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- PDB-4p5o: Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~... -

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基本情報

登録情報
データベース: PDB / ID: 4p5o
タイトルStructure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action
要素
  • Cullin-1
  • DCN1-like protein 1
  • E3 ubiquitin-protein ligase RBX1
  • NEDD8
  • NEDD8-conjugating enzyme Ubc12
キーワードLIGASE / Nedd8 / Cullin / Neddylation / Complex / Ubc12 / Dcn1 / ubiquitin
機能・相同性
機能・相同性情報


E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / positive regulation of protein neddylation / ubiquitin-like protein binding / Parkin-FBXW7-Cul1 ubiquitin ligase complex / regulation of protein neddylation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress ...E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / positive regulation of protein neddylation / ubiquitin-like protein binding / Parkin-FBXW7-Cul1 ubiquitin ligase complex / regulation of protein neddylation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation / ubiquitin conjugating enzyme binding / NEDD8 ligase activity / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / Prolactin receptor signaling / TGF-beta receptor signaling activates SMADs / cullin family protein binding / regulation of postsynapse assembly / regulation of proteolysis / anatomical structure morphogenesis / protein monoubiquitination / regulation of protein ubiquitination / ubiquitin ligase complex / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / negative regulation of insulin receptor signaling pathway / post-translational protein modification / intrinsic apoptotic signaling pathway / T cell activation / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / animal organ morphogenesis / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / cellular response to amino acid stimulus / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Recognition of DNA damage by PCNA-containing replication complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of canonical Wnt signaling pathway / Iron uptake and transport / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / DNA Damage Recognition in GG-NER / RING-type E3 ubiquitin transferase / protein modification process / Degradation of beta-catenin by the destruction complex / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / modification-dependent protein catabolic process / NOTCH1 Intracellular Domain Regulates Transcription / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / G1/S transition of mitotic cell cycle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Formation of Incision Complex in GG-NER / protein tag activity / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / Regulation of RAS by GAPs / positive regulation of protein catabolic process / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / cellular response to UV / UCH proteinases / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity
類似検索 - 分子機能
Cullin; Chain C, Domain 2 / Cullin Repeats / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / 5 helical Cullin repeat like / Nedd8-like ubiquitin / UBA-like domain ...Cullin; Chain C, Domain 2 / Cullin Repeats / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / 5 helical Cullin repeat like / Nedd8-like ubiquitin / UBA-like domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Herpes Virus-1 / Ribosomal Protein S5; domain 2 / Ubiquitin-conjugating enzyme/RWD-like / EF-hand / Recoverin; domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Roll / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
NEDD8-conjugating enzyme Ubc12 / E3 ubiquitin-protein ligase RBX1 / Cullin-1 / Ubiquitin-like protein NEDD8 / DCN1-like protein 1
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: 3.1071 Å
データ登録者Scott, D.C. / Schulman, B.A.
資金援助 米国, 2件
組織認可番号国
Howard Hughes Medical Institute (HHMI) 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM069530 米国
引用ジャーナル: Cell / 年: 2014
タイトル: Structure of a RING E3 Trapped in Action Reveals Ligation Mechanism for the Ubiquitin-like Protein NEDD8.
著者: Scott, D.C. / Sviderskiy, V.O. / Monda, J.K. / Lydeard, J.R. / Cho, S.E. / Harper, J.W. / Schulman, B.A.
履歴
登録2014年3月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年7月2日Provider: repository / タイプ: Initial release
改定 1.12017年9月6日Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
カテゴリ: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
改定 1.22019年11月20日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32020年1月29日Group: Advisory / Derived calculations / Refinement description
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_close_contact / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list
改定 2.02023年12月27日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_poly / struct_conn / struct_conn_type
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _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

