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- PDB-5c1a: p97-N750D/R753D/M757D/Q760D in complex with ATP-gamma-S -

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基本情報

登録情報
データベース: PDB / ID: 5c1a
タイトルp97-N750D/R753D/M757D/Q760D in complex with ATP-gamma-S
要素Transitional endoplasmic reticulum ATPase
キーワードHYDROLASE / AAA ATPase / ERAD / VCP / CDC48
機能・相同性
機能・相同性情報


: / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex / protein-DNA covalent cross-linking repair / cytoplasm protein quality control ...: / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex / protein-DNA covalent cross-linking repair / cytoplasm protein quality control / positive regulation of protein K63-linked deubiquitination / positive regulation of oxidative phosphorylation / : / aggresome assembly / mitotic spindle disassembly / deubiquitinase activator activity / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / cellular response to misfolded protein / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / stress granule disassembly / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / MHC class I protein binding / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / HSF1 activation / translesion synthesis / interstrand cross-link repair / ATP metabolic process / proteasomal protein catabolic process / Protein methylation / endoplasmic reticulum unfolded protein response / ERAD pathway / Attachment and Entry / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / negative regulation of smoothened signaling pathway / macroautophagy / positive regulation of protein-containing complex assembly / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / establishment of protein localization / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of non-canonical NF-kappaB signal transduction / ADP binding / ABC-family proteins mediated transport / autophagy / positive regulation of protein catabolic process / cytoplasmic stress granule / Aggrephagy / azurophil granule lumen / KEAP1-NFE2L2 pathway / Ovarian tumor domain proteases / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / Neddylation / cellular response to heat / ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / ciliary basal body / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle / lipid binding / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum / protein-containing complex / ATP hydrolysis activity / RNA binding
類似検索 - 分子機能
Vps4 C terminal oligomerisation domain / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / : ...Vps4 C terminal oligomerisation domain / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / : / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Transitional endoplasmic reticulum ATPase
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: 3.8 Å
データ登録者Haenzelmann, P. / Schindelin, H.
引用ジャーナル: Structure / 年: 2016
タイトル: Structural Basis of ATP Hydrolysis and Intersubunit Signaling in the AAA+ ATPase p97.
著者: Hanzelmann, P. / Schindelin, H.
履歴
登録2015年6月13日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02016年1月13日Provider: repository / タイプ: Initial release
改定 1.12016年1月20日Group: Database references
改定 1.22024年1月10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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_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

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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: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
E: Transitional endoplasmic reticulum ATPase
F: Transitional endoplasmic reticulum ATPase
G: Transitional endoplasmic reticulum ATPase
H: Transitional endoplasmic reticulum ATPase
I: Transitional endoplasmic reticulum ATPase
J: Transitional endoplasmic reticulum ATPase
K: Transitional endoplasmic reticulum ATPase
L: Transitional endoplasmic reticulum ATPase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,083,96560
ポリマ－1,070,82412
非ポリマー13,14148
水00
1
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
E: Transitional endoplasmic reticulum ATPase
F: Transitional endoplasmic reticulum ATPase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)541,98330
ポリマ－535,4126
非ポリマー6,57124
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area56850 Å2
ΔGint-285 kcal/mol
Surface area176690 Å2
手法PISA
2
G: Transitional endoplasmic reticulum ATPase
H: Transitional endoplasmic reticulum ATPase
I: Transitional endoplasmic reticulum ATPase
J: Transitional endoplasmic reticulum ATPase
K: Transitional endoplasmic reticulum ATPase
L: Transitional endoplasmic reticulum ATPase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)541,98330
ポリマ－535,4126
非ポリマー6,57124
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area56430 Å2
ΔGint-291 kcal/mol
Surface area175470 Å2
手法PISA
単位格子
Length a, b, c (Å)182.669, 145.470, 251.397
Angle α, β, γ (deg.)90.000, 109.770, 90.000
Int Tables number4
Space group name H-MP1211
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
71chain G
81chain H
91chain I
101chain J
111chain K
121chain L

