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- PDB-3ebb: PLAP/P97 complex -

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基本情報

登録情報
データベース: PDB / ID: 3ebb
タイトルPLAP/P97 complex
要素
  • PHOSPHOLIPASE A2-ACTIVATING PROTEIN
  • TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATP
キーワードCHAPERONE / ARMADILLO REPEAT / STRUCTURAL GENOMICS CONSORTIUM / SGC / WD repeat / ATP-binding / Disease mutation / Lipid-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Transport / Ubl conjugation pathway
機能・相同性
機能・相同性情報


positive regulation of synaptic vesicle recycling / negative regulation of protein K63-linked ubiquitination / positive regulation of phospholipase A2 activity / ubiquitin recycling / phospholipase A2 activator activity / positive regulation of neuron migration / positive regulation of dendrite extension / : / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / flavin adenine dinucleotide catabolic process ...positive regulation of synaptic vesicle recycling / negative regulation of protein K63-linked ubiquitination / positive regulation of phospholipase A2 activity / ubiquitin recycling / phospholipase A2 activator activity / positive regulation of neuron migration / positive regulation of dendrite extension / : / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / 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 / : / mitotic spindle disassembly / aggresome assembly / 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 / prostaglandin metabolic process / 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 / proteasomal protein catabolic process / ATP metabolic process / Protein methylation / endoplasmic reticulum unfolded protein response / phospholipid metabolic process / ERAD pathway / Attachment and Entry / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / ubiquitin binding / 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 / nervous system development / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / Neddylation / cellular response to heat / cellular response to lipopolysaccharide / 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 / inflammatory response
類似検索 - 分子機能
PUL domain / PLAA family ubiquitin binding domain / PFU domain superfamily / PUL domain / PFU (PLAA family ubiquitin binding) / PFU domain profile. / PUL domain profile. / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain ...PUL domain / PLAA family ubiquitin binding domain / PFU domain superfamily / PUL domain / PFU (PLAA family ubiquitin binding) / PFU domain profile. / PUL domain profile. / 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 / : / Leucine-rich Repeat Variant / Aspartate decarboxylase-like domain superfamily / Leucine-rich Repeat Variant / 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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
類似検索 - ドメイン・相同性
Transitional endoplasmic reticulum ATPase / Phospholipase A-2-activating protein
類似検索 - 構成要素
生物種HOMO SAPIENS (ヒト)
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: 1.9 Å
データ登録者Walker, J.R. / Qiu, L. / Akutsu, M. / Slessarev, Y. / Amaya, M.F. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. ...Walker, J.R. / Qiu, L. / Akutsu, M. / Slessarev, Y. / Amaya, M.F. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
引用ジャーナル: J.Biol.Chem. / 年: 2010
タイトル: Structure and function of the PLAA/Ufd3-p97/Cdc48 complex.
著者: Qiu, L. / Pashkova, N. / Walker, J.R. / Winistorfer, S. / Allali-Hassani, A. / Akutsu, M. / Piper, R. / Dhe-Paganon, S.