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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: Cullin-1
B: E3 ubiquitin-protein ligase RBX1
E: DCN1-like protein 1
I: NEDD8-conjugating enzyme Ubc12
K: NEDD8
C: Cullin-1
D: E3 ubiquitin-protein ligase RBX1
F: DCN1-like protein 1
G: NEDD8-conjugating enzyme Ubc12
H: NEDD8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)217,83916
ポリマ－217,44710
非ポリマー3926
水00
1
A: Cullin-1
B: E3 ubiquitin-protein ligase RBX1
E: DCN1-like protein 1
I: NEDD8-conjugating enzyme Ubc12
K: NEDD8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)108,9208
ポリマ－108,7235
非ポリマー1963
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Cullin-1
D: E3 ubiquitin-protein ligase RBX1
F: DCN1-like protein 1
G: NEDD8-conjugating enzyme Ubc12
H: NEDD8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)108,9208
ポリマ－108,7235
非ポリマー1963
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)89.105, 129.606, 119.940
Angle α, β, γ (deg.)90.00, 111.79, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 5種, 10分子 ACBDEFIGKH

#1: タンパク質 Cullin-1 / CUL-1


分子量: 42722.051 Da / 分子数: 2 / 変異: L421E, V451E, V452K, Y455K, K720R / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CUL1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q13616
#2: タンパク質 E3 ubiquitin-protein ligase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / Rbx1 / Regulator of cullins 1


分子量: 12089.677 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: RBX1, RNF75, ROC1 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P62877, 合成酵素; C-N結合を形成; 酸-D-アミノ酸リガーゼ（ペプチド合成）
#3: タンパク質 DCN1-like protein 1 / DCUN1 domain-containing protein 1 / Defective in cullin neddylation protein 1-like protein 1 / ...DCUN1 domain-containing protein 1 / Defective in cullin neddylation protein 1-like protein 1 / Squamous cell carcinoma-related oncogene


分子量: 23237.461 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: DCUN1D1, DCUN1L1, RP42, SCCRO / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q96GG9
#4: タンパク質 NEDD8-conjugating enzyme Ubc12 / NEDD8 carrier protein / NEDD8 protein ligase / Ubiquitin-conjugating enzyme E2 M


分子量: 21754.795 Da / 分子数: 2 / 変異: N103S, C111S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2M, UBC12 / 発現宿主: Trichoplusia ni (イラクサキンウワバ)
参照: UniProt: P61081, 合成酵素; C-N結合を形成; 酸-D-アミノ酸リガーゼ（ペプチド合成）
#5: タンパク質 NEDD8 / Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / ...Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / Ubiquitin-like protein Nedd8


分子量: 8919.289 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: NEDD8 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q15843

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非ポリマー , 1種, 6分子

#6: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Zn

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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: 2.96 Å3/Da / 溶媒含有率: 58.41 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 11% PEG3350, 0.2M ammonium citrate, 10mM ATP / PH範囲: 6.5-6.9

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データ収集

回折平均測定温度: 80 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-E / 波長: 0.97912 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2013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: 0.97912 Å / 相対比: 1
反射解像度: 3.1→50 Å / Num. obs: 45594 / % possible obs: 99.9 % / 冗長度: 3.6 % / Net I/σ(I): 13.46

