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- PDB-6h0g: Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4) -

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基本情報

登録情報
データベース: PDB / ID: 6h0g
タイトルStructure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4)
要素
  • DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DDB1 (DNA damage binding protein 1),DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
  • Protein cereblon
  • Zinc finger protein 692
キーワードSIGNALING PROTEIN / E3 ubiquitin ligase / drug mediated protein-interaction / targeted protein degradation
機能・相同性
機能・相同性情報


negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Generic Transcription Pathway / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding ...negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Generic Transcription Pathway / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / regulation of gluconeogenesis / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / locomotory exploration behavior / cullin family protein binding / viral release from host cell / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / nucleotide-excision repair / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / DNA-binding transcription repressor activity, RNA polymerase II-specific / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / apoptotic process / DNA damage response / regulation of transcription by RNA polymerase II / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / extracellular exosome / zinc ion binding / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
類似検索 - 分子機能
: / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) ...: / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / PUA-like superfamily / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
類似検索 - ドメイン・相同性
S-Pomalidomide / DNA damage-binding protein 1 / Protein cereblon / Zinc finger protein 692
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: 4.25 Å
データ登録者Bunker, R.D. / Petzold, G. / Thoma, N.H.
資金援助3件
組織認可番号国
European UnionHorizon 2020 No. 666068
European Molecular Biology OrganizationAdvanced Fellowship aALTF 761-2016
European UnionHuman Frontier Science Program Long-Term Fellowship LT000210/2014
引用ジャーナル: Science / 年: 2018
タイトル: Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN.
著者: Sievers, Q.L. / Petzold, G. / Bunker, R.D. / Renneville, A. / Slabicki, M. / Liddicoat, B.J. / Abdulrahman, W. / Mikkelsen, T. / Ebert, B.L. / Thoma, N.H.
履歴
登録2018年7月9日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02018年11月7日Provider: repository / タイプ: Initial release
改定 1.12018年11月14日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 2.02019年4月17日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_mutation / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
改定 2.12024年1月17日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DDB1 (DNA damage binding protein 1),DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
B: Protein cereblon
C: Zinc finger protein 692
D: DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DDB1 (DNA damage binding protein 1),DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
E: Protein cereblon
F: Zinc finger protein 692
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)297,34812
ポリマ－296,5406
非ポリマー8086
水00
1
A: DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DDB1 (DNA damage binding protein 1),DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
B: Protein cereblon
C: Zinc finger protein 692
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)148,6746
ポリマ－148,2703
非ポリマー4043
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DDB1 (DNA damage binding protein 1),DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
E: Protein cereblon
F: Zinc finger protein 692
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)148,6746
ポリマ－148,2703
非ポリマー4043
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)112.510, 99.530, 166.940
Angle α, β, γ (deg.)90.000, 108.490, 90.000
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質 DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DDB1 (DNA damage binding protein 1),DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


分子量: 95773.695 Da / 分子数: 2
変異: Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller ...変異: Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG)
由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DDB1, XAP1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q16531
#2: タンパク質 Protein cereblon


分子量: 48976.117 Da / 分子数: 2 / 変異: N-terminally truncated (1-40 aa deleted) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CRBN, AD-006 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q96SW2
#3: タンパク質・ペプチド Zinc finger protein 692


分子量: 3520.015 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: ZNF692 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9BU19
#4: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn
#5: 化合物 ChemComp-Y70 / S-Pomalidomide / 2-[(3S)-2,6-ジオキソ-3-ピペリジニル]-4-アミノイソインドリン-1,3-ジオン


分子量: 273.244 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C13H11N3O4

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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: 3.12 Å3/Da / 溶媒含有率: 60.62 %
結晶化温度: 293 K / 手法: 蒸気拡散法
詳細: Protein-drug solution: 350 uM ZNF692-ZF4, 70 uM DDB1/CRBN, 80 uM pomalidomide and in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: 14.1% (w/v) PEG 5K MME and 70 mM Tris-HCl pH 7.5