NCSドメイン領域:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: MG / End label comp-ID: MG / Auth seq-ID: 21 - 904 / Label seq-ID: 20

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA - P
2chain BBB - T
3chain CCC - X
4chain DDD - BA
5chain EEE - FA
6chain FFF - JA
7chain GGG - NA
8chain HHH - RA
9chain III - VA
10chain JJJ - ZA
11chain KKK - DB
12chain LLL - HB

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要素

#1: タンパク質
Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


分子量: 89235.352 Da / 分子数: 12 / 変異: N750D, R753D, M757D, Q760D / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: VCP / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P55072, vesicle-fusing ATPase
#2: 化合物...
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE / ATP-γ-S


分子量: 523.247 Da / 分子数: 24 / 由来タイプ: 合成 / 式: C10H16N5O12P3S
コメント: ATP-gamma-S, エネルギー貯蔵分子類似体*YM
#3: 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: 24 / 由来タイプ: 合成 / 式: Mg

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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: 2.94 Å3/Da / 溶媒含有率: 58.1 %
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: 9-9.5% PEG 4000, 0.4-0.5 M magnesium acetate, 0.1 M sodium-citrate pH 5.6

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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: ESRF / ビームライン: ID29 / 波長: 0.97625 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2014年7月7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: 0.97625 Å / 相対比: 1
反射解像度: 3.8→49.05 Å / Num. obs: 120767 / % possible obs: 98.9 % / 冗長度: 5.8 % / Biso Wilson estimate: 146.75 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.062 / Net I/σ(I): 8 / Num. measured all: 702900
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.8-3.8661.8711.13585059700.5010.80899.2
20.81-49.055.40.05929.138517180.9930.02890.5

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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
Aimless0.1.27データスケーリング
MxCuBEデータ収集
PHENIX精密化
PDB_EXTRACT3.15データ抽出
PHASER位相決定
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 3CF3

