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基本情報

登録情報
データベース: PDB / ID: 5vgz
タイトルConformational Landscape of the p28-Bound Human Proteasome Regulatory Particle
要素
  • (26S proteasome non-ATPase regulatory subunit ...) x 10
  • (26S proteasome regulatory subunit ...) x 6
  • 26S proteasome complex subunit SEM1
キーワードHYDROLASE / p28 / 26S proteasome / regulatory particle / 19S / gankyrin
機能・相同性
機能・相同性情報


positive regulation of inclusion body assembly / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; オメガペプチターゼ / integrator complex / proteasome accessory complex / meiosis I / positive regulation of proteasomal protein catabolic process ...positive regulation of inclusion body assembly / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; オメガペプチターゼ / integrator complex / proteasome accessory complex / meiosis I / positive regulation of proteasomal protein catabolic process / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / proteasome regulatory particle, base subcomplex / negative regulation of programmed cell death / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Regulation of ornithine decarboxylase (ODC) / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / K63-linked deubiquitinase activity / Impaired BRCA2 binding to RAD51 / proteasome binding / regulation of protein catabolic process / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / blastocyst development / transcription factor binding / general transcription initiation factor binding / endopeptidase activator activity / proteasome assembly / polyubiquitin modification-dependent protein binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / mRNA export from nucleus / regulation of proteasomal protein catabolic process / enzyme regulator activity / ERAD pathway / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / inclusion body / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / stem cell differentiation / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / double-strand break repair via homologous recombination / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / P-body / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / HDR through Homologous Recombination (HRR) / Metalloprotease DUBs / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / cytoplasmic ribonucleoprotein granule / Regulation of PTEN stability and activity / Interleukin-1 signaling / double-strand break repair via nonhomologous end joining / Orc1 removal from chromatin / Regulation of RAS by GAPs
類似検索 - 分子機能
: / Ubiquitin interaction motif / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / DSS1/SEM1 / 26S proteasome regulatory subunit RPN5, C-terminal domain / : ...: / Ubiquitin interaction motif / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / DSS1/SEM1 / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome subunit RPN2, N-terminal domain / DSS1_SEM1 / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S Proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S Proteasome non-ATPase regulatory subunit 7/8 / : / 26S proteasome regulatory subunit 7, OB domain / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / Ubiquitin-interacting motif. / PCI/PINT associated module / von Willebrand factor type A domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / HEAT repeats / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / von Willebrand factor A-like domain superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Armadillo-like helical / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
類似検索 - ドメイン・相同性
26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 ...26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome complex subunit SEM1 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 13
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.5 Å
データ登録者Lu, Y. / Wu, J. / Dong, Y. / Chen, S. / Sun, S. / Ma, Y.B. / Ouyang, Q. / Finley, D. / Kirschner, M.W. / Mao, Y.
引用ジャーナル: Mol Cell / 年: 2017
タイトル: Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle.
著者: Ying Lu / Jiayi Wu / Yuanchen Dong / Shuobing Chen / Shuangwu Sun / Yong-Bei Ma / Qi Ouyang / Daniel Finley / Marc W Kirschner / Youdong Mao /
要旨: The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of ...The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of AAA-ATPases, which is guided by at least four RP assembly chaperones in mammals: PAAF1, p28/gankyrin, p27/PSMD9, and S5b. Using cryogenic electron microscopy, we analyzed the non-AAA structure of the p28-bound human RP at 4.5 Å resolution and determined seven distinct conformations of the Rpn1-p28-AAA subcomplex within the p28-bound RP at subnanometer resolutions. Remarkably, the p28-bound AAA ring does not form a channel in the free RP and spontaneously samples multiple "open" and "closed" topologies at the Rpt2-Rpt6 and Rpt3-Rpt4 interfaces. Our analysis suggests that p28 assists the proteolytic core particle to select a specific conformation of the ATPase ring for RP engagement and is released in a shoehorn-like fashion in the last step of the chaperone-mediated proteasome assembly.
履歴
登録2017年4月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年8月23日Provider: repository / タイプ: Initial release
改定 1.12018年8月22日Group: Data collection / Database references / カテゴリ: pdbx_related_exp_data_set
Item: _pdbx_related_exp_data_set.data_reference / _pdbx_related_exp_data_set.metadata_reference
改定 1.22023年8月16日Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible / _refine.ls_d_res_high / _refine.ls_d_res_low

