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- PDB-8cob: Crystal structure of human PCNA in complex with ERCC6L2 PIP box p... -

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基本情報

登録情報
データベース: PDB / ID: 8cob
タイトルCrystal structure of human PCNA in complex with ERCC6L2 PIP box peptide
要素
  • DNA excision repair protein ERCC-6-like 2
  • Proliferating cell nuclear antigen
キーワードDNA BINDING PROTEIN / ERCC6L2 / RAD26L / HEBO / PCNA / CENTROMERE ASSOCIATED REPLICATION FACTOR
機能・相同性
機能・相同性情報


positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / MutLalpha complex binding ...positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / MutLalpha complex binding / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / replisome / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / translesion synthesis / mismatch repair / response to cadmium ion / estrous cycle / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / epithelial cell differentiation / male germ cell nucleus / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / liver regeneration / Translesion synthesis by POLI / replication fork / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of DNA replication / nuclear estrogen receptor binding / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / damaged DNA binding / chromosome, telomeric region / nuclear body / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus
類似検索 - 分子機能
Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / :
類似検索 - ドメイン・相同性
Proliferating cell nuclear antigen
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: 2.73 Å
データ登録者Ariza, A.
資金援助 英国, 1件
組織認可番号国
Cancer Research UK16304 英国
引用ジャーナル: Cell Rep / 年: 2023
タイトル: ERCC6L2 mitigates replication stress and promotes centromere stability.
著者: Carnie, C.J. / Armstrong, L. / Sebesta, M. / Ariza, A. / Wang, X. / Graham, E. / Zhu, K. / Ahel, D.
履歴
登録2023年2月27日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年4月19日Provider: repository / タイプ: Initial release
改定 1.12024年2月7日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.22024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: Proliferating cell nuclear antigen
B: DNA excision repair protein ERCC-6-like 2
C: Proliferating cell nuclear antigen
D: DNA excision repair protein ERCC-6-like 2
E: Proliferating cell nuclear antigen
F: DNA excision repair protein ERCC-6-like 2


分子量 (理論値)分子数
合計 (水以外)91,0886
ポリマ－91,0886
非ポリマー00
水1,15364
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-49 kcal/mol
Surface area34080 Å2
単位格子
Length a, b, c (Å)67.694, 109.082, 139.396
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
12
22
32