3cf3


解像度: 3.8→49.047 Å / SU ML: 0.57 / 交差検証法: NONE / σ(F): 1.34 / 位相誤差: 29.45 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2536 6032 5 %
Rwork0.1903 114583 -
obs0.1935 120615 98.64 %
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: 525.88 Å2 / Biso mean: 199.2002 Å2 / Biso min: 88.03 Å2
精密化ステップサイクル: final / 解像度: 3.8→49.047 Å
タンパク質核酸リガンド溶媒全体
原子数69306 0 1080 0 70386
Biso mean--139.46 --
残基数----8829
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00571213
X-RAY DIFFRACTIONf_angle_d1.00496323
X-RAY DIFFRACTIONf_chiral_restr0.03810796
X-RAY DIFFRACTIONf_plane_restr0.00512659
X-RAY DIFFRACTIONf_dihedral_angle_d17.16227696
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A53541X-RAY DIFFRACTION14.46TORSIONAL
12B53541X-RAY DIFFRACTION14.46TORSIONAL
13C53541X-RAY DIFFRACTION14.46TORSIONAL
14D53541X-RAY DIFFRACTION14.46TORSIONAL
15E53541X-RAY DIFFRACTION14.46TORSIONAL
16F53541X-RAY DIFFRACTION14.46TORSIONAL
17G53541X-RAY DIFFRACTION14.46TORSIONAL
18H53541X-RAY DIFFRACTION14.46TORSIONAL
19I53541X-RAY DIFFRACTION14.46TORSIONAL
110J53541X-RAY DIFFRACTION14.46TORSIONAL
111K53541X-RAY DIFFRACTION14.46TORSIONAL
112L53541X-RAY DIFFRACTION14.46TORSIONAL
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 (%)
3.8-3.84320.39251940.33243810400499
3.8432-3.88840.38311960.3313828402499
3.8884-3.93580.36632110.31443813402499
3.9358-3.98560.37541900.29273773396399
3.9856-4.0380.36682000.28763851405199
4.038-4.09330.31322240.27273767399199
4.0933-4.15170.27931990.26543841404099
4.1517-4.21370.29171800.24083762394299
4.2137-4.27950.30382090.24413784399398
4.2795-4.34960.31711840.22513684386895
4.3496-4.42450.27811940.21193833402799
4.4245-4.50490.26992210.2063799402099
4.5049-4.59150.26831960.19893855405199
4.5915-4.68520.25682150.19133828404399
4.6852-4.7870.24851890.183800398999
4.787-4.89820.2591850.19373843402899
4.8982-5.02060.25712060.18893840404699
5.0206-5.15620.2622140.18093796401099
5.1562-5.30770.26132190.19353764398398
5.3077-5.47890.27671870.20033766395397
5.4789-5.67440.29982030.20883848405199
5.6744-5.90120.28462080.19353838404699
5.9012-6.16930.28361900.19743867405799
6.1693-6.49390.30572270.21113829405699
6.4939-6.89970.27171960.18833873406999
6.8997-7.43080.22132170.16343751396897
7.4308-8.17550.211940.15523886408099
8.1755-9.35140.18191840.13233900408499
9.3514-11.75490.14861840.12163843402797
11.7549-49.05120.25522160.18843911412797
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9559-0.68761.00412.9076-0.44383.46750.0809-0.03710.41760.0553-0.1733-0.3907-0.50630.49930.1311.478-0.2637-0.00171.5290.10941.9548207.371342.508672.4768
21.3747-0.69431.80654.4629-0.93654.4766-0.1067-0.0120.37460.3795-0.0827-0.2435-0.28020.09710.21020.9238-0.03080.02951.2092-0.03341.3016195.465516.505872.8478
32.4104-1.2820.4481.6925-0.26731.9164-0.2437-0.15790.31590.32730.11340.1902-0.3864-0.1780.07121.44810.12490.20371.655-0.2531.8189160.573121.668486.8482
41.9802-1.08890.9144.1008-0.12843.4446-0.28080.44080.3447-0.99460.30640.03210.21840.4919-0.06671.53530.1030.26082.2440.29881.2471181.573118.738519.9879
53.0021.66352.03384.05090.21375.2184-0.18310.3640.2094-0.17490.01160.1098-0.05180.00380.12961.020.10940.02341.3462-0.0651.1252181.36162.982543.991
63.09881.3177-0.52573.26011.47992.2639-0.15460.37090.7276-0.2420.0020.6139-0.1539-0.46070.11340.83190.0576-0.03181.4112-0.01791.578146.3677.756258.7944
72.63880.07470.25245.02470.47782.11730.02051.043-0.3448-0.7786-0.2270.09080.2299-0.40770.12621.72880.0521-0.13971.9558-0.53191.4431168.4685-42.925116.8937