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解析

ソフトウェア名称: PHENIX / バージョン: (phenix.refine: 1.8.2_1309) / 分類: 精密化
精密化構造決定の手法: 分子置換 / 解像度: 3.1071→42.133 Å / SU ML: 0.46 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 33.61 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2843 2309 5.08 %
Rwork0.2274 --
obs0.2303 45452 99.51 %
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
精密化ステップサイクル: LAST / 解像度: 3.1071→42.133 Å
タンパク質核酸リガンド溶媒全体
原子数13571 0 6 0 13577
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00913857
X-RAY DIFFRACTIONf_angle_d1.23618683
X-RAY DIFFRACTIONf_dihedral_angle_d16.3095225
X-RAY DIFFRACTIONf_chiral_restr0.0492052
X-RAY DIFFRACTIONf_plane_restr0.0062393
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1071-3.17470.39361350.34422559X-RAY DIFFRACTION95
3.1747-3.24850.37931440.32732678X-RAY DIFFRACTION100
3.2485-3.32970.40221440.32592733X-RAY DIFFRACTION100
3.3297-3.41970.36181380.3162698X-RAY DIFFRACTION100
3.4197-3.52030.36051590.26662667X-RAY DIFFRACTION100
3.5203-3.63380.33911460.26182701X-RAY DIFFRACTION100
3.6338-3.76360.32651400.25122688X-RAY DIFFRACTION100
3.7636-3.91420.25671470.24462691X-RAY DIFFRACTION100
3.9142-4.09220.32691160.22212732X-RAY DIFFRACTION100
4.0922-4.30780.28781540.19852690X-RAY DIFFRACTION100
4.3078-4.57730.25981580.18942673X-RAY DIFFRACTION100
4.5773-4.93030.2571490.17722737X-RAY DIFFRACTION100
4.9303-5.42550.25081540.19812710X-RAY DIFFRACTION100
5.4255-6.20840.2571500.21762715X-RAY DIFFRACTION100
6.2084-7.81380.28381380.21962723X-RAY DIFFRACTION100
7.8138-42.13650.21641370.19432748X-RAY DIFFRACTION98
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)
14.0433-0.6538-0.30333.0226-0.6731.2550.0872-0.0268-0.36750.27450.0272-0.0857-0.09840.1388-0.11070.75060.1031-0.09130.74560.01810.5876-6.23221.216717.0742
21.02250.728-0.64871.20320.19481.9546-0.1066-0.311-0.19450.5651-0.03830.22150.4198-0.62840.21221.67780.19210.35331.7881-0.03561.4806-14.62616.484539.5488
32.1924-0.0755-0.9275.78163.27455.15820.44280.66420.61080.0399-1.72670.6171-0.6434-1.37271.05841.41870.23990.25991.2822-0.13911.2468-10.129323.739648.4746
43.81090.69831.13732.5883-0.5622.9863-0.3705-1.2627-0.310.90730.1253-0.51120.64460.18290.21562.3540.1634-0.56091.68310.04631.48484.775817.504853.185
52.0627-1.54980.7292.3883-0.50292.69040.4989-0.53080.48380.2202-0.68130.8648-0.18880.82610.11261.71350.1304-0.10881.7426-0.30891.1249-0.079628.294146.5798
62.4140.2822-0.27353.91740.0671.8716-0.2904-0.1068-0.02160.0330.3161-0.778-0.02960.03070.07990.77270.0657-0.0370.8281-0.01441.08720.67318.63512.5658
72.0743-2.3647-3.21612.62343.59894.8185-0.5163-1.07860.2841-0.41110.85640.4343-0.5229-1.28640.08341.45710.4910.59231.57740.38751.9615-15.396217.459545.0437
8-0.0285-0.0357-0.0161-0.04370.01480.01650.5844-0.3261-0.3235-0.81870.07991.51830.2044-0.0088-0.45461.96510.2570.24631.0973-0.05111.7241-2.3886-6.272335.4071
93.6121-1.60092.29814.16811.43213.2815-0.1571-0.6597-0.06552.31080.25550.17250.756-0.3455-0.30651.67260.2254-0.09271.15660.00531.184412.0854-14.529838.3583
108.6984-2.632.03311.554-1.36591.996-0.6268-0.1323-0.1532-0.0648-0.6979-0.2943-0.4519-0.02451.0121.76880.3451-0.1131.28370.07510.903222.733-14.799139.8744
