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- PDB-4xvu: Structure of Get3 bound to the transmembrane domain of Nyv1 -

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基本情報

登録情報
データベース: PDB / ID: 4xvu
タイトルStructure of Get3 bound to the transmembrane domain of Nyv1
要素
  • ATPase GET3
  • Antibody heavy chain
  • Antibody light chain
  • Nyv1 TMD
キーワードHYDROLASE/TRANSPORT PROTEIN / membrane protein targeting complex / HYDROLASE-TRANSPORT PROTEIN complex
機能・相同性
機能・相同性情報


GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / 加水分解酵素; 酸無水物に作用 / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to arsenic-containing substance / response to metal ion / protein folding chaperone ...GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / 加水分解酵素; 酸無水物に作用 / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to arsenic-containing substance / response to metal ion / protein folding chaperone / guanyl-nucleotide exchange factor activity / unfolded protein binding / response to heat / cellular response to oxidative stress / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / cytosol
類似検索 - 分子機能
Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / P-loop containing nucleotide triphosphate hydrolases / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / P-loop containing nucleotide triphosphate hydrolases / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
ADENOSINE-5'-TRIPHOSPHATE / ATPase GET3
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.35 Å
データ登録者Mateja, A. / Paduch, M. / Chang, H.-Y. / Szydlowska, A. / Kossiakoff, A.A. / Hegde, R.S. / Keenan, R.J.
資金援助 米国, 3件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM086487 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01 GM094588 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM087519 米国
引用ジャーナル: Science / 年: 2015
タイトル: Protein targeting. Structure of the Get3 targeting factor in complex with its membrane protein cargo.
著者: Mateja, A. / Paduch, M. / Chang, H.Y. / Szydlowska, A. / Kossiakoff, A.A. / Hegde, R.S. / Keenan, R.J.
履歴
登録2015年1月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年3月18日Provider: repository / タイプ: Initial release
改定 1.12017年9月20日Group: Author supporting evidence / Derived calculations / Source and taxonomy
カテゴリ: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
改定 1.22019年12月25日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32023年9月27日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
改定 1.42024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: ATPase GET3
B: ATPase GET3
C: Antibody heavy chain
D: Antibody light chain
E: Antibody heavy chain
F: Antibody light chain
G: ATPase GET3
H: ATPase GET3
I: Antibody heavy chain
J: Antibody light chain
K: Antibody heavy chain
L: Antibody light chain
g: Nyv1 TMD
a: Nyv1 TMD
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)359,08824
ポリマ－356,83114
非ポリマー2,25710
水14,556808
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area39710 Å2
ΔGint-333 kcal/mol
Surface area123260 Å2
手法PISA
単位格子
Length a, b, c (Å)79.440, 109.230, 111.350
Angle α, β, γ (deg.)63.050, 77.740, 70.170
Int Tables number1
Space group name H-MP1

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要素

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抗体 , 2種, 8分子 CEIKDFJL

#2: 抗体
Antibody heavy chain


分子量: 24560.430 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens, synthetic construct
解説: Obtained by phage display from a library of human IgG antibody fragment, the CDRs are completely synthetic
プラスミド: RH2.2 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)/pRIL
#3: 抗体
Antibody light chain


分子量: 23671.266 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens, synthetic construct
解説: Obtained by phage display from a library of human IgG antibody fragment, the CDRs are completely synthetic
プラスミド: RH2.2 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)/pRIL

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タンパク質 / タンパク質・ペプチド , 2種, 6分子 ABGHga

#1: タンパク質
ATPase GET3 / Arsenical pump-driving ATPase / Arsenite-stimulated ATPase / Golgi to ER traffic protein 3 / Guided ...Arsenical pump-driving ATPase / Arsenite-stimulated ATPase / Golgi to ER traffic protein 3 / Guided entry of tail-anchored proteins 3


