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- PDB-3ihp: Covalent Ubiquitin-Usp5 Complex -

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基本情報

登録情報
データベース: PDB / ID: 3ihp
タイトルCovalent Ubiquitin-Usp5 Complex
要素
  • Ubiquitin
  • Ubiquitin carboxyl-terminal hydrolase 5
キーワードHYDROLASE / PROTEASE / THIOL PROTEASE / UBL CONJUGATION PATHWAY / METAL-BINDING / ZINC-FINGER / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Acetylation / Alternative splicing / Phosphoprotein / Zinc / Cytoplasm / Isopeptide bond / Nucleus / Ubl conjugation
機能・相同性
機能・相同性情報


regulation protein catabolic process at presynapse / : / : / protein modification process => GO:0036211 / negative regulation of T cell mediated immune response to tumor cell / protein K48-linked deubiquitination / deubiquitinase activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits ...regulation protein catabolic process at presynapse / : / : / protein modification process => GO:0036211 / negative regulation of T cell mediated immune response to tumor cell / protein K48-linked deubiquitination / deubiquitinase activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of ubiquitin-dependent protein catabolic process / protein deubiquitination / Viral mRNA Translation / Maturation of protein E / Maturation of protein E / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / L13a-mediated translational silencing of Ceruloplasmin expression / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / TCF dependent signaling in response to WNT / cytosolic ribosome / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / APC/C:Cdc20 mediated degradation of Securin / activated TAK1 mediates p38 MAPK activation / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / Regulation of signaling by CBL / NIK-->noncanonical NF-kB signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / SCF-beta-TrCP mediated degradation of Emi1 / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR3 signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Fanconi Anemia Pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex
類似検索 - 分子機能
Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain / Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / UBA-like domain / : / Ubiquitin-associated (UBA) domain / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein ...Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain / Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / UBA-like domain / : / Ubiquitin-associated (UBA) domain / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / UBA/TS-N domain / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Ubiquitin associated domain / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Cysteine proteinases / Zinc/RING finger domain, C3HC4 (zinc finger) / Cathepsin B; Chain A / Herpes Virus-1 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Helicase, Ruva Protein; domain 3 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
ETHANAMINE / Polyubiquitin-C / Ubiquitin carboxyl-terminal hydrolase 5 / Isoform Short of Ubiquitin carboxyl-terminal hydrolase 5 / Ubiquitin-60S ribosomal protein L40
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: 2.8 Å
データ登録者Walker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
引用ジャーナル: To be Published
タイトル: Covalent Ubiquitin-Usp5 Complex
著者: Walker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
履歴
登録2009年7月30日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02009年12月29日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22023年9月6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 / struct_ref_seq_dif / 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_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_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.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_type.id / _struct_ref_seq_dif.details / _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: Ubiquitin carboxyl-terminal hydrolase 5
B: Ubiquitin carboxyl-terminal hydrolase 5
C: Ubiquitin
D: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)208,1969
ポリマ－207,9394
非ポリマー2565
水57632
1
A: Ubiquitin carboxyl-terminal hydrolase 5
C: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)104,0804
ポリマ－103,9702
非ポリマー1102
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-8 kcal/mol
Surface area35540 Å2
手法PISA
2
B: Ubiquitin carboxyl-terminal hydrolase 5
D: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)104,1165
ポリマ－103,9702
非ポリマー1463
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-19 kcal/mol
Surface area36140 Å2
手法PISA
単位格子
Length a, b, c (Å)68.295, 188.845, 207.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
12C
22D

NCSドメイン領域:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 835
2114B1 - 835
1124C1 - 76
2124D1 - 76

NCSアンサンブル:
ID
2
1

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要素

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タンパク質 , 2種, 4分子 ABCD

#1: タンパク質 Ubiquitin carboxyl-terminal hydrolase 5 / Ubiquitin thioesterase 5 / Ubiquitin-specific-processing protease 5 / Deubiquitinating enzyme 5 / ...Ubiquitin thioesterase 5 / Ubiquitin-specific-processing protease 5 / Deubiquitinating enzyme 5 / Isopeptidase T


分子量: 95449.883 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ISOT, USP5 / プラスミド: PET28a-LIC / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 (DE3)
参照: UniProt: P45974-2, UniProt: P45974*PLUS, EC: 3.1.2.15
#2: タンパク質 Ubiquitin


分子量: 8519.778 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RPS27A, UBA52, UBA80, UBB, UBC, UBCEP1, UBCEP2 / プラスミド: PTBY2 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): B21 (DE3) / 参照: UniProt: P62988, UniProt: P0CG48*PLUS

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非ポリマー , 4種, 37分子

#3: 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
#4: 化合物 ChemComp-NEH / ETHANAMINE / エチルアミン


分子量: 45.084 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H7N
#5: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 32 / 由来タイプ: 天然 / 式: H2O