履歴
登録2008年8月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02009年2月24日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22014年4月2日Group: Source and taxonomy
改定 1.32024年10月9日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: PHOSPHOLIPASE A2-ACTIVATING PROTEIN
B: PHOSPHOLIPASE A2-ACTIVATING PROTEIN
C: PHOSPHOLIPASE A2-ACTIVATING PROTEIN
D: PHOSPHOLIPASE A2-ACTIVATING PROTEIN
E: TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATP
F: TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATP
G: TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATP
H: TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATP
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)139,3929
ポリマ－139,3688
非ポリマー241
水8,431468
1
A: PHOSPHOLIPASE A2-ACTIVATING PROTEIN
B: PHOSPHOLIPASE A2-ACTIVATING PROTEIN
E: TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATP
F: TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATP
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,7085
ポリマ－69,6844
非ポリマー241
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: PHOSPHOLIPASE A2-ACTIVATING PROTEIN
D: PHOSPHOLIPASE A2-ACTIVATING PROTEIN
G: TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATP
H: TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATP


分子量 (理論値)分子数
合計 (水以外)69,6844
ポリマ－69,6844
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)103.384, 68.651, 143.975
Angle α, β, γ (deg.)90.00, 103.45, 90.00
Int Tables number5
Space group name H-MC121

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要素

#1: タンパク質
PHOSPHOLIPASE A2-ACTIVATING PROTEIN / PLAP / PLA2P / DOA1


分子量: 33685.805 Da / 分子数: 4 / 断片: PUL DOMAIN, residues 511-795 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 遺伝子: PLAA, PLAP, FLJ11281, FLJ12699 / プラスミド: PET28-LIC / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: Q9Y263
#2: タンパク質・ペプチド
TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATP / 15S MG(2+)-ATPASE P97 SUBUNIT / VALOSIN-CONTAINING PROTEIN / VCP


分子量: 1156.070 Da / 分子数: 4 / 断片: C-TERMINAL PEPTIDE, residues 797-806 / 由来タイプ: 合成 / 詳細: OCCURS NATURALLY IN HUMANS / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P55072
#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: 1 / 由来タイプ: 合成 / 式: Mg
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 468 / 由来タイプ: 天然 / 式: H2O
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 30% PEG 4000, 0.1 M TRIS, PH 8.50, 0.2 M MGCL2, , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: 23-ID-B / 波長: 0.97945 / 波長: 0.97945 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2008年8月10日 / 詳細: MIRRORS
放射モノクロメーター: DOUBLE CRYSTAL / 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: 0.97945 Å / 相対比: 1
反射解像度: 1.9→50 Å / Num. all: 76756 / Num. obs: 76756 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 9.7 % / Rsym value: 0.064 / Net I/σ(I): 24.7
反射 シェル解像度: 1.9→1.97 Å / 冗長度: 3.1 % / Mean I/σ(I) obs: 3.2089 / Num. unique all: 7669 / Rsym value: 0.514 / % possible all: 99.6

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解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