82.90842.27680.82764.90810.49432.97650.08780.0146-0.3104-0.0027-0.14090.35440.1552-0.29130.11281.0108-0.0203-0.04881.6091-0.30471.3122173.9878-31.181542.4374
90.9673-0.34620.05763.5528-0.22171.60320.18310.0975-0.44420.28070.05610.82140.3344-0.0822-0.21921.031-0.12890.10051.7625-0.25061.995140.7415-26.200557.1387
101.7017-1.55650.12842.4417-2.01152.1199-0.03040.1299-0.2411-0.338-0.31670.03180.5866-0.58850.2312.3565-0.16370.00721.6796-0.36961.9501181.2494-80.769165.0992
111.19020.06280.70762.8623-1.15314.95610.03680.157-0.219-0.18560.20690.56830.3978-0.2519-0.17971.2651-0.11380.07291.4443-0.32911.4571181.9841-52.398469.4498
121.8912-0.31710.55841.2404-0.74252.94740.0291-0.3826-0.5230.30010.23870.23470.4864-0.4736-0.31021.3539-0.22910.36411.54930.07481.9877148.5473-45.944684.2952
135.42080.71120.95873.17980.90995.0864-0.23860.0777-0.05820.225-0.0723-0.07050.38720.03920.32341.55380.1101-0.05951.17980.13711.2803209.6979-57.0886116.177
140.9292-0.34011.16143.19090.06795.7985-0.0779-0.1947-0.0092-0.00340.18020.14220.1977-0.2245-0.08351.03560.01190.10441.3330.01261.3416197.2693-39.052697.7213
151.4008-0.4382-0.31241.53270.97341.2205-0.0346-0.4991-0.02280.6842-0.02940.26930.3448-0.04550.08731.723-0.15310.41711.97120.0811.5335162.3322-31.9948112.3954
163.47560.96260.42894.2575-0.92054.3027-0.31860.10690.1086-0.04380.03530.0654-0.153-0.1750.32191.5512-0.0068-0.21541.2886-0.24621.3088220.65174.8417120.7649
172.00270.24750.38485.51590.08732.04780.03410.05090.2795-0.0194-0.03420.0959-0.1541-0.0325-0.00321.21860.015-0.00641.2163-0.07681.0581203.2404-4.61999.9633
181.1975-0.34870.28783.1446-1.27140.5651-0.1297-0.23560.18410.87060.11690.4416-0.52040.10280.04951.82810.05350.44491.8296-0.22981.4946168.72731.8363113.7587
192.5483-0.02140.44052.31632.10051.75970.2326-0.3489-0.14960.38350.1808-0.12880.7774-0.5048-0.39981.5921-0.31080.00481.55950.47671.6403230.4749-70.409779.685
202.05920.02431.68692.9160.0833.67460.1823-0.0438-0.12340.2596-0.0147-0.1279-0.00330.0675-0.19331.2183-0.06610.30011.21860.02541.3122232.8868-47.453262.7128
211.98810.54850.50872.55771.1342.69030.21750.4481-0.40960.03340.1482-0.25350.91860.4129-0.35431.50330.2520.20691.4939-0.08561.5191266.4871-52.678347.225
222.33040.19830.31341.150.37324.31350.0135-0.0702-0.12220.0134-0.34260.94640.18510.07680.26181.9307-0.114-0.2951.4166-0.00262.0937203.9059-70.271922.6065
231.00430.60711.85083.0740.3593.92490.29040.3543-0.3975-0.23460.04260.31920.17920.1188-0.22131.14270.03730.15741.4824-0.10991.4337218.601-47.224931.0903
241.85830.17780.95210.4461-1.15163.1650.07910.3929-0.0396-0.29250.0314-0.30560.44290.5157-0.14361.46230.25580.4281.7468-0.32761.3175252.8129-52.4515.8047
252.6417-0.7472-0.59564.1311-0.43450.95-0.17860.71860.3916-0.60870.23290.4855-0.4493-0.3868-0.02381.7710.0839-0.37122.1196-0.01541.6648199.5983-17.0144-10.8526
263.05760.61141.53473.2562-0.19833.23260.17650.47160.03-0.0175-0.23840.267-0.1420.12350.12511.30850.02070.07741.3966-0.10591.2844216.3413-17.696312.5571
271.42320.27390.04653.0662-0.48341.2803-0.50420.5523-0.0785-0.50660.3328-0.3153-0.20560.17670.20471.5125-0.05170.33252.0823-0.12961.183250.5447-22.5685-1.3911
281.98170.34630.88712.39731.68952.0508-0.12710.38410.1686-0.1186-0.24420.3419-0.63640.19990.45112.11840.191-0.42171.42740.13482.1068218.351836.875115.1799
291.83531.60131.2255.34580.97361.497-0.1075-0.03340.4322-0.1906-0.26180.3986-0.32110.13060.39351.30420.0661-0.03671.38080.04671.485226.880712.494127.2834