分子量: 39392.605 Da / 分子数: 4 / 変異: D57N / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: GET3, ARR4, YDL100C, D2371 / プラスミド: pCDF1b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)/pRIL
参照: UniProt: Q12154, 加水分解酵素; 酸無水物に作用
#4: タンパク質・ペプチド Nyv1 TMD


分子量: 3166.895 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
プラスミド: pET28 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)/pRIL

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非ポリマー , 4種, 818分子

#5: 化合物
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP


分子量: 507.181 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / コメント: ATP, エネルギー貯蔵分子*YM
#6: 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: 4 / 由来タイプ: 合成 / 式: Mg
#7: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 808 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY
配列の詳細The sequence of the bound Nyv1 TMD peptide is: MGSHHHHHHSQKVKNITLLTFTIILFVSAAFMFFYLW However, due ...The sequence of the bound Nyv1 TMD peptide is: MGSHHHHHHSQKVKNITLLTFTIILFVSAAFMFFYLW However, due to relatively poor local density, this chain was modeled as a poly-alanine helix.

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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: 2.25 Å3/Da / 溶媒含有率: 45.36 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 15% PEG 3350, 25 mM succinic acid pH 7.0

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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: 24-ID-C / 波長: 0.9795 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2014年3月10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: 0.9795 Å / 相対比: 1
反射解像度: 2.35→69.38 Å / Num. obs: 123349 / % possible obs: 95 % / 冗長度: 3.2 % / Net I/σ(I): 5.9
反射 シェル解像度: 2.35→2.43 Å / 冗長度: 3 % / Mean I/σ(I) obs: 1.8 / % possible all: 85

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
xia2データ削減
PHASER位相決定
Coot3.15モデル構築
精密化構造決定の手法: 分子置換
開始モデル: 2woj, 3pgf

2woj

3pgf


解像度: 2.35→69.376 Å / SU ML: 0.29 / 交差検証法: FREE R-VALUE / σ(F): 2 / 位相誤差: 24.47 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2335 6207 5.03 %
Rwork0.1971 117129 -
obs0.1989 123336 94.58 %
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: 267.48 Å2 / Biso mean: 67.0967 Å2 / Biso min: 23.66 Å2
精密化ステップサイクル: final / 解像度: 2.35→69.376 Å
タンパク質核酸リガンド溶媒全体
原子数22998 0 175 808 23981
Biso mean--40.71 46.69 -
残基数----2990
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00523644
X-RAY DIFFRACTIONf_angle_d0.95332072
X-RAY DIFFRACTIONf_chiral_restr0.0363639
X-RAY DIFFRACTIONf_plane_restr0.0044072
X-RAY DIFFRACTIONf_dihedral_angle_d12.8358553
LS精密化 シェル