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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: SLS / ビームライン: X06SA / 波長: 1.000043 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2017年5月29日
放射モノクロメーター: SI(111) silicon crista / 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: 1.000043 Å / 相対比: 1
反射解像度: 4.17→48.6 Å / Num. obs: 24386 / % possible obs: 92 % / 冗長度: 4.034 % / Biso Wilson estimate: 156.11 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.233 / Rrim(I) all: 0.267 / Χ2: 0.986 / Net I/σ(I): 3.99 / Num. measured all: 98372 / Scaling rejects: 59
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
4.17-4.273.4743.1490.454867190114010.1553.6473.7
4.27-4.393.9321.9760.756079191415460.3012.2680.8
4.39-4.523.9051.5510.896768184917330.3791.77893.7
4.52-4.663.921.211.166551178416710.5011.38893.7
4.66-4.813.8481.0051.346134171915940.5311.1692.7
4.81-4.983.7830.9041.555970171815780.5591.04691.9
4.98-5.173.670.9171.475321158914500.6181.06291.3
5.17-5.383.7440.7091.875264158114060.6730.81888.9
5.38-5.623.9990.6682.045610150914030.7230.76793
5.62-5.893.9670.5632.425256143413250.7640.64792.4
5.89-6.214.270.5842.655654137913240.7230.66896
6.21-6.594.5770.4993.425831128112740.8040.56599.5
6.59-7.044.480.3554.395461123012190.8910.40499.1
7.04-7.64.2780.2665.684804114711230.9270.30497.9
7.6-8.334.3650.1638.084391104510060.9720.18596.3
8.33-9.314.5770.1111.6843349539470.9870.12499.4
9.31-10.754.4360.08114.7237008438340.9920.09298.9
10.75-13.174.1470.07416.2529367197080.9920.08498.5
13.17-18.634.0830.06916.3422095735410.9940.07894.4
18.63-48.64.0660.06317.5212323263030.9960.07192.9

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解析

ソフトウェア
名称バージョン分類
BUSTER2.11.7精密化
XDSJun 1, 2017 BUILT=20170923データ削減
XSCALEJun 1, 2017 BUILT=20170923データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5FQD