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構造の表示

ムービー
  • 登録構造単位
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-8672
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
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: 26S proteasome regulatory subunit 7
B: 26S proteasome regulatory subunit 4
C: 26S proteasome regulatory subunit 8
D: 26S proteasome regulatory subunit 6B
E: 26S proteasome regulatory subunit 10B
F: 26S proteasome regulatory subunit 6A
U: 26S proteasome non-ATPase regulatory subunit 1
V: 26S proteasome non-ATPase regulatory subunit 3
W: 26S proteasome non-ATPase regulatory subunit 12
X: 26S proteasome non-ATPase regulatory subunit 11
Y: 26S proteasome non-ATPase regulatory subunit 6
Z: 26S proteasome non-ATPase regulatory subunit 7
a: 26S proteasome non-ATPase regulatory subunit 13
b: 26S proteasome non-ATPase regulatory subunit 4
c: 26S proteasome non-ATPase regulatory subunit 14
d: 26S proteasome non-ATPase regulatory subunit 8
e: 26S proteasome complex subunit SEM1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)535,26918
ポリマ－535,20317
非ポリマー651
水00
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_5551
Buried area63690 Å2
ΔGint-344 kcal/mol
Surface area233450 Å2

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要素

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26S proteasome regulatory subunit ... , 6種, 6分子 ABCDEF

#1: タンパク質 26S proteasome regulatory subunit 7 / 26S proteasome AAA-ATPase subunit RPT1 / Proteasome 26S subunit ATPase 2 / Protein MSS1


分子量: 9309.589 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMC2, MSS1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P35998
#2: タンパク質 26S proteasome regulatory subunit 4 / P26s4 / 26S proteasome AAA-ATPase subunit RPT2 / Proteasome 26S subunit ATPase 1


分子量: 7969.963 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMC1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P62191
#3: タンパク質 26S proteasome regulatory subunit 8 / 26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / ...26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / Thyroid hormone receptor-interacting protein 1 / TRIP1 / p45/SUG


分子量: 13603.661 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMC5, SUG1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P62195
#4: タンパク質 26S proteasome regulatory subunit 6B / 26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ...26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ATPase 4 / Tat-binding protein 7 / TBP-7


分子量: 12341.005 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMC4, MIP224, TBP7 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P43686
#5: タンパク質 26S proteasome regulatory subunit 10B / 26S proteasome AAA-ATPase subunit RPT4 / Proteasome 26S subunit ATPase 6 / Proteasome subunit p42


分子量: 12197.259 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMC6, SUG2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P62333
#6: タンパク質 26S proteasome regulatory subunit 6A / 26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / ...26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / Tat-binding protein 1 / TBP-1


分子量: 12942.888 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMC3, TBP1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P17980

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26S proteasome non-ATPase regulatory subunit ... , 10種, 10分子 UVWXYZabcd

#7: タンパク質 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome subunit p112


分子量: 103755.023 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q99460
#8: タンパク質 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit RPN3 / 26S proteasome regulatory subunit S3 / Proteasome subunit p58


分子量: 55703.727 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD3 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O43242
#9: タンパク質 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit p55


分子量: 52979.359 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD12 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O00232
#10: タンパク質 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit S9 / 26S proteasome ...26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit S9 / 26S proteasome regulatory subunit p44.5


分子量: 43427.055 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD11 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O00231
#11: タンパク質 26S proteasome non-ATPase regulatory subunit 6 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit S10 / Breast cancer- ...26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit S10 / Breast cancer-associated protein SGA-113M / Phosphonoformate immuno-associated protein 4 / Proteasome regulatory particle subunit p44S10 / p42A