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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: 3.22 Å3/Da / 溶媒含有率: 61.82 %
結晶化温度: 298 K / pH: 6.5
詳細: Crystals of the covalent ubiquitin complex of Usp5 were grown at 298 K using the hanging drop method by mixing equal volumes of protein solution (25 mg/ml) and Crystallization Buffer (1.45 M ...詳細: Crystals of the covalent ubiquitin complex of Usp5 were grown at 298 K using the hanging drop method by mixing equal volumes of protein solution (25 mg/ml) and Crystallization Buffer (1.45 M ammonium sulfate, 0.1 M bis-Tris, pH 6.5, 0.2 M sodium acetate, 5% ethyleneglycol and 1 mM dithiothreitol). The crystals were cryoprotected by immersion in Paratone N in paraffin oil 30% (v/v) and placed in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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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: 0.97918
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2007年6月11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: 0.97918 Å / 相対比: 1
反射解像度: 2.8→35 Å / Num. obs: 66229 / % possible obs: 98 % / Observed criterion σ(I): -3 / 冗長度: 5.4 % / Rsym value: 0.101 / Net I/σ(I): 17.1
反射 シェル解像度: 2.8→2.9 Å / 冗長度: 5.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.845 / % possible all: 94.6

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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
PHASER位相決定
REFMAC5.5.0102精密化
HKL-2000データ削減
HKL-2000データスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRIES 2IBI, 2G43, 2DAK, 2DAG