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

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.37670.26771580.25053083324175
2.3767-2.40470.30321770.24853509368684
2.4047-2.4340.27512220.25263830405295
2.434-2.46480.28412180.24813954417295
2.4648-2.49720.31572060.24163964417095
2.4972-2.53150.27862280.24133956418496
2.5315-2.56760.25962070.23993952415996
2.5676-2.60590.29642080.24263983419196
2.6059-2.64670.27682240.23413961418596
2.6467-2.69010.30062150.23383911412696
2.6901-2.73650.28221920.23434014420696
2.7365-2.78620.29452050.24423935414095
2.7862-2.83980.29082190.24293917413695
2.8398-2.89780.27572210.23623961418297
2.8978-2.96080.29141890.23613972416196
2.9608-3.02970.2761970.22524031422897
3.0297-3.10540.27352180.22363969418796
3.1054-3.18940.2552010.22324004420596
3.1894-3.28320.26751960.22493928412495
3.2832-3.38920.26052400.223859409994
3.3892-3.51030.22462070.20063873408094
3.5103-3.65090.23122190.19543962418197
3.6509-3.8170.2122170.18684038425597
3.817-4.01820.20022050.17783968417397
4.0182-4.270.21012080.16853961416995
4.27-4.59960.18492100.1513781399192
4.5996-5.06230.16971920.14324020421297
5.0623-5.79460.19872080.16614008421697
5.7946-7.29930.21932040.19063874407894
7.2993-69.4060.19621960.17143951414796
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)
11.2567-0.5088-0.50872.1843-0.37441.62460.07850.2140.0177-0.7089-0.21180.8763-0.0091-0.09550.11210.51620.0254-0.25740.348-0.0480.553493.34665.1195216.1567
24.6467-1.406-0.15541.41660.09582.26250.0057-0.28361.40880.65770.41520.5269-0.9737-1.1838-0.24770.54970.2240.16790.79790.12680.809986.275273.2886240.4545
34.6955-0.23350.07742.33760.55064.4505-0.0913-0.2288-0.24570.401-0.10481.33390.1001-0.67960.09620.4529-0.06580.00180.4986-0.02560.986685.129558.8806229.8388
43.6325-0.95490.99274.81861.46511.54110.1148-0.1773-0.2294-0.5157-0.20890.96020.0619-0.07830.06410.47490.0039-0.14820.2778-0.05250.508698.969152.0894220.4223
53.3771-0.97340.06462.41860.66531.28010.09720.48210.0414-1.2425-0.1446-0.1821-0.08380.20920.07870.7580.0148-0.04970.4078-0.01150.3084110.059658.1839209.0401
64.4126-0.52240.37034.0290.13961.9807-0.0324-0.4766-0.08310.49410.03880.24630.3008-0.08370.00630.34390.00130.00780.3265-0.01330.2248112.597256.3248243.5164
71.00920.01780.20453.35790.02493.3481-0.0070.06850.1063-0.06860.0402-0.2464-0.01360.08-0.0240.2057-0.0330.0080.2967-0.0170.3552115.855167.9194234.0221
82.513-0.78880.42373.4812-0.07661.38610.17370.3295-0.5962-0.6683-0.32610.7718-0.2174-0.3030.21460.2275-0.0343-0.07870.2535-0.0310.357194.6241102.3498220.4402
91.7511-0.60420.72361.0647-0.30041.54720.15620.04170.0486-0.312-0.0218-0.3159-0.0894-0.1381-0.13830.2843-0.01760.04650.31990.01310.3994101.32795.8946223.2825
101.1542-0.19730.15322.71870.21581.59730.1218-0.6736-0.03890.7453-0.08540.00680.37590.0620.00420.2612-0.09330.05240.37690.01830.373798.872492.6922232.9508
112.1164-0.9717-1.13012.50580.63011.90440.00670.4809-0.2936-0.4538-0.14040.1150.0777-0.14320.10660.32330.02130.00180.4262-0.0680.411893.341691.9807222.9826
121.1010.01330.39751.7922-0.36060.19870.0068-0.25040.3695-0.0065-0.05060.2754-0.25440.18810.04580.2541-0.02830.03160.4408-0.02950.4597.1167103.473228.4893
