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- PDB-2n8a: 1H, 13C and 15N chemical shift assignments and solution structure... -

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基本情報

登録情報
データベース: PDB / ID: 2n8a
タイトル1H, 13C and 15N chemical shift assignments and solution structure for PARP-1 F1F2 domains in complex with a DNA single-strand break
要素
  • DNA (45-MER)
  • Poly [ADP-ribose] polymerase 1
キーワードTRANSFERASE
機能・相同性
機能・相同性情報


NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / regulation of base-excision repair / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis ...NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / regulation of base-excision repair / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / positive regulation of single strand break repair / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / regulation of catalytic activity / negative regulation of adipose tissue development / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / mitochondrial DNA metabolic process / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / replication fork reversal / ATP generation from poly-ADP-D-ribose / positive regulation of necroptotic process / transcription regulator activator activity / HDR through MMEJ (alt-NHEJ) / positive regulation of DNA-templated transcription, elongation / signal transduction involved in regulation of gene expression / NAD+ ADP-ribosyltransferase / cellular response to zinc ion / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / NAD+-protein-aspartate ADP-ribosyltransferase activity / mitochondrial DNA repair / protein poly-ADP-ribosylation / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / NAD+-protein-glutamate ADP-ribosyltransferase activity / response to aldosterone / positive regulation of mitochondrial depolarization / positive regulation of cardiac muscle hypertrophy / NAD+-protein mono-ADP-ribosyltransferase activity / R-SMAD binding / nuclear replication fork / negative regulation of transcription elongation by RNA polymerase II / protein autoprocessing / site of DNA damage / macrophage differentiation / NAD+ poly-ADP-ribosyltransferase activity / decidualization / 転移酵素; グリコシル基を移すもの; 五炭糖残基を移すもの / POLB-Dependent Long Patch Base Excision Repair / positive regulation of SMAD protein signal transduction / positive regulation of double-strand break repair via homologous recombination / SUMOylation of DNA damage response and repair proteins / nucleosome binding / protein localization to chromatin / nucleotidyltransferase activity / telomere maintenance / transforming growth factor beta receptor signaling pathway / negative regulation of innate immune response / nuclear estrogen receptor binding / response to gamma radiation / mitochondrion organization / Downregulation of SMAD2/3:SMAD4 transcriptional activity / cellular response to nerve growth factor stimulus / DNA Damage Recognition in GG-NER / protein-DNA complex / protein modification process / positive regulation of protein localization to nucleus / Dual Incision in GG-NER / histone deacetylase binding / Formation of Incision Complex in GG-NER / cellular response to insulin stimulus / cellular response to amyloid-beta / NAD binding / cellular response to UV / nuclear envelope / double-strand break repair / regulation of protein localization / site of double-strand break / cellular response to oxidative stress / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / damaged DNA binding / positive regulation of canonical NF-kappaB signal transduction / chromosome, telomeric region / nuclear body / innate immune response / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / DNA damage response / chromatin binding / protein kinase binding / chromatin / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity
類似検索 - 分子機能
Zinc finger, PARP-type / first zn-finger domain of poly(adp-ribose) polymerase-1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 ...Zinc finger, PARP-type / first zn-finger domain of poly(adp-ribose) polymerase-1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / : / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / Poly [ADP-ribose] polymerase 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法溶液NMR / simulated annealing
Model detailslowest energy, model1
データ登録者Neuhaus, D. / Eustermann, S. / Yang, J. / Wu, W.
引用ジャーナル: Mol.Cell / 年: 2015
タイトル: Structural Basis of Detection and Signaling of DNA Single-Strand Breaks by Human PARP-1.
著者: Eustermann, S. / Wu, W.F. / Langelier, M.F. / Yang, J.C. / Easton, L.E. / Riccio, A.A. / Pascal, J.M. / Neuhaus, D.
履歴
登録2015年10月8日登録サイト: BMRB / 処理サイト: RCSB
改定 1.02015年12月2日Provider: repository / タイプ: Initial release
改定 1.12015年12月23日Group: Database references
改定 1.22016年10月5日Group: Structure summary
改定 1.32016年10月19日Group: Other
改定 1.42024年5月1日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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集合体