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETLEULEU(chain 'A' and (resid 1 through 7 or resid 9...AA1 - 61 - 6
121GLYGLYVALVAL(chain 'A' and (resid 1 through 7 or resid 9...AA9 - 159 - 15
131ALAALAASPASP(chain 'A' and (resid 1 through 7 or resid 9...AA18 - 4118 - 41
141HISHISGLYGLY(chain 'A' and (resid 1 through 7 or resid 9...AA44 - 5644 - 56
151THRTHRTHRTHR(chain 'A' and (resid 1 through 7 or resid 9...AA5959
161CYSCYSCYSCYS(chain 'A' and (resid 1 through 7 or resid 9...AA6262
171ASNASNTHRTHR(chain 'A' and (resid 1 through 7 or resid 9...AA65 - 8965 - 89
181ASPASPGLUGLU(chain 'A' and (resid 1 through 7 or resid 9...AA97 - 10497 - 104
191LYSLYSVALVAL(chain 'A' and (resid 1 through 7 or resid 9...AA110 - 111110 - 111
1101TYRTYRLEULEU(chain 'A' and (resid 1 through 7 or resid 9...AA114 - 118114 - 118
1111LEULEUVALVAL(chain 'A' and (resid 1 through 7 or resid 9...AA121 - 123121 - 123
1121LEULEUGLUGLU(chain 'A' and (resid 1 through 7 or resid 9...AA126 - 130126 - 130
1131TYRTYRSERSER(chain 'A' and (resid 1 through 7 or resid 9...AA133 - 141133 - 141
1141PHEPHEILEILE(chain 'A' and (resid 1 through 7 or resid 9...AA144 - 154144 - 154
1151ALAALACYSCYS(chain 'A' and (resid 1 through 7 or resid 9...AA157 - 162157 - 162
1161ASPASPSERSER(chain 'A' and (resid 1 through 7 or resid 9...AA165 - 170165 - 170
1171LEULEUGLNGLN(chain 'A' and (resid 1 through 7 or resid 9...AA175 - 184175 - 184
1181ALAALAMETMET(chain 'A' and (resid 1 through 7 or resid 9...AA194 - 199194 - 199
1191PROPROALAALA(chain 'A' and (resid 1 through 7 or resid 9...AA202 - 208202 - 208
1201TYRTYRGLUGLU(chain 'A' and (resid 1 through 7 or resid 9...AA211 - 238211 - 238
1211ILEILEPROPRO(chain 'A' and (resid 1 through 7 or resid 9...AA241 - 253241 - 253
2221METMETLEULEU(chain 'C' and (resid 1 through 7 or resid 9...CC1 - 61 - 6
2231GLYGLYVALVAL(chain 'C' and (resid 1 through 7 or resid 9...CC9 - 159 - 15
2241ALAALAASPASP(chain 'C' and (resid 1 through 7 or resid 9...CC18 - 4118 - 41
2251HISHISGLYGLY(chain 'C' and (resid 1 through 7 or resid 9...CC44 - 5644 - 56
2261THRTHRTHRTHR(chain 'C' and (resid 1 through 7 or resid 9...CC5959
2271CYSCYSCYSCYS(chain 'C' and (resid 1 through 7 or resid 9...CC6262
2281ASNASNTHRTHR(chain 'C' and (resid 1 through 7 or resid 9...CC65 - 8965 - 89
2291ASPASPGLUGLU(chain 'C' and (resid 1 through 7 or resid 9...CC97 - 10497 - 104
2301LYSLYSVALVAL(chain 'C' and (resid 1 through 7 or resid 9...CC110 - 111110 - 111
2311TYRTYRLEULEU(chain 'C' and (resid 1 through 7 or resid 9...CC114 - 118114 - 118
2321LEULEUVALVAL(chain 'C' and (resid 1 through 7 or resid 9...CC121 - 123121 - 123
2331LEULEUGLUGLU(chain 'C' and (resid 1 through 7 or resid 9...CC126 - 130126 - 130
2341TYRTYRSERSER(chain 'C' and (resid 1 through 7 or resid 9...CC133 - 141133 - 141
2351PHEPHEILEILE(chain 'C' and (resid 1 through 7 or resid 9...CC144 - 154144 - 154
2361ALAALACYSCYS(chain 'C' and (resid 1 through 7 or resid 9...CC157 - 162157 - 162
2371ASPASPSERSER(chain 'C' and (resid 1 through 7 or resid 9...CC165 - 170165 - 170
2381LEULEUGLNGLN(chain 'C' and (resid 1 through 7 or resid 9...CC175 - 184175 - 184
2391ALAALAMETMET(chain 'C' and (resid 1 through 7 or resid 9...CC194 - 199194 - 199
2401PROPROALAALA(chain 'C' and (resid 1 through 7 or resid 9...CC202 - 208202 - 208
2411TYRTYRGLUGLU(chain 'C' and (resid 1 through 7 or resid 9...CC211 - 238211 - 238
2421ILEILEPROPRO(chain 'C' and (resid 1 through 7 or resid 9...CC241 - 253241 - 253
3431METMETLEULEU(chain 'E' and (resid 1 through 7 or resid 9...EE1 - 61 - 6
3441GLYGLYVALVAL(chain 'E' and (resid 1 through 7 or resid 9...EE9 - 159 - 15
3451ALAALAASPASP(chain 'E' and (resid 1 through 7 or resid 9...EE18 - 4118 - 41
3461HISHISGLYGLY(chain 'E' and (resid 1 through 7 or resid 9...EE44 - 5644 - 56
3481THRTHRTHRTHR(chain 'E' and (resid 1 through 7 or resid 9...EE5959
3491CYSCYSCYSCYS(chain 'E' and (resid 1 through 7 or resid 9...EE6262
3501ASNASNTHRTHR(chain 'E' and (resid 1 through 7 or resid 9...EE65 - 8965 - 89
3511ASPASPGLUGLU(chain 'E' and (resid 1 through 7 or resid 9...EE97 - 10497 - 104
3521LYSLYSVALVAL(chain 'E' and (resid 1 through 7 or resid 9...EE110 - 111110 - 111
3531TYRTYRLEULEU(chain 'E' and (resid 1 through 7 or resid 9...EE114 - 118114 - 118
3541LEULEUVALVAL(chain 'E' and (resid 1 through 7 or resid 9...EE121 - 123121 - 123
3551LEULEUGLUGLU(chain 'E' and (resid 1 through 7 or resid 9...EE126 - 130126 - 130
3561TYRTYRSERSER(chain 'E' and (resid 1 through 7 or resid 9...EE133 - 141133 - 141
3571PHEPHEILEILE(chain 'E' and (resid 1 through 7 or resid 9...EE144 - 154144 - 154
3581ALAALACYSCYS(chain 'E' and (resid 1 through 7 or resid 9...EE157 - 162157 - 162
3591ASPASPSERSER(chain 'E' and (resid 1 through 7 or resid 9...EE165 - 170165 - 170
3601LEULEUGLNGLN(chain 'E' and (resid 1 through 7 or resid 9...EE175 - 184175 - 184
3611ALAALAMETMET(chain 'E' and (resid 1 through 7 or resid 9...EE194 - 199194 - 199
3621PROPROALAALA(chain 'E' and (resid 1 through 7 or resid 9...EE202 - 208202 - 208
3631TYRTYRGLUGLU(chain 'E' and (resid 1 through 7 or resid 9...EE211 - 238211 - 238
3641ILEILEPROPRO(chain 'E' and (resid 1 through 7 or resid 9...EE241 - 253241 - 253
1652GLYGLYPHEPHEchain 'B'BB797 - 8064 - 13
2662GLYGLYPHEPHEchain 'D'DD797 - 8064 - 13
3672GLYGLYPHEPHE(chain 'F' and resid 797 through 807)FF797 - 8064 - 13