131.2879-1.89670.05537.1366-0.47350.58270.073-0.04450.0276-0.87850.17730.3989-0.0339-0.2245-0.51240.336-0.06370.03880.29070.07940.488110.347392.3345223.1999
141.04670.4040.1921.7569-0.71481.027-0.38050.08470.02070.37830.25550.4962-0.24430.19280.25850.2676-0.0714-0.01010.35270.02160.505889.6857116.6637224.0858
151.2878-1.1891-0.29251.5281-0.15962.59990.2615-1.0701-0.05960.2705-0.3225-1.2498-0.430.224-0.25970.5299-0.1575-0.01090.466-0.02080.6868104.503142.9871224.2421
161.92320.7059-0.07972.61860.46891.1669-0.48050.38450.1537-0.61250.8867-0.6667-0.37740.3631-0.35170.5215-0.12370.08520.4912-0.1160.487599.5107130.8698219.2099
171.3318-0.05550.70431.88150.12381.65280.02610.5704-0.0543-0.14380.3005-0.6249-0.4283-0.1074-0.37440.4135-0.03810.11020.4187-0.06260.5007102.453128.0814223.3037
184.09654.3165-1.89436.4233-3.01514.04250.00180.14840.5301-0.26480.8914-0.8752-0.79360.0913-0.63270.5402-0.06980.2320.3899-0.12370.8741106.0016136.5305220.5265
192.12380.21710.15111.84520.07311.4359-0.51290.63580.0105-0.96020.592-0.42080.0942-0.0675-0.20770.826-0.29590.14210.7782-0.05560.640499.3218135.7177213.2347
203.59780.7353-0.5763.3209-0.19392.56820.0899-0.04590.8620.0596-0.02750.3186-0.0392-0.9663-0.0111.01630.0231-0.08730.6856-0.02260.583795.9672140.756216.5398
214.22622.9062-0.31432.5410.00882.70440.1007-0.54780.31370.37250.0096-0.69730.0721-0.35860.04190.2781-0.08970.05340.4356-0.05310.8205120.4694108.7674235.2838
222.9082-0.75810.87693.3693-0.1791.36050.0286-0.00870.43990.0759-0.0706-0.1785-0.1163-0.05140.03630.1859-0.02860.04150.28620.00150.3964118.8086100.5089230.2747
230.20130.2467-0.09271.80670.13290.0474-0.3921-0.03320.70440.1365-0.1721-1.0149-0.16990.2163-0.21530.0242-0.2253-0.07050.3576-0.07641.4391122.5229124.6601229.1654
243.58491.7086-1.06843.23950.17762.8336-0.0835-0.132-0.02480.53710.0047-0.528-0.1114-0.14920.10220.4583-0.0379-0.09320.33050.00680.4291104.152135.5305234.247
253.83160.53-0.95733.09730.59182.6480.1513-0.0859-0.02270.2059-0.327-0.5538-0.2888-0.17160.09930.471-0.0102-0.09370.33750.00280.4663106.6102137.6634234.4511
261.4679-0.99570.55385.34690.48752.409-0.1461-0.30240.17420.89730.15540.41060.15730.02050.05980.37610.00430.10350.2964-0.02110.3628109.974125.6996233.3669
270.70520.3580.19897.8497-0.86370.9432-0.0641-0.1043-0.07690.55060.05190.2164-0.08290.0229-0.05480.19120.03850.04510.3273-0.00270.2396112.82999.481226.7937
283.3729-0.6402-0.41733.45180.59953.44970.0698-0.1334-0.27480.27710.1354-0.0623-0.01070.0011-0.13830.2908-0.0289-0.00610.31270.05590.3784117.818-11.0333227.6569
295.0468-1.01050.03344.8320.22462.55280.2278-0.38960.2281-1.0729-0.04460.9307-0.4546-0.1714-0.40030.4518-0.0848-0.04030.30080.00740.5223104.12515.5872208.0651
301.04330.08160.21394.75520.17760.7148-0.082-0.03360.148-0.61260.06920.3191-0.2712-0.00650.01970.3071-0.0096-0.02730.2828-0.00370.2906108.382915.9023212.9493
311.1017-0.1089-0.83372.23150.06232.65210.0122-0.0076-0.06950.3-0.05060.2721-0.1242-0.03370.08440.22860.03690.05250.31950.0310.2784101.0133-8.8158219.8582
322.97260.3064-0.84741.6194-0.83073.5303-0.1188-0.2976-0.4380.06340.10710.05120.3207-0.12190.04620.24760.02920.06920.29210.05390.392102.7399-13.4088219.8346