302.37761.45281.13553.08430.96032.4218-0.31990.76070.3671-0.51850.21640.0206-0.3720.60820.10641.0711-0.25120.27821.88550.37131.0509261.3087.188613.6848
312.3119-0.2270.35140.7445-0.58542.32990.13110.26720.52790.448-0.39810.3552-0.4186-0.46710.33152.19620.0802-0.0561.5825-0.36731.7547243.194137.497973.3642
323.5434-0.33391.9613.7622-0.18492.96480.0518-0.13670.19510.1554-0.37490.0198-0.1930.12750.22421.27420.0130.24041.4473-0.04121.2287240.426212.601159.3811
333.3025-0.19750.33812.7183-0.99114.66430.00180.32160.68530.0865-0.1697-0.5291-0.18060.61020.11080.7171-0.03280.21581.27010.12021.2704275.1936.536646.3819
342.0786-0.54110.90093.2995-1.10190.219-0.1845-0.48860.06260.31590.3787-0.2160.3499-0.1434-0.26692.1796-0.15040.22481.7167-0.08631.2227250.9732-16.709104.7441
352.6224-0.91872.48015.0421-0.29413.46640.0798-0.11310.02660.2943-0.2857-0.1179-0.09740.1560.10141.2105-0.23760.35291.3357-0.00131.1001244.2688-17.501476.9455
362.3219-0.15790.40394.444-0.31481.15780.2865-0.3131-0.26360.2897-0.1818-0.98580.3068-0.0004-0.08691.001-0.01370.08461.42350.19861.3677277.4102-23.456261.8767
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 200 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 201 through 460 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 461 through 770 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 21 through 200 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 201 through 460 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 461 through 770 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 21 through 200 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 201 through 460 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 461 through 770 )C0
10X-RAY DIFFRACTION10chain 'D' and (resid 21 through 200 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 201 through 460 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 461 through 770 )D0
13X-RAY DIFFRACTION13chain 'E' and (resid 21 through 200 )E0
14X-RAY DIFFRACTION14chain 'E' and (resid 201 through 460 )E0
15X-RAY DIFFRACTION15chain 'E' and (resid 461 through 770 )E0
16X-RAY DIFFRACTION16chain 'F' and (resid 21 through 200 )F0
17X-RAY DIFFRACTION17chain 'F' and (resid 201 through 460 )F0
18X-RAY DIFFRACTION18chain 'F' and (resid 461 through 770 )F0
19X-RAY DIFFRACTION19chain 'G' and (resid 21 through 200 )G0
20X-RAY DIFFRACTION20chain 'G' and (resid 201 through 460 )G0
21X-RAY DIFFRACTION21chain 'G' and (resid 461 through 770 )G0
22X-RAY DIFFRACTION22chain 'H' and (resid 21 through 200 )H0
23X-RAY DIFFRACTION23chain 'H' and (resid 201 through 460 )H0
24X-RAY DIFFRACTION24chain 'H' and (resid 461 through 770 )H0
25X-RAY DIFFRACTION25chain 'I' and (resid 21 through 200 )I0
26X-RAY DIFFRACTION26chain 'I' and (resid 201 through 460 )I0
27X-RAY DIFFRACTION27chain 'I' and (resid 461 through 770 )I0
28X-RAY DIFFRACTION28chain 'J' and (resid 21 through 200 )J0
29X-RAY DIFFRACTION29chain 'J' and (resid 201 through 460 )J0
30X-RAY DIFFRACTION30chain 'J' and (resid 461 through 770 )J0
31X-RAY DIFFRACTION31chain 'K' and (resid 21 through 200 )K0
32X-RAY DIFFRACTION32chain 'K' and (resid 201 through 460 )K0
33X-RAY DIFFRACTION33chain 'K' and (resid 461 through 770 )K0
34X-RAY DIFFRACTION34chain 'L' and (resid 21 through 200 )L0
35X-RAY DIFFRACTION35chain 'L' and (resid 201 through 460 )L0
36X-RAY DIFFRACTION36chain 'L' and (resid 461 through 770 )L0

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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