SOLVE位相決定
RESOLVEモデル構築
REFMAC5.2.0019精密化
HKL-2000データ削減
HKL-2000データスケーリング
RESOLVE位相決定
精密化構造決定の手法: 単波長異常分散 / 解像度: 1.9→41.49 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.805 / SU ML: 0.115 / 交差検証法: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.167 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
Rfactor反射数%反射Selection details
Rfree0.24837 3849 5 %RANDOM
Rwork0.18777 ---
obs0.19079 72714 98.85 %-
all-76756 --
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK
原子変位パラメータBiso mean: 17.331 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.45 Å2
2---0.36 Å20 Å2
3---0.37 Å2
精密化ステップサイクル: LAST / 解像度: 1.9→41.49 Å
タンパク質核酸リガンド溶媒全体
原子数8139 0 1 468 8608
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228380
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.98611354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.83251083
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73826.219320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.782151562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9371520
X-RAY DIFFRACTIONr_chiral_restr0.0870.21375
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026062
X-RAY DIFFRACTIONr_nbd_refined0.2070.24142
X-RAY DIFFRACTIONr_nbtor_refined0.2980.26046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2438
X-RAY DIFFRACTIONr_metal_ion_refined0.1350.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.216
X-RAY DIFFRACTIONr_mcbond_it0.721.55590
X-RAY DIFFRACTIONr_mcangle_it1.14728731
X-RAY DIFFRACTIONr_scbond_it2.02733101
X-RAY DIFFRACTIONr_scangle_it2.9534.52623
LS精密化 シェル解像度: 1.9→1.949 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.33 296 -
Rwork0.236 5373 -
obs--99.18 %
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)
18.47020.170910.35024.8614-0.2312.6871-0.3590.50620.098-0.04090.0798-0.4032-0.18150.57040.2792-0.01720.06580.06670.1349-0.04850.06511.54333.471417.0742
26.46463.23590.70964.2227-1.41981.28820.4067-0.5894-0.46960.3403-0.2188-0.20860.1195-0.1219-0.18780.0943-0.00940.02280.0415-0.00820.0359-13.0161-12.417620.3139
320.6363-7.66-2.66757.70745.10986.34190.212-0.7163-0.02710.2069-0.28910.78160.479-0.95550.0771-0.102-0.10670.0590.12170.07710.0885-29.3366-14.070513.7091
410.5402-5.48162.76255.844-3.38713.23750.12950.3806-0.1872-0.2537-0.255-0.06310.15690.14930.12560.0455-0.00590.01440.012-0.00190.0487-12.9566-16.69586.6152
53.71290.5725-1.00852.6502-0.06754.1736-0.00150.1456-0.0481-0.1170.03510.083-0.0517-0.1514-0.03360.06390.0152-0.00230.0285-0.0270.0514-16.6508-5.75039.8369
62.3962-0.0768-0.74331.6518-0.73122.2563-0.04770.03940.0393-0.03550.0518-0.0246-0.0192-0.069-0.00410.06120.0238-0.00330.0535-0.03190.0697-13.42822.31713.8579
78.4153-3.0727-7.82296.4084.303723.084-0.048-0.06870.3612-0.12110.1756-0.0375-0.45680.2593-0.12770.0387-0.0004-0.0037-0.01210.00960.0781-10.489111.637112.2426
84.08040.1572-2.73823.1386-1.06514.49560.0208-0.30190.03420.1211-0.03080.0466-0.11860.05580.010.06130.0313-0.04540.1035-0.04170.0812-6.71336.198222.4545