登録構造単位
A: Poly [ADP-ribose] polymerase 1
B: DNA (45-MER)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)38,1094
ポリマ－37,9782
非ポリマー1312
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
NMR アンサンブル
データ基準
コンフォーマー数 (登録 / 計算)78 / 78Total, Tensor and NOE xplor energies simultaneously below thresholds (6000, 1500 and 2 kcal.mol-1 respectively)
代表モデルモデル #1lowest energy
詳細The assembly is a hetero-dimer made of one chain of Poly [ADP-Ribose] Polymerase 1 and one chain of DNA (45-MER).

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要素

#1: タンパク質 Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / NAD(+) ADP-ribosyltransferase 1 / ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1


分子量: 24106.572 Da / 分子数: 1 / 断片: residues 1-214 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PARP1, ADPRT, PPOL / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / Variant (発現宿主): DE3 / 参照: UniProt: P09874, NAD+ ADP-ribosyltransferase
#2: DNA鎖 DNA (45-MER)


分子量: 13871.856 Da / 分子数: 1 / 由来タイプ: 合成
#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

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実験情報

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実験

実験手法: 溶液NMR
NMR実験
Conditions-IDExperiment-IDSolution-IDタイプ
1112D 1H-15N TROSY
1212D 1H-13C HMQC
131TROSY-NHCACB (optimized for CB)
141TROSY-HNCA
151TROSY-HN(CO)CA
1622D 1H-15N TROSY
1722D 1H-13C HMQC
182TROSY-HNCA
192TROSY-HN(CO)CA
11032D 1H-15N TROSY
11143D 1H-13C-1H NOESY-HMQC
1125HMCM(CG)CBCA
11362D 1H-1H NOESY
11463D 13C-13C-1H HMQC-NOESY-HMQC
11563D 1H-13C-1H NOESY-HMQC
11672D 1H-13C HSQC aromatic
11782D 1H-1H NOESY filtered to accept 13C-1H in w2
11882D 1H-1H NOESY filtered to accept 13C-1H in w2 (no decoupling in w1)
11992D 1H-1H NOESY filtered to accept 13C-1H in w2
12092D 1H-1H NOESY filtered to accept 13C-1H in w2 (no decoupling in w1)
121102D 1H-1H NOESY filtered to accept 13C-1H in w2 (no decoupling in w1)
122112D 1H-1H NOESY filtered to accept 13C-1H in w2
123122D 1H-13C HSQC aliphatic
124122D 1H-1H NOESY filtered to accept 13C-1H in w2
125132D 1H-1H TOCSY
126132D 1H-1H NOESY
227142D 1H-1H TOCSY
228142D 1H-1H NOESY
129152D 1H-1H NOESY
330162D 1H-15N TROSY
331172D 1H-15N TROSY
NMR実験の詳細Text: Sample numbers used here correspond to those used in the supplementary material for the primary citation