332.2943-0.5514-0.11152.7393-0.04752.89440.01030.1301-0.11590.0167-0.05850.19450.22440.11590.06930.27450.0532-0.02470.2941-0.00950.22576.871676.9943192.3762
342.7249-0.5155-0.84071.81860.13753.1421-0.03140.09060.02580.0475-0.02730.3060.0487-0.25690.09930.25940.0304-0.04410.3189-0.02280.317866.822585.3598187.0809
351.5840.0798-1.39851.3756-0.63863.2259-0.08910.12190.0266-0.1267-0.0512-0.58880.31180.50580.17140.31160.0654-0.04320.51810.01880.376192.252282.9398180.511
361.96810.2202-0.51932.3948-0.29814.0395-0.06070.11680.1247-0.13990.02260.4642-0.1304-0.6073-0.0050.39560.0222-0.10820.47210.01330.348361.052479.4593162.6822
371.66620.9704-0.32861.6436-0.46842.674-0.0835-0.1774-0.2428-0.1950.11850.54060.4034-0.74610.03660.4526-0.0375-0.08860.4896-0.05980.45955.309170.0334164.2002
383.22431.04281.25722.99540.24162.682-0.048-0.2021-0.31290.24040.2888-0.17330.19920.1072-0.06220.61560.18230.09970.41250.07160.427279.682466.3977168.0476
391.9222-0.21411.62861.9801-0.31371.8535-0.11030.3686-0.1878-0.36680.0582-0.39670.28190.59640.06530.50040.10490.1240.5367-0.01480.289386.417471.1609160.9949
402.98960.31640.35623.645-0.64183.35050.3826-0.8998-0.10211.1288-0.43730.1259-0.08590.08630.11960.68410.0840.02160.4712-0.01950.407774.734440.6229195.4954
411.7273-0.1153-0.81093.0477-0.07972.3564-0.0958-0.14130.04240.5038-0.10490.38910.2235-0.2610.28840.469-0.01160.03720.4876-0.06310.354272.173647.8832187.7861
421.1240.55790.12753.06850.02241.66020.0978-0.4271-0.33660.6429-0.1256-0.14550.45320.00210.07910.81370.04270.05820.54930.0150.452876.58826.7973192.7604
435.8217-1.76520.84792.0798-0.21842.4795-0.10380.6737-0.7804-0.1449-0.2164-0.15790.43470.5384-0.08391.08040.0520.25520.87870.0940.785783.286612.5953201.4335
442.8127-0.8747-0.99162.5176-0.25452.36380.0570.6802-0.3938-0.6347-0.42110.36060.1281-0.69230.34630.68010.0070.01180.5789-0.1250.412175.818232.6968165.7638
452.0631-0.0599-0.5062.0593-0.45573.2741-0.1349-0.1261-0.22160.0072-0.0571-0.08460.8293-0.02290.13940.6970.00320.07890.3664-0.0480.308580.720130.0786175.2744
460.183-0.3412-0.06530.7697-0.50963.1625-0.33350.1566-0.3013-0.2578-0.02570.20240.3333-1.00460.37521.4122-0.11190.11370.7421-0.03520.694574.96316.1491184.0708
472.2921-0.59520.60481.7148-0.68492.63110.0292-0.3469-0.784-0.4347-0.29610.07921.2276-0.36670.03391.3219-0.14420.18220.69570.0320.699372.49027.3544188.4217
481.3766-2.2187-0.24413.65790.33960.0677-0.9705-0.1072-0.9132-0.73270.429-0.57240.9663-0.47940.75382.183-0.52550.47111.19380.04521.187273.8394-3.7232186.4593
492.27270.13130.02352.7158-0.25543.50550.25830.0957-0.1342-0.8446-0.48210.5428-0.589-0.10360.26460.4495-0.0225-0.11650.35820.0080.417268.9739117.2567157.9132
502.13390.06461.37471.9144-0.37692.1247-0.1847-0.10840.0611-0.43690.2074-0.0298-0.2287-0.21780.00950.38860.0079-0.02820.3926-0.0030.308673.5009111.3395165.0991
512.4577-0.6206-1.15963.82521.72533.8902-0.0823-0.3623-0.10190.2139-0.22210.61790.3444-0.44250.43860.28990.0419-0.02410.5118-0.03360.402566.0675107.8012170.0063
522.22480.22790.81422.4741-0.15821.8569-0.373-0.11420.5421-0.19260.05410.2956-0.3179-0.23150.35930.43320.026-0.09820.4477-0.01860.365568.8107113.9053163.6141
532.0005-0.43670.69633.3796-0.6872.185-0.40960.05580.3593-0.1132-0.09850.1079-0.5759-0.2670.33560.3714-0.0124-0.12840.39230.00940.279673.4118118.7262163.4297