96.5339-0.8587-1.95084.8611-0.901314.190.01530.4370.0689-0.7051-0.1486-0.28920.13930.41120.13340.08220.01230.02270.02890.02330.1006-0.217514.395914.3174
103.8381-0.585-0.29353.3837-0.34726.2970.1566-0.1488-0.07430.2399-0.0147-0.0957-0.12980.0611-0.14190.05090.0125-0.0160.086-0.02130.08121.93758.140125.2614
115.7926-2.29323.06244.2321-3.06347.8206-0.45610.2970.87890.0161-0.0046-0.6624-0.45920.20680.46070.0105-0.0808-0.0547-0.0051-0.01760.13476.612119.073221.8401
124.2475-10.42921.137360.812812.18556.6770.2014-0.95340.02584.1803-1.0571-1.35150.54040.5410.85560.2865-0.0704-0.0680.28190.00060.00259.44285.408935.2074
137.03041.30090.074311.9157-5.36427.46910.15570.34970.23990.3184-0.037-0.0667-0.32780.9671-0.11860.0005-0.02170.00280.1211-0.06110.052912.78110.441626.1938
1410.294-6.5414-2.370235.02420.428312.1454-0.09260.4013-0.5013-0.93380.00320.4025-0.7466-0.41970.08940.01290.0147-0.00420.03240.07660.1365-10.4006-25.141214.0523
159.01576.92464.24826.90972.96953.4334-0.1835-0.07460.518-0.2051-0.04380.4003-0.2876-0.04920.22730.0430.0165-0.030.06250.03050.08171.8583-18.623914.8221
1630.3257-11.317312.235610.7222-4.32946.9138-0.1943-0.45730.01170.21170.2410.1912-0.1841-0.2684-0.04670.0420.01240.02650.0321-0.03260.038317.9737-5.869629.468
174.5528-4.17165.91558.881-11.519820.1026-0.1553-0.0380.31030.0593-0.3769-0.70880.21770.83490.5322-0.0162-0.0242-0.0230.0292-0.0050.10231.4294-7.049727.5435
188.4354-3.44773.41751.4175-1.54784.12170.1840.23320.2426-0.2554-0.2984-0.17290.1175-0.09960.11440.05280.03450.03880.03530.0110.067917.556-3.038413.9574
191.2925-0.03820.32382.4265-0.15472.69650.02380.13130.1471-0.07150.045-0.17420.04810.0777-0.06890.02140.00840.03090.0718-0.00380.088621.7877-14.649616.9385
201.9673-0.1330.17691.43380.32131.6770.0503-0.0703-0.08450.16140.0579-0.07650.04310.1337-0.10820.04530.00150.00580.05210.01240.082917.2668-23.627221.5069
213.69721.6801-1.9887.0435-9.417118.65-0.16780.1527-0.2483-0.12570.137-0.11070.341-0.22620.03070.02180.01240.01020.0132-0.02770.060214.4496-31.231115.4056
221.642-0.38740.0242.08210.415.4648-0.0084-0.059-0.05270.13410.0547-0.03870.1350.0913-0.04630.0443-0.01120.02390.07370.02590.12256.2768-27.586722.9397
232.5278-0.6493-0.07842.95830.1963.16710.00260.004-0.1345-0.03180.02470.04020.23260.0713-0.02730.0811-0.0260.02250.06830.04180.12060.3213-32.264220.0982
245.62834.296-2.388912.257-9.495325.2310.02090.2089-0.4587-0.48220.08960.4289-0.14060.0342-0.11050.02390.0102-0.0177-0.01380.00060.0897-5.2589-41.623810.6672
254.3341-2.00471.018627.599710.42998.8769-0.2287-0.4658-0.40240.4915-0.181.19840.2358-0.10810.40870.0377-0.02310.15980.06010.17920.1165-10.1764-34.480626.9633
263.3311-1.1811-0.176711.34469.844312.4730.04090.0759-0.3920.1237-0.27020.62260.2704-0.64610.2293-0.0327-0.03230.03330.04110.06340.1944-12.5708-31.457119.5466
273.43722.59855.67053.49932.289911.9528-0.0476-0.17910.25330.0388-0.00570.27950.1751-0.24950.05330.1053-0.04510.0720.0315-0.02960.0768-26.71755.04750.7876
2811.1353-11.38-0.194513.46990.72440.15360.42170.548-0.3298-0.2633-0.58360.41250.0124-0.01750.16190.0958-0.0681-0.02920.07140.04970.0135-3.7279-10.996751.6167