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質 Proliferating cell nuclear antigen / PCNA / Cyclin


分子量: 28795.752 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PCNA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P12004
#2: タンパク質・ペプチド DNA excision repair protein ERCC-6-like 2


分子量: 1566.798 Da / 分子数: 3 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
参照: 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 64 / 由来タイプ: 天然 / 式: H2O
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3 Å3/Da / 溶媒含有率: 58.97 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.5 / 詳細: 25% (w/v) PEG3350, 100 mM BIS-TRIS pH 5.5

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: MASSIF-1 / 波長: 0.966 Å
検出器タイプ: DECTRIS PILATUS3 2M / 検出器: PIXEL / 日付: 2017年10月28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: 0.966 Å / 相対比: 1
反射解像度: 2.73→48.56 Å / Num. obs: 28128 / % possible obs: 99.9 % / 冗長度: 5 % / Biso Wilson estimate: 48.91 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.059 / Rrim(I) all: 0.133 / Net I/σ(I): 10.5
反射 シェル解像度: 2.73→2.86 Å / 冗長度: 4.8 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 3 / Num. unique obs: 3678 / CC1/2: 0.5 / Rpim(I) all: 0.272 / Rrim(I) all: 0.599 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
PHENIXdev_3126精密化
XDSデータ削減
Aimless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: 5MLO