分子量: 44336.906 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD6, KIAA0107, PFAAP4 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q15008
#12: タンパク質 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit S12 / Mov34 protein ...26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit S12 / Mov34 protein homolog / Proteasome subunit p40


分子量: 32382.094 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD7, MOV34L / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P51665
#13: タンパク質 26S proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit S11 / 26S proteasome ...26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit S11 / 26S proteasome regulatory subunit p40.5


分子量: 42734.988 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD13 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9UNM6
#14: タンパク質 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory ...26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory factor 1 / ASF / Multiubiquitin chain-binding protein


分子量: 20866.023 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD4, MCB1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P55036
#15: タンパク質 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit RPN11 / 26S proteasome-associated PAD1 homolog 1


分子量: 32329.355 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD14, POH1 / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: O00487, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; オメガペプチターゼ
#16: タンパク質 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit S14 / p31


分子量: 30039.699 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD8 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P48556

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タンパク質 / 非ポリマー , 2種, 2分子 e

#17: タンパク質 26S proteasome complex subunit SEM1 / 26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot ...26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot malformation type 1 protein / Sem1


分子量: 8284.611 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SEM1, C7orf76, DSS1, SHFDG1, SHFM1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P60896
#18: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 1 / 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: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: Proteasome regulatory particle / タイプ: COMPLEX / Entity ID: #1-#17 / 由来: RECOMBINANT
由来(天然)生物種: Homo sapiens (ヒト)
由来(組換発現)生物種: Homo sapiens (ヒト)
緩衝液pH: 7.5
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: ETHANE

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電子顕微鏡撮影

実験機器
モデル: Talos Arctica / 画像提供: FEI Company
顕微鏡モデル: FEI TECNAI ARCTICA
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD
撮影電子線照射量: 50 e/Å2
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)

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解析

ソフトウェア名称: PHENIX / バージョン: 1.11.1_2575: / 分類: 精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成解像度: 4.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 117471 / 対称性のタイプ: POINT
精密化解像度: 4.5→4.5 Å / SU ML: 1.24 / σ(F): 0 / 位相誤差: 69.72 / 立体化学のターゲット値: MLHL
Rfactor反射数%反射
Rfree0.4468 2086 0.32 %
Rwork0.487 --
obs0.4869 652306 99.92 %
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
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.00537363
ELECTRON MICROSCOPYf_angle_d1.05750457
ELECTRON MICROSCOPYf_dihedral_angle_d9.82422980
ELECTRON MICROSCOPYf_chiral_restr0.0585767
ELECTRON MICROSCOPYf_plane_restr0.0076469
精密化 TLS