2920.78947.2581-4.66435.7423-0.22225.141-0.11390.02450.1758-0.08930.4239-0.44930.09880.4189-0.31-0.0804-0.0259-0.0481-0.01890.05050.148715.0094-12.8857.7203
3014.21582.06581.82083.55380.97341.11540.0342-0.4433-0.26190.4272-0.2925-0.1333-0.1063-0.09850.25830.1144-0.0611-0.0450.01850.06010.029-2.7952-16.747263.6876
313.96980.1798-1.60773.5455-1.59922.7447-0.12-0.04120.08540.2857-0.2459-0.4161-0.20470.28130.36590.096-0.0982-0.13370.00670.0850.07534.2204-7.008360.4561
326.79652.3246-2.92465.6533-3.62276.0571-0.1378-0.32950.19340.9421-0.252-0.753-0.55530.31640.38980.2149-0.0718-0.2538-0.07150.03560.0735-0.30781.810262.6674
334.6057-1.9502-1.55123.86350.91073.9084-0.09830.07950.240.5717-0.1096-0.3849-0.12140.05320.20780.1438-0.0684-0.13950.0270.07930.0691-4.44651.20855.8843
347.57863.8414-14.37886.7284-9.804729.2053-0.1756-0.13560.39270.8928-0.3770.1134-1.90930.10370.55260.4083-0.1151-0.3472-0.18110.008-0.0074-5.319811.772760.5743
359.803415.77744.295238.36339.37912.35090.58270.80960.046-1.84630.1006-3.2538-0.71760.3563-0.68330.06330.04380.05250.16260.22830.122-0.970410.248445.026
365.8388-2.6596-4.05694.2871.61415.63960.02510.1205-0.01550.4392-0.223-0.0283-0.43720.06150.19790.1539-0.065-0.09210.04830.040.0185-12.59167.117352.6197
375.1511-3.1452-7.71515.03236.169523.6303-0.0683-0.0975-0.03320.44890.0350.0076-0.07050.3060.03330.11-0.0333-0.03820.0126-0.01610.0416-13.113316.653350.9043
380.97050.09140.88981.7479-0.74711.73470.07260.02570.03520.1509-0.160.1109-0.195-0.04310.08730.1119-0.0093-0.01030.0516-0.01350.0358-19.30414.282444.245
395.1174-4.1597-2.167312.29653.95054.47510.2580.1408-0.0345-0.1833-0.26180.4308-0.2101-0.20730.00380.0713-0.0053-0.00550.0518-0.01010.0359-25.21539.630640.0915
408.0117-1.98731.47342.90250.01572.3919-0.2921-0.12180.48010.18280.0495-0.2089-0.1484-0.20710.24260.0155-0.0508-0.02970.0282-0.01050.0576-12.9485-19.456955.0114
4120.82629.70226.58310.15613.88954.6730.3271-0.1481-0.197-0.0494-0.29140.2945-0.0579-0.1061-0.03560.10030.055-0.0344-0.0028-0.01650.0479-35.8496-6.901237.0162
426.21763.11293.52994.20310.94364.30250.0479-0.36480.23360.4369-0.13480.1541-0.4586-0.1010.08690.08620.02310.03190.0167-0.01130.0421-36.7414-3.262450.7022
433.7643-1.26572.56971.5742-1.48069.2417-0.0331-0.18440.1678-0.0110.12870.1117-0.1304-0.1078-0.09560.04790.0143-0.0261-0.0096-0.01290.1082-33.9037-13.443747.5087
449.1906-2.0708-2.14433.53370.355115.47730.3270.2191-0.8001-0.02310.01180.8680.4149-0.6723-0.3387-0.0356-0.0248-0.1377-0.07010.01510.2459-35.2594-23.329448.2098
454.4713-1.22460.47162.698-2.65063.77190.0921-0.2548-0.19190.1003-0.0250.1778-0.0980.1259-0.06720.02660.0162-0.04250.0378-0.01470.1099-27.0619-20.6451.9348
4614.8505-3.8634-4.35247.496313.234240.0442-0.13010.1395-1.8513-0.2431-0.27170.82740.23220.52370.4019-0.0685-0.0629-0.0564-0.1285-0.01380.3252-27.8627-32.18549.9446
474.5726-1.6645-0.0623.8716-2.900212.72630.1243-0.0692-0.3191-0.0189-0.24390.22210.0106-0.12360.11970.0359-0.0081-0.04160.0694-0.02310.1645-19.1582-26.331251.2076