5fqd


解像度: 4.25→48.6 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.843 / 交差検証法: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.991
Rfactor反射数%反射Selection details
Rfree0.256 1140 4.9 %RANDOM
Rwork0.221 ---
obs0.223 23287 93.3 %-
原子変位パラメータBiso max: 750 Å2 / Biso mean: 152.81 Å2 / Biso min: 53.68 Å2
Baniso -1Baniso -2Baniso -3
1-25.5038 Å20 Å2-34.4595 Å2
2--23.6223 Å20 Å2
3----49.1261 Å2
Refine analyzeLuzzati coordinate error obs: 0.84 Å
精密化ステップサイクル: final / 解像度: 4.25→48.6 Å
タンパク質核酸リガンド溶媒全体
原子数19888 0 44 0 19932
Biso mean--75 --
残基数----2512
拘束条件
Refine-IDタイプ数Restraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d8876SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes6376HARMONIC5
X-RAY DIFFRACTIONt_it40090HARMONIC20
X-RAY DIFFRACTIONt_nbd11SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2666SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact44376SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d40090HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg72515HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion14.05
LS精密化 シェル解像度: 4.25→4.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
Rfactor反射数%反射
Rfree0.2722 21 4.51 %
Rwork0.2633 445 -
all0.2637 466 -
obs--75.32 %
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)
12.58080.5299-0.19986.73082.87432.9229-0.4436-0.82730.02571.36040.09171.0147-0.4293-0.78720.35190.50080.23630.01321.23390.20990.9937-19.07279.2801-29.7091
26.3314-0.8807-1.1895.03632.33995.162-0.1999-2.03410.97020.92920.12640.1389-0.89930.72470.07341.34420.1794-0.41131.4889-0.09970.6706-6.703227.9169-20.9247
3-1.9494-1.60473.53019.97066.09072.5790.4622-1.0009-0.14771.80550.56610.1035-0.2477-0.0293-1.02831.59770.199-0.41841.51980.05371.15692.097615.0011-14.4594
44.66260.3423-2.16863.78060.81069.081-0.1819-0.9482-0.24150.4871-0.0613-0.78950.33280.61470.24320.01590.3116-0.18410.61310.41880.900911.9828-2.3474-42.5633
56.52240.0227-1.84484.2262-0.55444.3143-0.41460.4641-0.2329-0.83320.1440.90680.7667-0.97640.27060.0472-0.2004-0.22360.5430.22830.9758-10.3939-2.4997-59.4721
67.53143.3544-3.342913.6645-2.95025.39660.8577-0.42121.2962-0.0840.1350.792-0.9293-0.8033-0.99270.73630.365-0.03010.4872-0.06180.4418-11.595444.4941-72.8451
76.7704-5.73237.92336.0507-5.684311.8203-0.522-0.2318-0.1314-0.12480.66150.3076-0.8212-1.095-0.13950.4271-0.1111-0.39640.60390.03390.7961-16.442725.6828-66.0439
82.4087-1.9706-3.81780-1.58661.29410.1144-1.59561.42091.51530.3992-0.9398-1.6320.498-0.51370.60540.0941-0.31250.99230.01751.33346.8122.771-46.3604
93.6122.5806-0.95668.2466-5.691410.8305-0.0949-0.78860.17750.2059-0.2589-1.2329-0.60.74730.35380.057-0.0012-0.0875-0.1983-0.12781.13637.392837.3123-73.4339
105.3869-10.1918-2.078919.8145-0.110724.8106-0.23880.27731.7101-0.7830.509-1.5156-0.52490.8989-0.27020.1745-0.1739-0.4505-0.1695-0.13840.31433.252352.213-94.5782
1129.6808-11.70041.637925.50388.741940.43080.3249-0.2705-2.2826-0.04610.13380.57342.2051-0.7937-0.4587-0.1611-0.4839-0.0275-0.2341-0.01270.91541.372940.8733-95.8041
124.7959-0.86860.61312.9137-1.86987.8617-0.0171-0.79210.30120.52820.27821.0389-0.5706-0.6858-0.26110.43160.02390.25960.0631-0.20880.8738-74.904574.0731-28.2647
139.67443.7004-0.879313.963-3.52987.7556-0.16590.93940.2099-0.60620.36020.4486-0.2786-0.2789-0.19430.222-0.11880.15-0.3659-0.34680.5605-67.149180.847-49.9601
1411.6704-0.17293.297510.2844-9.574312.8735-0.3167-0.23691.08170.6964-0.3741-0.3849-1.43530.21270.69080.4252-0.24040.012-0.1943-0.81780.5195-58.143991.1534-39.9265
153.6101-0.73070.1075.0872-1.42662.0278-0.1946-0.9027-0.42231.3095-0.1109-0.63650.05210.30570.30550.9252-0.08640.03790.7288-0.19690.4629-50.786658.189-16.3145
1616.05791.6355-4.805510.80451.911.39360.16050.402-0.5069-0.2471-0.45591.46971.0323-0.0450.29550.41970.1-0.3116-0.6043-0.01581.4344-64.096527.9212-56.1496
175.22124.80323.605113.34841.80892.12141.07640.1692-0.97911.3838-0.72981.776610.0193-0.34650.57520.21190.0173-0.41150.04691.637-69.331627.6129-48.9552
1818.24619.68775.90514.221-5.06761.909-0.02680.97180.995-0.81931.03110.64360.97890.3189-1.00430.76010.0206-0.0099-0.1910.08220.8143-54.632165.3662-42.6858
1922.67112.9396-3.824123.902-13.1621.9954-0.33750.25220.5632-2.8288-0.38910.0053-0.18552.82850.72650.1890.02590.077-0.2023-0.07820.8145-46.450560.7927-38.7291
2013.14067.7959-12.727216.89869.67536.4913-0.12792.67080.6234-2.1699-0.03010.7735-1.17780.59360.1580.60550.0009-0.0681-0.10070.30550.9345-47.972948.2576-52.9363
214.9012-0.6773-0.753413.68256.46476.326-0.09650.3357-0.54680.02030.6131-0.78550.15541.6005-0.51660.16910.0662-0.0434-0.16160.01460.9875-44.537629.4443-52.4409
2221.2694-1.9416-7.0256.639-4.6335-2.17390.28580.8303-1.2667-0.2072-0.5314-0.0890.9237-0.10740.24560.98320.56680.14020.7552-0.16041.4898-48.25540.9761-68.0048
2312.2907-5.9677-16.088217.20923.421723.73950.1109-0.9439-0.79882.69890.0041-0.55150.43191.4854-0.1150.89710.1148-0.23860.3286-0.21441.1974-46.95967.5425-55.582
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 176}A1 - 176
2X-RAY DIFFRACTION2{A|177 - 248}A177 - 248
3X-RAY DIFFRACTION3{A|249 - 299}A249 - 299
4X-RAY DIFFRACTION4{A|300 - 856}A300 - 856
5X-RAY DIFFRACTION5{A|857 - 1140}A857 - 1140
6X-RAY DIFFRACTION6{B|42 - 163}B42 - 163
7X-RAY DIFFRACTION7{B|164 - 200}B164 - 200
8X-RAY DIFFRACTION8{B|201 - 262}B201 - 262
9X-RAY DIFFRACTION9{B|263 - 442}B263 - 442
10X-RAY DIFFRACTION10{C|413 - 428}C413 - 428
11X-RAY DIFFRACTION11{C|429 - 442}C429 - 442
12X-RAY DIFFRACTION12{D|1 - 176}D1 - 176
13X-RAY DIFFRACTION13{D|177 - 248}D177 - 248
14X-RAY DIFFRACTION14{D|249 - 299}D249 - 299
15X-RAY DIFFRACTION15{D|300 - 1140}D300 - 1140
16X-RAY DIFFRACTION16{E|42 - 147}E42 - 147
17X-RAY DIFFRACTION17{E|148 - 192}E148 - 192
18X-RAY DIFFRACTION18{E|193 - 216}E193 - 216
19X-RAY DIFFRACTION19{E|217 - 249}E217 - 249
20X-RAY DIFFRACTION20{E|250 - 276}E250 - 276
21X-RAY DIFFRACTION21{E|277 - 442}E277 - 442
22X-RAY DIFFRACTION22{F|413 - 417}F413 - 417
23X-RAY DIFFRACTION23{F|418 - 442}F418 - 442

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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