540.06750.2065-0.12950.5874-0.42380.2787-0.40240.2460.4551-0.0836-0.60340.0145-0.81640.3406-0.41542.2666-0.1837-1.82350.55430.81820.982471.2547152.2572160.2169
550.603-1.34480.52053.6107-0.8110.5089-0.55521.01130.4629-1.09450.30340.7498-1.57490.0933-0.14321.8617-0.2347-0.46040.71240.17220.577175.014145.5958158.4837
560.3456-0.47260.2150.6211-0.31850.19230.7940.33270.1977-0.0577-0.7776-0.0403-0.25520.4190.09692.1839-0.3189-0.40070.99230.27681.153973.9334150.3233151.1588
572.79531.22580.04980.557-0.07610.257-0.05110.28880.78610.24210.05090.3654-0.2239-0.26310.08482.3054-0.2198-0.55680.74410.45850.95969.4352155.5841153.2843
581.88181.0851-0.24054.1573-0.03783.1210.1244-0.56640.00580.2437-0.2852-0.2184-0.2945-0.03510.15080.3947-0.0774-0.01870.47250.04640.339986.7665121.3863180.2433
593.5830.72060.90253.83731.08830.8051-0.17720.1369-0.0572-0.247-0.1658-0.8751-0.14380.21430.05330.4376-0.0299-0.00050.44990.05930.41991.3893116.3606173.9359
601.1684-0.23031.21873.57540.0431.4312-0.07880.0884-0.0193-0.1454-0.0294-0.2669-0.13640.02940.18010.4287-0.01630.00220.4309-0.01640.3184.8371118.667175.2278
610.0232-0.3036-0.06314.64050.73280.14440.1220.08670.45630.0614-0.3907-0.8679-0.9732-0.07650.29020.6291-0.1245-0.00520.43410.00480.504591.4627141.1208173.543
621.91760.8062-0.0313.6517-2.21152.22590.120.14330.2863-0.65750.43731.3407-0.3822-0.2718-0.12661.65710.0681-0.82430.3859-0.0911.670866.8372156.4116165.1211
633.26791.16491.83413.8937-0.28552.9374-0.287-0.70690.7598-1.145-0.3461.4721-0.593-0.37140.46270.72090.0075-0.25510.5015-0.12760.831777.0889147.0947173.0526
641.2341-0.1868-1.22840.00640.08181.156-0.3312-1.01921.2436-0.9597-0.40661.8803-1.1552-0.31680.3761.3250.4237-0.59130.7263-0.47111.970369.8594156.4906175.1501
65-0.00030.00510.0040.004-0.00430.0057-0.28810.38140.0795-0.10680.4756-0.0042-0.02690.1485-0.15421.3916-0.14820.4991.3059-0.02842.647545.235181.9454176.2154
661.16420.8462-0.71461.7520.47661.6572-0.0952-0.02060.21960.50770.2460.46580.3186-0.114-0.39821.157-0.1940.38651.2194-0.16291.219487.991959.0516247.8828
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 89 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 135 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 215 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 285 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 286 through 352 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 178 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 179 through 352 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 20 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 21 through 48 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 49 through 70 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 71 through 86 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 87 through 102 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 103 through 115 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 116 through 128 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 129 through 143 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 144 through 166 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 167 through 184 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 185 through 197 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 198 through 212 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 213 through 225 )C0