4824.7513-9.12995.242435.364916.441849.1747-0.6032-2.3678-1.29722.8655-0.39772.10822.0933-2.24431.0010.1364-0.18090.14410.11540.08910.1172-19.8589-37.503257.7544
4910.76728.1597-3.713314.7107-6.79598.7545-0.24980.7773-0.2997-1.19320.0690.09630.6273-0.02240.18080.03590.0684-0.02650.0763-0.036-0.0459-14.3145-32.079543.3764
501.1378-1.57710.53216.9991-0.89012.67840.0072-0.01720.00040.6069-0.0621-0.07080.2581-0.21250.05490.09-0.0633-0.00160.0508-0.00050.0673-10.9554-34.369956.0854
515.85795.0619-1.55114.8603-2.29895.3332-0.11310.2371-0.3691-0.7454-0.0381-0.46220.34480.14580.15110.01830.08120.03270.04090.01740.0286-3.3337-32.218945.1259
527.9962-0.23262.539720.6778-6.542621.09240.2431-0.2377-0.2046-0.3847-0.3297-1.12080.59750.68630.0866-0.03590.0240.02250.05430.02260.1126-1.3865-32.416254.1258
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA531 - 53940 - 48
2X-RAY DIFFRACTION2AA540 - 55849 - 67
3X-RAY DIFFRACTION3AA559 - 57568 - 84
4X-RAY DIFFRACTION4AA576 - 59685 - 105
5X-RAY DIFFRACTION5AA597 - 635106 - 144
6X-RAY DIFFRACTION6AA636 - 675145 - 184
7X-RAY DIFFRACTION7AA676 - 688185 - 197
8X-RAY DIFFRACTION8AA689 - 711198 - 220
9X-RAY DIFFRACTION9AA712 - 733221 - 242
10X-RAY DIFFRACTION10AA734 - 753243 - 262
11X-RAY DIFFRACTION11AA754 - 775263 - 284
12X-RAY DIFFRACTION12AA776 - 782285 - 291
13X-RAY DIFFRACTION13AA783 - 795292 - 304
14X-RAY DIFFRACTION14BB531 - 53540 - 44
15X-RAY DIFFRACTION15BB536 - 54645 - 55
16X-RAY DIFFRACTION16BB547 - 55856 - 67
17X-RAY DIFFRACTION17BB559 - 57468 - 83
18X-RAY DIFFRACTION18BB575 - 59284 - 101
19X-RAY DIFFRACTION19BB593 - 636102 - 145
20X-RAY DIFFRACTION20BB637 - 672146 - 181
21X-RAY DIFFRACTION21BB673 - 689182 - 198
22X-RAY DIFFRACTION22BB690 - 713199 - 222
23X-RAY DIFFRACTION23BB714 - 754223 - 263
24X-RAY DIFFRACTION24BB755 - 768264 - 277
25X-RAY DIFFRACTION25BB769 - 781278 - 290
26X-RAY DIFFRACTION26BB782 - 795291 - 304
27X-RAY DIFFRACTION27CC530 - 53939 - 48
28X-RAY DIFFRACTION28CC540 - 55549 - 64
29X-RAY DIFFRACTION29CC556 - 57265 - 81
30X-RAY DIFFRACTION30CC573 - 59182 - 100
31X-RAY DIFFRACTION31CC592 - 621101 - 130
32X-RAY DIFFRACTION32CC622 - 650131 - 159
33X-RAY DIFFRACTION33CC651 - 673160 - 182
34X-RAY DIFFRACTION34CC674 - 686183 - 195
35X-RAY DIFFRACTION35CC687 - 695196 - 204
36X-RAY DIFFRACTION36CC696 - 716205 - 225
37X-RAY DIFFRACTION37CC717 - 736226 - 245
38X-RAY DIFFRACTION38CC737 - 779246 - 288
39X-RAY DIFFRACTION39CC780 - 795289 - 304
40X-RAY DIFFRACTION40DD532 - 54641 - 55
41X-RAY DIFFRACTION41DD547 - 56656 - 75
42X-RAY DIFFRACTION42DD567 - 59976 - 108
43X-RAY DIFFRACTION43DD600 - 629109 - 138
44X-RAY DIFFRACTION44DD630 - 654139 - 163
45X-RAY DIFFRACTION45DD655 - 675164 - 184
46X-RAY DIFFRACTION46DD676 - 692185 - 201
47X-RAY DIFFRACTION47DD694 - 716203 - 225
48X-RAY DIFFRACTION48DD719 - 727228 - 236
49X-RAY DIFFRACTION49DD728 - 740237 - 249
50X-RAY DIFFRACTION50DD741 - 767250 - 276
51X-RAY DIFFRACTION51DD768 - 785277 - 294
52X-RAY DIFFRACTION52DD786 - 795295 - 304

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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