5mlo


解像度: 2.73→48.56 Å / SU ML: 0.3824 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 25.4455
Rfactor反射数%反射
Rfree0.2547 1405 5 %
Rwork0.197 --
obs0.1999 28073 99.8 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 63.35 Å2
精密化ステップサイクル: LAST / 解像度: 2.73→48.56 Å
タンパク質核酸リガンド溶媒全体
原子数5982 0 0 64 6046
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00716290
X-RAY DIFFRACTIONf_angle_d1.13928521
X-RAY DIFFRACTIONf_chiral_restr0.05471002
X-RAY DIFFRACTIONf_plane_restr0.00591100
X-RAY DIFFRACTIONf_dihedral_angle_d5.98595228
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.830.36051210.28762628X-RAY DIFFRACTION99.78
2.83-2.940.28161440.26272633X-RAY DIFFRACTION99.78
2.94-3.070.33961350.25582611X-RAY DIFFRACTION99.71
3.07-3.240.29591350.24142649X-RAY DIFFRACTION99.89
3.24-3.440.28491410.20692630X-RAY DIFFRACTION100
3.44-3.70.29551660.21012622X-RAY DIFFRACTION99.96
3.7-4.080.24611310.18022670X-RAY DIFFRACTION100
4.08-4.670.21621270.14332697X-RAY DIFFRACTION99.96
4.67-5.880.20151530.162708X-RAY DIFFRACTION99.62
5.88-48.560.22951520.19822820X-RAY DIFFRACTION99.3
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)
14.45909493831-0.2550222804-0.5111689568138.000565629270.4423438493623.63403309158-0.3695173550981.1724016315-0.417267249422-0.6909423928340.225596063685-0.3824833606230.6842923679450.09264286271190.05643436490760.42154311453-0.03973205283590.1986781904560.679799005258-0.06797763726520.48353261694743.0343709069116.033177742-10.8241031048
26.593352879340.6148480719460.3331180177269.37711039698-2.109505625544.72172652248-0.2919023144190.747763726106-0.7861475184140.1442844725920.036019667491-0.0955262282680.888480943818-0.4132227113830.2096026804630.606644038527-0.2394950465510.2777310473010.575888458957-0.2366923821690.62349946720533.1613337544107.404301457-6.20168094381
35.762929308686.380280419520.9530137069777.182577209551.235176903320.415250551738-0.4414464661041.752973642040.070524081208-0.9538798519890.645404446309-0.5967164468810.4077449766730.286969554461-0.3348260067610.623219215334-0.01487845472240.1606461270521.282782533840.04614135109610.6981499760646.7634602311127.706454925-16.9402328068
41.69157449651-0.559150054747-0.5751016273892.00718677082-0.02136571689351.40751738138-0.0669895381952-0.1008505941930.1422016945840.224309826833-0.0753234361779-0.097166318235-0.04487059396060.602176495915-0.229333282503-0.3057161889920.0412670242310.0876148769020.4167263037750.1628591909570.84157945496248.7388510221137.5010485497.50682785929
52.51637696786-0.547735854124-1.445353681432.54030431534-0.06415865466661.569412388640.1697421769020.134649780138-0.2378263576510.1034455508340.07153757979-0.206593910240.0151852360510.701982026605-0.1807952249770.005846105932230.09528704368440.03409436295780.9618674869440.1699741904141.0537863064854.9760765058136.6567170069.70003844023
63.438304200180.524501398284-0.504764173940.6714507736820.06606075369291.444867439510.02932655264870.5015633076370.124457246508-0.1896715098570.0438546482811-0.03116871517430.1404481544260.2918600647380.02820343169170.05206999905970.08659305656130.09630883294720.5355901110430.1846485842210.63186158799548.5290883714131.028769393-1.95835158196
77.65926957462-3.58303286852-2.41523389896.201485733443.051347202498.125485266070.3942705405070.9568006410860.435541771773-0.741417643111-0.324747998456-1.04946137645-1.033401252730.511303388793-0.2007577319160.3714728786660.007613214232550.1046230086540.627880327420.3247225948440.76998843334346.8776549683140.211849083-14.2920250845
81.747815828991.17774239731-0.5201099339561.498030996790.5709165291661.26647687874-0.2295865475750.343408705516-0.415828441088-0.0965235665410.01579978117760.196549148354-0.0096673512797-0.04808097160460.1316592424340.3979151482450.005869193661570.2285134685480.09473906488-0.07020821086120.7646886229512.8731691487106.59090631822.1029800152
91.681865467160.5449833321411.055986687138.47924715459-0.1238268820013.95783488492-0.0224959502129-0.0559188044080.2158869260430.200745554851-0.056917999139-0.112295192164-0.2973151817190.09141988383390.07144959350630.3847565041470.03864065781830.1111658993090.09984746327970.04071376883710.6842915106626.6291030042115.85690959331.4936936701
101.59882470645-2.22593475701-1.144583214863.328299389632.348534112413.0357198152-0.54901111560.261355996671-0.9977518555620.172002567558-0.02109214086530.29921751610.325509284562-0.6319840992651.107962918010.839940794698-0.06697459368530.2960542842270.519929005626-0.3109010541771.2272492768-4.54544416238102.70010203911.2456398107