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試料調製

詳細
Solution-ID内容溶媒系
1Sample 1: 0.2 mM [U-15N; U-13C; U-2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 95% H2O/5% D2O95% H2O/5% D2O
2Sample 2: 0.2 mM [U-15N; U-13C; U-70% 2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 95% H2O/5% D2O95% H2O/5% D2O
3Sample 3: 0.2 mM [U-98% 2H; U-98% 15N] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 95% H2O/5% D2O95% H2O/5% D2O
4Sample 4a: 0.2 MM PARP-1 1-214, Uniform [2H,15N,13C], back-labeled with [1H,13C] in the delta-methyl groups of Ile and all methyl groups of Leu and Val residues, using sodium [4-13C, 3,3-2H2] alpha-ketobutyrate and sodium [3- 2H, 4,4'-13C2] alpha-ketoisovalerate as precursors to maximize protonation of methyl groups, for use in NOE experiments; sodium [3-2H, 4,4'-13C2] alpha-ketoisovalerate was prepared from sodium [4,4'-13C2] alpha-ketoisovalerate by exchange with 2H2O at pH 12.5 and 45 C for 3 hrs. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 95% H2O/5% D2O95% H2O/5% D2O
5Sample 4b: 0.2 MM PARP-1 1-214, Uniform [2H,15N,13C], back-labeled with [1H,13C] in the delta-methyl groups of Ile and all methyl groups of Leu and Val residues, using sodium [3,3-2H2,13C4] alpha-ketobutyrate and sodium [3- 2H,13C5] alpha-ketoisovalerate as precursors to produce linear chains of 13C in the sidechains of Val and Leu, for use in assignment experiments to link methyl signals to C-alpha signals. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 100% D2O100% D2O
6Sample 5: 0.2 MM PARP-1 1-214, Uniform [2H,15N,13C], back-labeled with [1H,13C] in the methyl groups of Met residues in addition to Ile, Leu and Val methyl groups as in sample 4a. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 100% D2O100% D2O
7Sample 6: 0.2 MM PARP-1 1-214, Uniform [2H,15N,13C]; back-labeled with [1H,13C] in the methyl groups of Ile, Leu and Val methyl groups as in sample 4a and [1H,13C,15N] Phe residues. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 100% D2O100% D2O
8Sample 7: 0.2 MM PARP-1 1-214, Sortase ligated, block-labelled sample. (N.B. residues 103 and 104 of WT sequence deleted, additional residues LPETGGG inserted between residues 102 and 105; this sample was not used for making any assignments of residues in this region, which is in the flexible linker between domains). Labelling for residues 1-102 (and LPET of insertion): uniform [1H,12C,15N]. Labelling for residues 105-214 (and GGG of insertion): [2H,15N,13C] back-labeled with [1H,13C] Ile, Leu Val and Met methyl groups labeled as in sample 5. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 100% D2O100% D2O
9Sample 8: 0.2 MM PARP-1 1-214, Sortase ligated, block-labelled sample. (N.B. residues 103 and 104 of WT sequence deleted, additional residues LPETGGG inserted between residues 102 and 105; this sample was not used for making any assignments of residues in this region, which is in the flexible linker between domains). Labelling for residues 1-102 (and LPET of insertion): uniform [1H,12C,15N]. Labelling for residues 105-214 (and GGG of insertion): [2H,15N,13C] back labeled with [1H,13C] Met methyl groups as in sample 5 and [13C,15N,1H] Arg residues. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 100% D2O100% D2O
10Sample 9: 0.2 MM PARP-1 1-214, Sortase ligated, block-labelled sample. (N.B. residues 103 and 104 of WT sequence deleted, additional residues LPETGGG inserted between residues 102 and 105; this sample was not used for making any assignments of residues in this region, which is in the flexible linker between domains). Labelling for residues 1-102 (and LPET of insertion): [2H,15N,13C] back-labeled with Ile, Leu and Val methyl groups labeled as in sample 4a and [1H,13C,15N] Arg residues. Labelling for residues 105-214 (and GGG of insertion): uniform [1H,12C,15N]. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 95% H2O/5% D2O95% H2O/5% D2O
