION59chain 'M' and (resid 290 through 421 )
60X-RAY DIFFRACTION60chain 'N' and (resid 4 through 207 )
61X-RAY DIFFRACTION61chain 'N' and (resid 208 through 289 )
62X-RAY DIFFRACTION62chain 'N' and (resid 290 through 421 )
63X-RAY DIFFRACTION63chain 'O' and (resid 4 through 51 )
64X-RAY DIFFRACTION64chain 'O' and (resid 52 through 207 )
65X-RAY DIFFRACTION65chain 'O' and (resid 208 through 260 )
66X-RAY DIFFRACTION66chain 'O' and (resid 261 through 301 )
67X-RAY DIFFRACTION67chain 'O' and (resid 302 through 421 )
68X-RAY DIFFRACTION68chain 'P' and (resid 3 through 188 )
69X-RAY DIFFRACTION69chain 'P' and (resid 189 through 238 )
70X-RAY DIFFRACTION70chain 'P' and (resid 239 through 290 )
71X-RAY DIFFRACTION71chain 'P' and (resid 291 through 421 )
72X-RAY DIFFRACTION72chain 'J' and (resid 4 through 92 )
73X-RAY DIFFRACTION73chain 'J' and (resid 93 through 250 )
74X-RAY DIFFRACTION74chain 'J' and (resid 251 through 421 )

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万見について

-
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