111.04360.7676-0.61013.44150.38294.6706-0.0440.17590.25611.26460.2258-0.6470.48480.1575-0.11821.43140.28990.26330.97630.10560.886312.2358-4.254536.0432
124.11240.67980.43655.79380.43112.5542-0.8041-0.49620.69321.05170.81210.6836-0.3809-0.2323-0.1881.52570.26390.2611.04750.11271.39037.35570.717630.1189
133.64440.11150.22813.1016-0.28351.58020.0041-0.09880.1309-0.27170.09670.06530.04530.2113-0.03060.697-0.11740.09660.6886-0.00650.5608-6.197-21.788894.4016
144.20490.56780.84454.27110.97115.9578-0.96640.96360.2281-0.8635-0.61582.21110.0239-0.79981.25761.3992-0.0636-0.26451.6669-0.0851.4216-19.8167-8.521880.1962
150.95540.1038-0.23621.1051-0.66321.6686-0.18420.6034-0.2027-0.67640.00010.632-0.75640.02860.27021.5499-0.2349-0.44471.51030.01331.5976-12.7666-10.842268.5231
162.22070.11292.71717.6021.07583.4072-0.5583-0.2505-0.4974-0.25610.3447-0.2898-1.036-0.08250.12561.357-0.2113-0.28191.5689-0.21891.4327-6.1461-22.308962.7007
172.8760.4956-0.42251.5914-0.21090.5126-0.30520.6301-0.6472-0.3043-0.1607-0.196-0.33320.49430.58931.9569-0.16850.30821.7233-0.3071.10582.0782-24.678262.4673
182.4178-0.77620.62832.9380.29961.5854-0.27560.09740.01550.0720.2972-0.37620.01660.05110.05410.7563-0.07580.09190.8493-0.07550.991120.6815-9.257598.8811
196.50291.12720.70884.7543-0.05492.2942-0.66560.64730.41871.02990.976-0.3159-1.2802-0.0714-0.50731.5941-0.202-0.43041.07740.05111.39-12.9341-12.772170.4374
201.42130.7843-1.66670.4255-0.89711.94760.04520.17610.20330.3965-0.19510.21680.618-0.33940.13771.779-0.0094-0.2191.3449-0.16571.9094-2.32318.686475.0925
212.82052.1411-1.81212.39950.837.56721.10340.78280.3776-1.65940.50380.245-0.9219-0.7569-1.25551.7725-0.3952-0.11661.22180.11551.166611.532313.873973.5657
221.99241.135-9.64460.615-0.06942.0058-0.01320.61850.1797-0.2772-0.2966-0.44820.4768-0.17450.251.7134-0.2220.14931.2782-0.04090.881122.620814.185771.5491
231.74020.0932.55675.7324-0.03513.7159-0.480.3820.2718-0.48010.8793-0.4062-0.4781-0.3679-0.50841.6913-0.299-0.25581.20580.17021.30058.6073.544671.2353
245.5809-0.81681.72782.56620.85982.8256-0.0758-0.3405-1.4816-1.42070.6076-0.3130.4105-0.3534-0.56161.5703-0.328-0.18180.93720.05310.91210.57440.995279.1189
252.79780.04011.32073.1487-0.3221.11140.2344-1.7675-0.6408-0.5247-0.3786-0.8380.0127-0.45910.54691.44780.3151-0.26311.91380.0792.525453.7186-22.295133.1256
262.25810.9001-0.65582.17940.35021.8529-0.1984-0.2291-0.38250.5417-0.1433-1.9390.21510.30680.2561.16380.1613-0.04791.13980.24111.883955.9393-10.172826.8072
275.93932.00650.46445.3071-0.51513.64180.72370.6229-0.96230.0088-0.5337-0.6640.1756-0.19540.05371.06350.1285-0.06880.9651-0.38731.375348.5767-0.188916.8993
282.1402-0.0626-0.13982.7831-0.27951.96-0.1591-0.21310.60260.5589-0.0826-0.5812-0.0287-0.13040.20110.87390.0368-0.1330.8845-0.13721.265640.462813.0122.7035
290.54910.66590.39781.222-0.43071.5537-0.12630.54440.5419-0.732-0.7417-1.1639-0.18780.46940.77791.3978-0.270.4561.36270.09772.053654.568716.534576.4784
302.3325-0.24390.47262.09070.01171.4398-0.43740.44890.09630.0112-0.1171-0.069-0.32460.36970.35881.0695-0.2057-0.05711.19910.19441.658855.250910.381186.3849