手法: refined / Refine-ID: ELECTRON MICROSCOPY

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)
12.5332.6116-3.93232.6992-3.97876.3273-0.23430.687-0.715-0.51530.2147-0.60250.09741.66550.13773.5321-1.65623.06286.6832-1.14457.2632150.243379.092114.079
24.1512.9983-4.41572.2696-3.26194.85180.58631.34220.6345-1.56211.088-2.6567-0.46582.1178-1.28193.9703-0.53380.51585.5567-1.46922.9121148.425982.8821126.0707
34.80613.18890.98546.56884.18512.92861.73372.68282.2790.1695-2.34150.0037-1.5783-0.8914-0.94442.0031-0.09161.58412.88730.23692.6923161.5543102.3802131.4274
42.246-1.24722.21897.0714-0.15643.4713-1.76650.68740.82850.8727-0.67450.9509-1.53940.01841.70473.1722-2.57580.96842.3233-0.51062.2971163.5609107.2288133.0947
58.7505-3.28222.95864.9095-4.97055.04590.6105-0.38111.16642.1144-0.7346-0.1694-0.43861.18510.82884.8585-1.93641.43634.4793-2.91384.6905169.351102.476130.5279
60.90740.46061.33223.0418-0.36042.3430.5695-0.0852-0.82760.3520.29430.7080.03510.23290.79141.5192-2.32740.23752.845-1.17513.2178160.6863100.1127131.2639
79.02826.51847.86035.37855.04647.4231-1.805-4.9177-0.88861.49980.88664.46640.90314.15290.38230.97120.69171.82993.8347-0.04174.8076139.609885.6645116.109
83.48510.7914-3.25480.1734-0.73013.0311-0.383-0.23611.08120.4868-0.3418-1.7538-1.0423-0.58331.52263.06460.64620.45094.282-1.60033.5763153.940199.3378112.9653
92.14770.04564.81978.9708-6.1171.9990.7012-1.7871-0.70512.9568-0.2325-3.471-0.1944.8801-0.3292.9927-0.6785-1.56514.331-1.04452.1673163.060291.1412119.2069
105.86191.78923.28471.16120.38362.50820.24430.010.70730.3672-0.307-0.34690.48321.55730.6147-3.25982.78933.4311.0677-1.56871.5187154.638796.8608117.5607
116.21741.3897-0.44523.4716-4.11985.13520.60030.9532-2.0703-1.85790.34880.3128-0.34882.7327-0.7062.0386-1.2579-0.17443.5936-1.76834.1441156.144893.2133109.423
120.5111-0.87890.17571.9542-0.79620.53111.3644-0.49670.7506-2.5832-1.60050.6884-0.69143.3368-0.56861.68310.64050.25481.9585-0.14172.2162148.91295.6922113.836
132.7327-0.2035-0.04810.07630.74674.6923-0.34581.4457-0.2554-1.1515-0.07270.5661-1.26692.03770.1857.19181.39110.46062.7933-1.2181-1.848589.2213110.3355123.7236
144.3766-2.5273-1.32862.3238-2.24669.768-0.4424-0.0172.88561.3987-1.9089-0.1226-0.40942.99280.6579-5.94417.63545.4078-2.7158-4.4922-0.3657135.4465103.6251108.5049
151.50871.33150.32651.08840.36160.58810.2298-1.38961.2320.45120.366-0.1249-1.04860.5226-0.42356.64672.5254-0.27484.0994-3.14792.711579.8325104.7879129.4996
163.53034.0907-0.54834.5703-0.66080.3774-0.72750.20141.0913-0.4494-0.97811.5820.3449-0.92071.30072.9824-0.80051.59672.75180.6460.7782118.286120.0394124.5964
174.77952.4096-2.73411.29-1.82793.8788-0.5260.93690.6931-1.31940.70210.22040.2361-0.49981.29712.2963-2.34750.56391.97333.59722.0054128.7387118.7013115.3269
189.84675.8002-6.52433.4076-3.8974.4419-1.13611.43541.568-2.90420.59222.4021-0.6571-2.26020.03493.74110.0992-0.60984.31341.17831.8542127.2975126.0088117.3845
193.1132-0.144-0.77080.29231.22872.7926-0.6707-1.6369-2.16650.66890.1887-1.22240.33651.9832-0.43962.621-0.56163.40766.82391.60352.7845162.4434125.4882177.3484