11Sample 10: 0.2 MM PARP-1 1-214, Sortase ligated, block-labelled sample. (N.B. residues 103 and 104 of WT sequence deleted, additional residues LPETGGG inserted between residues 102 and 105; this sample was not used for making any assignments of residues in this region, which is in the flexible linker between domains). Labelling for residues 1-102 (and LPET of insertion): [2H,15N,13C] back-labeled with Ile, Leu and Val methyl groups labeled as in sample 4a and [1H,13C,15N] Phe residues. Labelling for residues 105-214 (and GGG of insertion): uniform [1H,12C,15N]. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 100% D2O100% D2O
12Sample 11: 0.2 mM see Sample details section PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 100% D2O100% D2O
13Sample 12: 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 100% D2O100% D2O
14Sample 13: 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 95% H2O/5% D2O95% H2O/5% D2O
15Sample 14: 0.2 mM [U-15N; U-13C; U-2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4, 100% D2O100% D2O
16Sample 15: 0.2 mM [U-15N; U-13C; U-2H] PARP-1 1, 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 uM ZnSO4, 200 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
17Sample 16: 0.2 mM [U-15N; U-13C; U-2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 uM ZnSO4, 200 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
試料
濃度 (mg/ml)構成要素Isotopic labelingSolution-ID
0.2 mMPARP-1 1-214-1[U-15N; U-13C; U-2H]1
0.2 mMDNA (45-MER)-21
50 mMTRIS-3[U-2H]1
1 mMDTT-4[U-2H]1
0.1 mMZnSO4-51
0.2 mMPARP-1 1-214-6[U-15N; U-13C; U-70% 2H]2
0.2 mMDNA (45-MER)-72
50 mMTRIS-8[U-2H]2
1 mMDTT-9[U-2H]2
0.1 mMZnSO4-102
0.2 mMPARP-1 1-214-11[U-98% 2H; U-98% 15N]3
0.2 mMDNA (45-MER)-123
50 mMTRIS-13[U-2H]3
1 mMDTT-14[U-2H]3
0.1 mMZnSO4-153
0.2 mMPARP-1 1-214-16see Sample details section4
0.2 mMDNA (45-MER)-174
50 mMTRIS-18[U-2H]4
1 mMDTT-19[U-2H]4
0.1 mMZnSO4-204
0.2 mMPARP-1 1-214-21see Sample details section5
0.2 mMDNA (45-MER)-225
50 mMTRIS-23[U-2H]5
1 mMDTT-24[U-2H]5
0.1 mMZnSO4-255
0.2 mMPARP-1 1-214-26see Sample details section6
0.2 mMDNA (45-MER)-276
50 mMTRIS-28[U-2H]6
1 mMDTT-29[U-2H]6
0.1 mMZnSO4-306
0.2 mMPARP-1 1-214-31see Sample details section7
0.2 mMDNA (45-MER)-327
50 mMTRIS-33[U-2H]7
1 mMDTT-34[U-2H]7
0.1 mMZnSO4-357
0.2 mMPARP-1 1-214-36see Sample details section8
0.2 mMDNA (45-MER)-378
50 mMTRIS-38[U-2H]8
1 mMDTT-39[U-2H]8
0.1 mMZnSO4-408
0.2 mMPARP-1 1-214-41see Sample details section9
0.2 mMDNA (45-MER)-429
50 mMTRIS-43[U-2H]9
1 mMDTT-44[U-2H]9
0.1 mMZnSO4-459
0.2 mMPARP-1 1-214-46see Sample details section10
0.2 mMDNA (45-MER)-4710
50 mMTRIS-48[U-2H]10
1 mMDTT-49[U-2H]10
0.1 mMZnSO4-5010
0.2 mMPARP-1 1-214-51see Sample details section11
0.2 mMDNA (45-MER)-5211
50 mMTRIS-53[U-2H]11
1 mMDTT-54[U-2H]11
0.1 mMZnSO4-5511
0.2 mMPARP-1 1-214-56see Sample details section12
0.2 mMDNA (45-MER)-5712
50 mMTRIS-58[U-2H]12
1 mMDTT-59[U-2H]12
0.1 mMZnSO4-6012
0.2 mMDNA (45-MER)-6113
50 mMTRIS-62[U-2H]13
1 mMDTT-63[U-2H]13
0.1 mMZnSO4-6413
0.2 mMDNA (45-MER)-6514
50 mMTRIS-66[U-2H]14
1 mMDTT-67[U-2H]14
0.1 mMZnSO4-6814
0.2 mMPARP-1 1-214-69[U-15N; U-13C; U-2H]15
0.2 mMDNA (45-MER)-7015
50 mMTRIS-71[U-2H]15
1 mMDTT-72[U-2H]15
0.1 mMZnSO4-7315
0.2 mMPARP-1 1-214-74[U-15N; U-13C; U-2H]16
50 mMTRIS-75[U-2H]16
1 mMDTT-76[U-2H]16
0.1 uMZnSO4-7716
200 mMsodium chloride-7816
0.2 mMPARP-1 1-214-79[U-15N; U-13C; U-2H]17
0.2 mMDNA (45-MER)-8017
50 mMTRIS-81[U-2H]17
1 mMDTT-82[U-2H]17
0.1 uMZnSO4-8317
200 mMsodium chloride-8417
試料状態
Conditions-IDイオン強度pH圧 (kPa)温度 (K)
10.00047.2ambient 310 K
20.00047.2ambient 300 K
30.17.2ambient 303 K