21X-RAY DIFFRACTION21chain 'D' and (resid 2 through 19 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 20 through 105 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 106 through 116 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 117 through 166 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 167 through 217 )D0
26X-RAY DIFFRACTION26chain 'E' and (resid 4 through 94 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 95 through 143 )E0
28X-RAY DIFFRACTION28chain 'E' and (resid 144 through 225 )E0
29X-RAY DIFFRACTION29chain 'F' and (resid 2 through 19 )F0
30X-RAY DIFFRACTION30chain 'F' and (resid 20 through 131 )F0
31X-RAY DIFFRACTION31chain 'F' and (resid 132 through 166 )F0
32X-RAY DIFFRACTION32chain 'F' and (resid 167 through 217 )F0
33X-RAY DIFFRACTION33chain 'G' and (resid 5 through 94 )G0
34X-RAY DIFFRACTION34chain 'G' and (resid 95 through 285 )G0
35X-RAY DIFFRACTION35chain 'G' and (resid 286 through 352 )G0
36X-RAY DIFFRACTION36chain 'H' and (resid 4 through 197 )H0
37X-RAY DIFFRACTION37chain 'H' and (resid 198 through 245 )H0
38X-RAY DIFFRACTION38chain 'H' and (resid 246 through 285 )H0
39X-RAY DIFFRACTION39chain 'H' and (resid 286 through 352 )H0
40X-RAY DIFFRACTION40chain 'I' and (resid 4 through 20 )I0
41X-RAY DIFFRACTION41chain 'I' and (resid 21 through 86 )I0
42X-RAY DIFFRACTION42chain 'I' and (resid 87 through 184 )I0
43X-RAY DIFFRACTION43chain 'I' and (resid 185 through 225 )I0
44X-RAY DIFFRACTION44chain 'J' and (resid 3 through 33 )J0
45X-RAY DIFFRACTION45chain 'J' and (resid 34 through 131 )J0
46X-RAY DIFFRACTION46chain 'J' and (resid 132 through 153 )J0
47X-RAY DIFFRACTION47chain 'J' and (resid 154 through 191 )J0
48X-RAY DIFFRACTION48chain 'J' and (resid 192 through 217 )J0
49X-RAY DIFFRACTION49chain 'K' and (resid 4 through 20 )K0
50X-RAY DIFFRACTION50chain 'K' and (resid 21 through 55 )K0
51X-RAY DIFFRACTION51chain 'K' and (resid 56 through 76 )K0
52X-RAY DIFFRACTION52chain 'K' and (resid 77 through 103 )K0
53X-RAY DIFFRACTION53chain 'K' and (resid 104 through 128 )K0
54X-RAY DIFFRACTION54chain 'K' and (resid 129 through 154 )K0
55X-RAY DIFFRACTION55chain 'K' and (resid 155 through 197 )K0
56X-RAY DIFFRACTION56chain 'K' and (resid 198 through 212 )K0
57X-RAY DIFFRACTION57chain 'K' and (resid 213 through 225 )K0
58X-RAY DIFFRACTION58chain 'L' and (resid 2 through 39 )L0
59X-RAY DIFFRACTION59chain 'L' and (resid 40 through 76 )L0
60X-RAY DIFFRACTION60chain 'L' and (resid 77 through 105 )L0
61X-RAY DIFFRACTION61chain 'L' and (resid 106 through 116 )L0
62X-RAY DIFFRACTION62chain 'L' and (resid 117 through 131 )L0
63X-RAY DIFFRACTION63chain 'L' and (resid 132 through 177 )L0
64X-RAY DIFFRACTION64chain 'L' and (resid 178 through 217 )L0
65X-RAY DIFFRACTION65chain 'g' and (resid 34 through 45 )g0
66X-RAY DIFFRACTION66chain 'a' and (resid 1 through 25 )a0

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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