204.2653-4.98845.56739.5426-4.22538.4727-0.4786-1.08230.6164-0.54861.2096-1.3085-0.6066-0.1655-0.6831-1.3842-2.39660.55872.16391.48730.4142138.852131.2482128.8914
214.22810.9956-0.40264.37061.05032.0445-0.6662-2.09911.32361.60371.8261.3646-1.27032.6776-0.67320.6828-0.09572.28722.4721-1.63791.3384136.2542138.9121137.7634
225.4863-0.32973.22525.33333.2355.5037-1.3858-1.88231.44781.44330.8250.7646-1.62381.43570.68820.7698-0.18291.77413.19530.16340.7863143.4496131.8152136.059
233.6807-2.53311.14971.9849-0.76710.3574-0.7531-3.63871.8851.24461.40731.70751.2887-2.0999-1.07153.2488-1.5163.31236.00360.54135.9402155.9925116.6259170.697
247.836-0.3444-0.16480.2540.84452.9451.0655-1.5938-0.37560.57850.07640.7543-1.20080.4001-0.60950.4950.19321.18644.4326-0.42963.6934158.2188117.7798136.6528
259.78831.61060.51823.2184-3.72895.0223-2.7281-1.546.3063-2.63933.4037-2.0994-9.7369-0.0153-1.50183.97950.11030.99674.37031.35244.2466149.7418136.0578145.8994
262.66053.60110.81951.99322.00639.6622-1.3980.53690.61771.7771-2.31033.60551.4567-3.08243.5668-0.33910.2431-1.14964.1869-0.48063.8394152.7176124.3003132.3915
270.5180.265-0.5192.23191.17311.4994-2.6848-0.59793.16023.1028-1.3528-7.24351.09758.12614.61891.99030.20150.51625.82730.30945.3369160.3012126.9751147.5506
284.47765.82437.66547.58039.9771.99980.57831.86843.17622.33780.5884-3.61843.49672.9225-0.94992.7660.45661.87515.2469-0.57935.3646161.9567122.9227137.8063
296.1534-5.8158-2.59566.29810.31416.78381.3948-0.6832-1.1744-0.37730.6891.63013.7363-3.5667-1.95551.49680.0571.93181.04692.40591.902150.3361116.1211139.1934
302.0571-1.9547-1.42944.59394.26997.28722.0408-1.09192.77390.64210.4855-1.079-2.27252.2094-2.52626.1918-2.2619-0.76482.68750.03515.4985166.0059120.5692140.2388
315.57581.64672.33442.06180.48928.78670.5085-0.44851.88070.45661.32631.2762-1.45251.19440.09616.36740.47293.98162.56251.8242-0.190643.5688128.7298136.4377
321.0017-0.14641.2291.99280.96684.84580.73581.17610.3165-1.0302-0.0859-0.6248-0.74571.3575-0.10791.74561.25736.17841.2543-3.1247-2.339255.4582103.7226137.3038
331.957-1.2641-1.64321.03461.53121.8091-0.8367-1.0952-1.06150.21170.005-0.36531.84040.177-0.82070.07523.7946.24945.4899-3.885-1.677168.826677.6437138.8319
340.4926-0.70170.24581.17560.11450.63260.725-0.2834-1.1265-0.2483-0.06290.2440.3259-0.87075.59092.38567.5978-0.69745.7733-4.61651.709699.752966.4436133.1864
350.1065-1.17120.1392.37960.78082.41940.6166-0.3742-2.5012.1471-0.17211.5699-0.3329-0.20330.34487.68426.5638-1.5940.7262-10.0041-4.243498.992483.7585134.9433
363.75242.5017-1.66774.0283-1.66631.18170.4145-0.4863-2.5364-0.0397-0.36670.39610.56110.1281-0.27684.28944.8661-2.80287.6461-2.9775.178978.800561.8632121.0287
372.18721.21270.3972.38081.17942.78690.8155-2.2761-0.2687-2.35630.0569-3.61620.74710.23081.32265.37850.70370.19428.2391-1.78638.919467.9268120.185191.1665
383.7846-1.44811.16392.1676-1.86551.58542.96037.329-8.4454-4.0794-3.62632.20125.91564.30810.65052.6944-9.39273.7184-3.13581.80030.185761.894132.3021108.0312
396.2237-3.7764-0.61166.8437-1.23692.5579-2.7193-0.59371.03894.8471.5171-3.3651-4.20792.15640.09350.5204-1.7335-0.85873.37560.3468-0.389573.0566160.7126127.7076