111.654143413570.606782131785-0.1619240394962.214524153560.8915706215034.02742804209-0.4835705138710.656890705646-0.72810107367-0.5854516105330.270234132502-0.5156189153150.6646336606590.2517827846470.03987780976650.684570310491-0.1410578378430.315750361960.446449354311-0.2391214400790.75656924425415.4867786709100.6399915092.85369276032
124.82202638849-4.14252326795-0.8714236362655.042144608422.399200350144.228495868140.4888347598280.580045049818-0.74850964082-0.547469343640.02882858528240.6119048593910.637992048683-0.336165971328-0.6600902795490.844835337085-0.5100304508130.1495508792371.02417543098-0.3320210411090.792779123852-2.38813932529103.563955746-1.70074987279
132.213081797060.3000174531790.4732589674361.4960676685-0.2131244662162.254758480030.0597845531481-0.141034407130.55525949260.135555710680.171593877189-0.243697976164-0.3845708984130.6274917056970.01416353401850.035262402935-0.40955224860.1074434508390.0492896517539-0.2003124260581.2132214441735.8620591254146.35893349332.3005632095
147.07799606824-0.538628407147-1.106765430422.448023252470.04170949414665.799594656010.03197579453090.03169170777590.1748599534630.122815492352-0.0848271459337-0.04054071455650.05948561445440.5755905217210.05903645144180.239065981093-0.06994217425420.08820616995980.390796311269-0.02381719372320.72083319294244.0198241961142.49817739621.5774687616
157.152575863784.68951959609-6.100953998293.06982491709-3.984491802475.37725506530.853071301881-0.5571699312131.600937510430.488384903985-0.446487763813-0.0655274696662-1.339068632020.435059741753-0.7110448670780.73983920513-0.02556741339580.253418780870.415075102943-0.08927822627591.1137262128824.7950670437153.40215092437.1324036577
164.0520748731.201129703390.9268236782854.041743399091.542510969984.36490669671-0.0302914556481-0.6596783312-0.5806718298590.691923784846-0.0428197450647-0.1879901300360.5951567645110.124955454035-0.04722555989630.382468181929-0.05058853641910.02508516562060.02193633547020.07943385312320.69139216960714.5446104633127.7969954239.9705267722
172.230134300131.28279430617-0.3730613931585.323250512180.4371804219032.4995648025-0.0628628035432-0.155670247583-0.1115693474190.133211518553-0.0873987358248-0.2721812552750.02363918297040.2307633175650.03716904793380.226175883809-0.03498359175330.03832029280810.0962675846494-0.03348822792770.52403174698119.6274574395136.82194671437.4921434104
185.24717803938-2.11372792885-0.4622669521385.010299426390.1687625879532.95356863335-0.156093626205-0.3971715724890.2469098057620.6354845097610.240792255744-0.540607070631-0.1149823898830.439883744688-0.2650376738350.238380299763-0.053567583229-0.01020529234470.225814911461-0.09434641688020.64872804854424.4576169495141.17908253338.2090917651
190.196045271389-0.2645216154491.313298648850.35791661488-1.775941323028.81292762052-0.263455692276-0.5441390535940.2804329933420.638997142106-0.01267190288851.94482744067-0.17041541392-1.624569005440.08318513844310.2632262827960.01885808611330.1514688694860.34439375117-0.04465109464020.8794653964997.04258558439147.61197185934.7926998839
201.94547698745-1.351322340960.2571697985982.980214559420.905558821043.941372811920.0591589243421-0.09197609571020.621583394045-0.1481697387070.01752294798250.423416265589-0.734440480818-0.215876656956-0.09821250754290.3377363970850.0510526976860.01099459616810.207214634572-0.1282325055940.81364617358414.4941158842152.71610839639.1847647246
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 117 )
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 134 )
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 173 )
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 202 )
6X-RAY DIFFRACTION6chain 'A' and (resid 203 through 255 )
7X-RAY DIFFRACTION7chain 'B' and (resid 797 through 807 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 65 )
9X-RAY DIFFRACTION9chain 'C' and (resid 66 through 117 )
10X-RAY DIFFRACTION10chain 'C' and (resid 118 through 134 )
11X-RAY DIFFRACTION11chain 'C' and (resid 135 through 255 )
12X-RAY DIFFRACTION12chain 'D' and (resid 797 through 807 )
13X-RAY DIFFRACTION13chain 'E' and (resid 1 through 65 )
14X-RAY DIFFRACTION14chain 'E' and (resid 66 through 117 )
15X-RAY DIFFRACTION15chain 'E' and (resid 118 through 134 )
16X-RAY DIFFRACTION16chain 'E' and (resid 135 through 202 )
17X-RAY DIFFRACTION17chain 'E' and (resid 203 through 240 )
18X-RAY DIFFRACTION18chain 'E' and (resid 241 through 255 )
19X-RAY DIFFRACTION19chain 'F' and (resid 796 through 800 )
20X-RAY DIFFRACTION20chain 'F' and (resid 801 through 807 )

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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