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NMR測定

NMRスペクトロメーター
タイプ製造業者モデル磁場強度 (MHz)Spectrometer-ID
Bruker Avance IBrukerAvance I8001
Bruker Avance II+BrukerAVANCE II7002
Bruker DMXBrukerDMX6003
Bruker DRXBrukerDRX5004

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解析

NMR software
名称バージョン開発者分類
X-PLOR NIH2.28Schwieters, Kuszewski, Tjandra and Clore構造決定
Sparky3.115Goddardchemical shift assignment
TopSpin2.1Bruker Biospin解析
Analysis2.4.1CCPNchemical shift assignment
Analysis2.4.1CCPNデータ解析
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxデータ解析
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clore精密化
精密化手法: simulated annealing / ソフトェア番号: 1
詳細: THE STRUCTURE WAS CALCULATED USING A COMBINED NMR/X-RAY PROTOCOL. NMR EVIDENCE ESTABLISHED THE TOPOLOGY OF THE COMPLEX TO BE A MONOMERIC ASSEMBLY IN WHICH DOMAIN F1 (PROTEIN RESIDUES 6-91) IS ...詳細: THE STRUCTURE WAS CALCULATED USING A COMBINED NMR/X-RAY PROTOCOL. NMR EVIDENCE ESTABLISHED THE TOPOLOGY OF THE COMPLEX TO BE A MONOMERIC ASSEMBLY IN WHICH DOMAIN F1 (PROTEIN RESIDUES 6-91) IS BOUND TO THE DNA STEM WITH THE 5' TERMINUS AND DOMAIN F2 (PROTEIN RESIDUES 109-200) TO THE DNA STEM WITH THE 3' TERMINUS; NMR FURTHER SHOWED THAT THE INDIVIDUAL BINDING MODES OF F1 AND F2 TO THEIR RESPECTIVE STEMS WAS EQUIVALENT (THOUGH IN A DIFFERENT CONTEXT) TO THOSE SEEN IN CRYSTAL STRUCTURES PDB 3ODA AND 3ODC RESPECTIVELY. TEMPLATE STRUCTURES WERE CREATED FROM 3ODA AND 3ODC (AND 1MSY AND 1RNG FOR THE DNA TETRALOOPS) AND USED TOGETHER WITH NON-CRYSTALLOGRAPHIC SYMMETRY TERMS IN XPLOR-NIH TO RETAIN THESE FEATURES IN THE CALCULATED STRUCTURES, WHILE THE RDC AND NOE DERIVED RESTRAINTS DEFINED THE OVERALL STRUCTURE. FULL DETAILS OF THE APPROACH AND THE CALCULATION PROTOCOL APPEAR IN THE PRIMARY REFERENCE AND CORRESPONDING SUPPLEMENTARY MATERIAL FOR THIS ENTRY.
NMR constraintsNOE constraints total: 18 / NOE intraresidue total count: 0 / NOE long range total count: 18 / NOE medium range total count: 0 / NOE sequential total count: 0
代表構造選択基準: lowest energy
NMRアンサンブルコンフォーマー選択の基準: Total, Tensor and NOE xplor energies simultaneously below thresholds (6000, 1500 and 2 kcal.mol-1 respectively)
計算したコンフォーマーの数: 78 / 登録したコンフォーマーの数: 78 / Maximum upper distance constraint violation: 0.177 Å

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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

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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

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  • 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。
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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

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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

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