400.79010.66950.66399.32835.69033.60610.47761.1396-3.7022-2.4075-0.2625-2.50372.41951.3898-1.98299.01952.14670.62988.32872.27978.5593194.029187.9706137.7977
418.53455.75650.50765.8807-1.41091.59011.77140.4855-1.11672.7559-0.0996-6.19962.207-0.5174-2.49729.69513.6922.31535.45360.75297.7317178.9063191.871143.5872
420.8215-0.07790.26320.10190.0530.2767-0.15310.3066-0.52010.2557-1.3133-0.4321.8069-1.0153-0.67246.23021.66885.83389.33083.32063.2624161.4751183.4712146.9982
433.4791-1.64483.25235.0371-0.48033.24890.68121.01720.2501-1.6645-2.9815-0.62330.0604-1.1271-0.7521-1.74252.30824.54694.7722-2.8775.1586138.6577177.7356165.9574
447.63970.0807-0.11933.04180.93893.7598-0.5827-1.03922.43281.47571.45351.24710.11642.56282.02242.05092.8275-2.01065.94860.67518.1087117.9344181.0921157.4514
455.50472.85550.9651.85170.31313.2337-0.3394-0.13090.3939-0.0679-0.96151.0612-0.85630.1301-0.07031.27260.5771-2.81045.8706-0.54245.9787107.8497170.3321147.8532
460.2578-0.83871.42585.1321-5.30397.06350.01760.0611-0.52131.898-0.6638-1.545-0.64821.0322-0.15632.73560.5768-2.45584.144-4.19348.0877110.4776139.2303163.0153
470.0450.14560.11291.2246-0.72892.5418-0.41870.16351.37330.25270.5307-1.3444-0.79231.2113-1.58975.09714.62992.87528.6315-1.60979.1945137.2547212.465880.6089
480.1976-0.06660.30260.0387-0.01140.80861.30550.75151.812-0.98450.2246-1.7624-0.03341.73521.33614.61796.65652.76016.7482-2.66828.8377129.2136191.508490.8664
493.41011.0668-1.60055.1441-2.55531.55470.948-0.8292-0.1288-0.891-0.0456-1.16930.5940.33980.88992.41874.99823.11916.4382-3.87934.9726131.2071193.0543119.276
501.6211-0.5398-0.59524.28972.39874.82920.5893-0.42850.08170.30580.64890.3581-0.7257-0.44472.2135-0.4325-3.98014.261.92826.05310.7968109.3413180.9885132.0342
517.2615-3.46310.84824.33082.20382.5918-0.86973.35212.0867-0.12110.3961-0.95090.5727-0.06191.96260.9997-0.35082.47932.3990.59141.564695.338141.757113.9738
526.0217-3.2012-5.18092.07432.73684.76722.57730.0286-2.3462-1.34750.287-3.42572.42480.5185-0.45778.43345.74471.03248.88-1.73827.435190.9381173.43571.6664
530.57440.1668-0.98910.5491-0.89492.34892.39462.46180.4411-3.243-0.6426-2.18362.70151.19682.0321.70745.4696-0.9015.6319-4.92484.5438101.3278165.054990.8174
541.2945-1.9704-1.63864.9279-2.86410.04420.7506-2.6787-0.5564.62771.8473-1.5328-0.7612-0.8948-0.4516-11.918313.97612.8093-4.4521-9.384-7.132791.5841172.7287116.7431
551.1876-0.56350.25080.1035-0.0385-0.04760.4205-0.4424-1.27561.0066-0.6109-0.5651-0.2595-0.8652-1.9308-1.64832.8589-7.41261.831-5.24285.3694128.5602116.9209167.3609
564.85992.88724.96267.08674.66336.0365-0.84110.09511.64860.8075-0.75910.66611.62291.99980.80263.38680.7673-3.8044.953-3.22535.0288119.9416124.9914160.4696
572.44951.60114.36381.30062.11526.4977-1.8877-0.33723.89982.15660.0051-1.9806-2.1856-1.3212-0.68360.5084-1.14011.09840.0801-1.2946.247899.0465135.7741145.709
582.4913-0.6125-0.68212.4125-1.29821.50783.70171.5475-2.96331.67920.1745-1.63831.30670.3068-0.05266.0913.4432-1.46936.81850.06257.022144.38139.414204.2671
592.8923-1.59210.42951.6891-0.32620.2296-0.3989-0.0620.1739-0.47930.67560.54070.39561.0620.25860.11380.2096-1.51326.07133.1796-0.2149119.1359151.9935192.8358