2ibi

2g43

2dak

2dag


解像度: 2.8→34.9 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.889 / SU B: 30.552 / SU ML: 0.272 / 交差検証法: THROUGHOUT / ESU R: 0.563 / ESU R Free: 0.343 / 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 CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUMOF TLS AND RESIDUAL U FACTORS.
Rfactor反射数%反射Selection details
Rfree0.27588 3298 5 %RANDOM
Rwork0.22431 ---
obs0.22688 62592 98.05 %-
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: MASK
原子変位パラメータBiso mean: 73.948 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.04 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→34.9 Å
タンパク質核酸リガンド溶媒全体
原子数11759 0 9 32 11800
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02212019
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.96716278
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97551491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01424.56557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.655152014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9231568
X-RAY DIFFRACTIONr_chiral_restr0.090.21803
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219149
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4691.57512
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.898212082
X-RAY DIFFRACTIONr_scbond_it1.27534507
X-RAY DIFFRACTIONr_scangle_it2.2374.54196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-ID数タイプRms dev position (Å)Weight position
11A4816medium positional0.610.5
22C600medium positional0.330.5
11A4816medium thermal0.392
22C600medium thermal0.452
LS精密化 シェル解像度: 2.8→2.872 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.358 234 -
Rwork0.303 4388 -
obs--94.21 %
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)
15.5849-0.65662.57990.46020.30025.1070.1846-0.1417-0.0265-0.08530.0434-0.06610.33110.0756-0.2280.4747-0.11320.01580.2297-0.05810.1774-77.4876-62.849-74.8262
24.29541.32050.41690.60720.31570.26540.1766-0.1414-0.0786-0.0657-0.1829-0.07420.0911-0.03690.00630.5287-0.04780.04670.26830.04210.1994-59.4187-53.906-79.8348
34.4352-0.8951-0.29064.73571.2625.4002-0.0974-0.1568-0.17090.21750.15970.59480.0747-0.4805-0.06220.3187-0.03310.12120.21890.0980.3092-37.1802-45.455-76.4435
42.6241-0.14810.5550.83340.36642.54110.07880.12610.0041-0.229-0.17530.02690.1955-0.27480.09650.3838-0.06690.03420.3538-0.08330.2193-61.6675-61.6046-53.8172
50.3761-0.5527-0.78581.14131.62181.8699-0.0119-0.20410.19880.14120.0937-0.14040.03640.3127-0.08190.3537-0.0529-0.01760.49690.10210.3658-40.4289-53.4996-32.822
60.49450.04710.17520.57310.57551.17920.0034-0.0387-0.01450.01250.0218-0.12260.05850.2655-0.02520.3258-0.05730.05390.3613-0.01330.32-41.726-54.8597-34.0322
70.23720.53810.04362.15991.9371.35210.00260.06820.2018-0.2921-0.52510.6153-0.2877-0.59220.52240.28580.0941-0.14290.536-0.18010.4833-61.4187-26.1704-21.0356
89.66931.8553-2.50125.8601-0.24423.22990.1754-0.01190.28740.2337-0.33150.2319-0.4319-0.53520.15610.17870.0385-0.02450.4626-0.16750.2691-73.7781-42.7836-37.4903
92.17110.5145-1.26461.01350.68253.8495-0.03520.2057-0.2945-0.0164-0.0001-0.08260.56830.17520.03540.40230.00620.09520.2688-0.03040.332-48.1201-68.0426-46.2916
103.90712.4008-1.86586.4874-0.08930.89840.0427-0.09490.1780.1649-0.02880.13850.07930.0285-0.01390.370.0069-0.05640.1965-0.05370.2209-74.187320.245813.983
112.73961.22090.02225.26060.3852.39240.2554-0.10250.00760.1474-0.32720.1233-0.1564-0.00870.07180.3872-0.0241-0.04670.1962-0.10990.2305-73.555722.594515.7112
120.1516-0.85430.6754.8296-2.26335.91370.0053-0.06340.0377-0.3756-0.3726-0.43980.70130.95860.36730.40880.21140.06530.44450.16180.3134-117.36919.5143-0.5808
132.31890.948-0.23281.96260.65721.4790.1141-0.0074-0.01840.01310.0908-0.1783-0.21110.1201-0.20490.3464-0.0033-0.0210.1949-0.06980.2979-90.228-2.358212.5205
140.6138-0.4922-0.64611.03681.11941.1945-0.01560.1181-0.2929-0.0505-0.10550.22690.0951-0.17620.1210.338-0.0196-0.08890.27260.01680.4306-114.7891-19.41063.2659
150.84090.37440.05050.61140.62231.2446-0.0084-0.0058-0.13780.0545-0.00390.10790.0851-0.15110.01220.29550.0278-0.0690.24910.01280.3523-108.894-23.0213.7434
160.2444-0.00350.34450.95332.23844.5937-0.00930.1990.1129-0.18890.3899-0.3216-0.22870.6045-0.38060.2337-0.14190.08030.496-0.18510.5427-90.9323-30.4362-26.2722
1712.6904-4.5425-0.26634.418-0.25359.17870.1094-0.14750.195-0.55740.3835-0.4683-0.27870.9051-0.4930.1296-0.06570.03750.3811-0.23780.3502-79.0098-15.7455-8.0439
182.1883-0.27670.52292.76640.41031.59540.1133-0.1560.01650.24080.00460.1281-0.0337-0.0129-0.11790.29480.0481-0.02130.2502-0.01540.2632-103.8947-10.9418.4682
198.98862.61230.2732.7594-5.61277.5587-0.2569-0.02940.47140.1498-0.168-0.1987-0.09770.30490.42490.2448-0.1347-0.02630.3346-0.10170.3338-47.0098-40.9947-30.8543
2015.1866-2.1986-5.44235.1025.17094.95080.2687-0.18750.6116-1.1581-0.0105-0.1977-1.36070.1192-0.25810.7129-0.12420.09930.20770.02060.4363-49.6866-34.2992-38.7771
2110.7048-0.0543-1.19414.61061.29572.51920.28810.9148-0.2322-0.7482-0.22810.317-0.5817-0.0393-0.060.3745-0.0049-0.0290.3633-0.01310.2418-55.5405-42.8028-42.0097
222.3848-1.7581-2.61213.012.42613.75170.0178-0.09070.3397-0.0862-0.0122-0.02240.02780.055-0.00560.3137-0.07420.00880.3783-0.01790.2829-53.1063-45.2677-38.3397
239.56493.95310.06339.4715-2.9852.9559-0.58280.1468-0.5257-0.03740.02920.48720.5536-0.42030.55360.4059-0.08910.05220.3398-0.17340.4919-105.6727-22.5102-10.05
2410.5793-5.51050.78525.16940.33914.41940.35731.1270.3187-0.8135-0.1994-0.1746-0.8415-0.2999-0.15790.38140.0398-0.04650.31990.01850.2591-103.0758-13.8639-15.89
2511.1447-1.1919-0.66382.77893.06723.15110.36020.00280.6687-0.50010.0557-0.3849-0.56410.1829-0.41590.4031-0.03440.01180.2197-0.01060.3357-97.5378-11.4251-6.8727
263.3145-2.3201-1.09763.913.06344.92350.02420.1122-0.2312-0.10950.23410.1053-0.25850.3012-0.25830.285-0.0265-0.05010.21380.02130.3441-99.1186-15.6076-5.3257
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 121
2X-RAY DIFFRACTION2A122 - 203
3X-RAY DIFFRACTION3A204 - 282
4X-RAY DIFFRACTION4A283 - 462
5X-RAY DIFFRACTION5A463 - 513
6X-RAY DIFFRACTION6A514 - 607
7X-RAY DIFFRACTION7A608 - 711
8X-RAY DIFFRACTION8A712 - 749
9X-RAY DIFFRACTION9A769 - 834
10X-RAY DIFFRACTION10B1 - 40
11X-RAY DIFFRACTION11B41 - 156
12X-RAY DIFFRACTION12B173 - 320
13X-RAY DIFFRACTION13B321 - 462
14X-RAY DIFFRACTION14B463 - 520
15X-RAY DIFFRACTION15B521 - 607
16X-RAY DIFFRACTION16B608 - 712
17X-RAY DIFFRACTION17B713 - 750
18X-RAY DIFFRACTION18B768 - 835
19X-RAY DIFFRACTION19C1 - 16
20X-RAY DIFFRACTION20C17 - 39
21X-RAY DIFFRACTION21C40 - 57
22X-RAY DIFFRACTION22C58 - 75
23X-RAY DIFFRACTION23D1 - 16
24X-RAY DIFFRACTION24D17 - 39
25X-RAY DIFFRACTION25D40 - 56
26X-RAY DIFFRACTION26D57 - 75

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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