312.0455-3.6934-0.48612.03214.3181.8606-0.66690.270.01920.80640.4784-0.0084-0.5611-0.13550.19241.29690.0034-0.55281.1519-0.15182.915458.6747-0.021196.6781
322.2236-0.43310.00973.0662-0.58121.31190.10730.07-0.2096-0.3194-0.2424-0.4232-0.0034-0.05460.08680.9654-0.04540.07630.9613-0.0831.33941.2337-11.835889.3513
330.6370.8277-0.91651.0272-0.46533.70860.37550.2245-0.4403-0.5965-0.6081-1.29730.31550.66880.86291.5505-0.10560.14761.71890.20251.936444.1736.501767.5904
341.38950.6886-0.18873.47320.18573.0239-0.13270.24-0.0084-0.52830.33010.2728-0.24060.2553-0.30240.7016-0.1182-0.09350.68140.01390.748916.899819.504695.8743
351.8611-0.0602-1.09052.4763-0.95472.2737-0.0128-0.1543-0.41930.0096-0.16110.08060.3599-0.17840.25660.7395-0.06430.04070.82070.0181.228311.010511.0585113.3096
362.7481-0.21741.0073.32850.05112.45050.0704-0.42560.47940.2213-0.1629-0.1066-0.1313-0.28650.06360.74070.0154-0.06630.7020.01560.727517.431823.9753118.2355
371.9994-0.79322.81384.1865-2.30141.64720.2462-0.52590.45760.41610.41620.0299-1.0306-0.2374-0.60962.1698-0.1969-1.17181.62960.36032.4074-6.169221.946385.9044
381.0883-1.15170.71731.1851-0.77380.45710.23340.3231-0.092-0.52060.18510.2118-0.4302-0.4522-0.01131.52820.088-0.27671.2894-0.00791.55620.082417.612881.6365
393.4571-2.1566-0.45814.4884-2.10052.99780.66970.5613-0.971-0.39490.54850.62971.04310.1244-0.85091.730.0407-0.13981.5530.07092.8789-13.84816.249492.3197
402.0281-1.8381.4254.8721.87954.27570.23720.5753-0.9503-0.44010.64280.49180.7770.4023-0.64031.7636-0.0292-0.57991.3441-0.43112.7534-6.1219.831985.4848
416.54681.5293-1.50973.6322-3.04194.23240.4248-0.70770.3891-0.8902-0.80830.5602-0.18890.79290.49511.3506-0.122-0.03131.25980.24131.7138-2.897114.352796.5829
422.0683-0.4145-0.12351.90760.3931.0397-0.5273-0.14660.27250.21270.0977-0.55410.6616-0.90440.6981.486-0.3365-0.00331.230.13231.4058-7.713324.103294.4957
432.06880.74693.30594.64124.36858.4172-0.79860.11760.8493-0.4382-0.72531.9913-0.1815-0.8961.28821.1131-0.1068-0.18210.9134-0.10421.48726.368511.48895.6006
442.9296-0.74350.87551.26321.13322.04680.1488-0.3092-0.19040.4848-0.7685-0.401-0.5774-0.11790.71921.9160.2874-0.61941.309-0.13531.561145.4778-5.679443.0751
451.15780.0185-0.3692.3880.89162.8483-0.2793-0.35870.14270.71450.29970.31470.37150.2679-0.04920.77620.17130.07130.744-0.04070.87317.9721-22.621816.7937
460.8644-0.4726-0.59331.04890.55163.0238-0.0288-0.14670.31510.2260.23290.3539-0.2459-0.0141-0.22260.74570.06150.08950.73730.04820.876514.0183-13.200110.9112
472.5314-1.3653-0.49682.633-0.12092.62210.12270.15930.1481-0.3089-0.01510.64520.1485-0.0956-0.09960.701-0.02-0.00990.75270.07090.970715.3415-20.4616-7.0478
480.8284-1.3548-0.22832.8214-1.07093.2803-0.1595-0.1566-0.19760.34380.0529-0.52041.4399-0.73630.17551.45840.02890.32690.96910.09391.2689-1.7191-20.146227.9734
496.32453.1789-1.25186.70321.03046.08420.0461-0.0103-0.2293-0.3483-1.39181.3507-0.6062-0.77941.02771.54560.14480.16461.5443-0.2222.4733-12.8853-17.513920.3605
501.78971.2184-0.25632.66671.90182.3660.8145-0.33841.3769-0.0340.32610.5414-0.9644-0.6673-0.67711.4830.09150.49761.1486-0.07972.1308-5.9463-10.211225.5658
516.49291.9909-0.46592.01351.54969.00681.53780.71030.1329-0.0554-0.76231.63180.63260.5173-0.99651.15610.2086-0.12741.24780.30922.198-0.2593-15.677516.0331
520.41990.38291.55126.11433.91086.7051-0.0501-0.17890.55020.03750.20760.76920.53540.0527-0.04721.93710.12490.20681.60390.20182.0696-9.0648-14.834310.5188
530.54540.04080.60860.0180.12010.83140.1017-0.2309-0.0979-0.52330.12880.4123-0.0854-0.2921-0.34171.55630.1690.30411.00790.10212.2476-4.9785-22.832218.2188
542.0077-2.78732.42088.23653.55182.9227-0.646-0.20560.2047-0.54410.39950.1455-0.9075-1.43590.0751.46460.3371-0.06971.20180.10820.81088.5571-9.323512.068
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 416:507)
2X-RAY DIFFRACTION2(chain A and resid 508:581)
3X-RAY DIFFRACTION3(chain A and resid 582:620)
4X-RAY DIFFRACTION4(chain A and resid 621:636)
5X-RAY DIFFRACTION5(chain A and resid 637:691)
6X-RAY DIFFRACTION6(chain A and resid 692:776)
7X-RAY DIFFRACTION7(chain B and resid 23:30)
8X-RAY DIFFRACTION8(chain B and resid 31:42)
9X-RAY DIFFRACTION9(chain B and resid 43:53)
10X-RAY DIFFRACTION10(chain B and resid 54:59)
11X-RAY DIFFRACTION11(chain B and resid 67:90)
12X-RAY DIFFRACTION12(chain B and resid 91:104)
13X-RAY DIFFRACTION13(chain C and resid 416:507)
14X-RAY DIFFRACTION14(chain C and resid 508:523)
15X-RAY DIFFRACTION15(chain C and resid 524:600)
16X-RAY DIFFRACTION16(chain C and resid 601:621)
17X-RAY DIFFRACTION17(chain C and resid 622:691)
18X-RAY DIFFRACTION18(chain C and resid 692:776)
19X-RAY DIFFRACTION19(chain D and resid 21:34)
20X-RAY DIFFRACTION20(chain D and resid 35:40)
21X-RAY DIFFRACTION21(chain D and resid 41:53)
22X-RAY DIFFRACTION22(chain D and resid 54:59)
23X-RAY DIFFRACTION23(chain D and resid 67:76)
24X-RAY DIFFRACTION24(chain D and resid 77:105)
25X-RAY DIFFRACTION25(chain E and resid 62:82)
26X-RAY DIFFRACTION26(chain E and resid 83:147)
27X-RAY DIFFRACTION27(chain E and resid 148:163)
28X-RAY DIFFRACTION28(chain E and resid 164:258)
29X-RAY DIFFRACTION29(chain F and resid 64:95)
30X-RAY DIFFRACTION30(chain F and resid 96:143)
31X-RAY DIFFRACTION31(chain F and resid 144:150)
32X-RAY DIFFRACTION32(chain F and resid 151:258)
33X-RAY DIFFRACTION33(chain G and resid 2:29)
34X-RAY DIFFRACTION34(chain G and resid 30:133)
35X-RAY DIFFRACTION35(chain G and resid 134:158)
36X-RAY DIFFRACTION36(chain G and resid 159:184)
37X-RAY DIFFRACTION37(chain H and resid 1:6)
38X-RAY DIFFRACTION38(chain H and resid 7:15)
39X-RAY DIFFRACTION39(chain H and resid 16:25)
40X-RAY DIFFRACTION40(chain H and resid 26:37)
41X-RAY DIFFRACTION41(chain H and resid 38:55)
42X-RAY DIFFRACTION42(chain H and resid 56:67)
43X-RAY DIFFRACTION43(chain H and resid 68:76)
44X-RAY DIFFRACTION44(chain I and resid 2:12)
45X-RAY DIFFRACTION45(chain I and resid 13:102)
46X-RAY DIFFRACTION46(chain I and resid 103:146)
47X-RAY DIFFRACTION47(chain I and resid 147:184)
48X-RAY DIFFRACTION48(chain K and resid 1:13)
49X-RAY DIFFRACTION49(chain K and resid 14:25)
50X-RAY DIFFRACTION50(chain K and resid 26:38)
51X-RAY DIFFRACTION51(chain K and resid 39:50)
52X-RAY DIFFRACTION52(chain K and resid 51:55)
53X-RAY DIFFRACTION53(chain K and resid 56:70)
54X-RAY DIFFRACTION54(chain K and resid 71:76)

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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