603.362-0.7536-0.30765.19724.4233.7014-4.30333.7142-1.6156-2.4157-2.4673.8766-0.56460.0645-0.5352-0.5137-4.1766-1.25660.05541.57735.9451102.3685156.5874172.2503
614.04011.83932.46572.16580.91398.22610.64491.3004-2.78251.07850.0342-1.6472-0.12750.7218-1.24655.1813.4464-0.38363.49690.47754.0845143.5604110.6349194.88
623.9299-0.1506-0.33722.78860.47152.21470.2830.6586-0.49660.45050.3263-0.73341.21531.0215-0.84510.82213.7716-1.00973.0533-3.35872.3326144.457106.7544187.9441
631.2453-0.3312-0.20822.07290.48110.71111.22530.69690.50910.01860.5962-0.63960.26040.1873-0.3040.33045.00690.28112.0963-3.39512.4702137.3383107.5722185.6215
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732.96535.0371-4.22278.9738-7.32436.10021.24960.46451.256-1.02390.1114-1.0618-1.02310.0818-0.92364.1010.64451.06343.6312-0.045510.1676107.7241137.5814148.7199
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779.8516-2.43435.59284.6287-0.53633.34240.5903-1.3639-4.10141.4447-0.4182.2423-1.5793-1.1147-0.20013.3486-0.31371.48843.4163-0.15642.289927.4517142.545130.956
785.6545-0.26282.27053.25321.90032.18220.3418-0.96810.57040.33451.2427-0.3052-1.3850.7763-0.23176.38714.08213.21594.93891.06314.668137.9133149.0414128.676
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802.30023.7233-1.2658.5289-3.06723.844-0.71540.45070.5977-1.20320.34872.47470.5367-1.05720.12241.8663-1.80840.66780.8405-0.76040.600645.5358167.08136.8091
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862.9402-1.24551.74660.5769-0.81871.16290.7352.1202-0.7611-1.5952-0.584-0.31430.4367-0.005-0.26866.73332.94640.91267.1699-1.80533.915883.1029163.129398.8409
877.1408-2.7590.32757.021-3.96632.50163.13890.8675-1.4806-0.740.58122.68333.53611.0988-3.94296.8851.3858-0.42246.8724-0.97662.743179.3805174.2192108.2507
882.8999-0.3389-3.83342.055-0.60385.61351.1072-0.56150.89480.1453-0.3125-1.0477-1.53041.6739-0.37553.3351-1.51610.6155.4132.43364.20683.5571193.5303114.5986
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1ELECTRON MICROSCOPY1chain 'A' and (resid 73 through 83 )
2ELECTRON MICROSCOPY2chain 'A' and (resid 84 through 88 )
3ELECTRON MICROSCOPY3chain 'A' and (resid 89 through 109 )
4ELECTRON MICROSCOPY4chain 'A' and (resid 110 through 130 )
5ELECTRON MICROSCOPY5chain 'A' and (resid 131 through 143 )
6ELECTRON MICROSCOPY6chain 'A' and (resid 144 through 155 )
7ELECTRON MICROSCOPY7chain 'B' and (resid 93 through 106 )
8ELECTRON MICROSCOPY8chain 'B' and (resid 107 through 114 )
9ELECTRON MICROSCOPY9chain 'B' and (resid 115 through 121 )
10ELECTRON MICROSCOPY10chain 'B' and (resid 122 through 139 )
11ELECTRON MICROSCOPY11chain 'B' and (resid 140 through 153 )
12ELECTRON MICROSCOPY12chain 'B' and (resid 154 through 165 )
13ELECTRON MICROSCOPY13chain 'C' and (resid 11 through 67 )
14ELECTRON MICROSCOPY14chain 'C' and (resid 68 through 128 )
15ELECTRON MICROSCOPY15chain 'D' and (resid 39 through 65 )
16ELECTRON MICROSCOPY16chain 'D' and (resid 66 through 99 )
17ELECTRON MICROSCOPY17chain 'D' and (resid 100 through 120 )
18ELECTRON MICROSCOPY18chain 'D' and (resid 121 through 145 )
19ELECTRON MICROSCOPY19chain 'E' and (resid 11 through 51 )
20ELECTRON MICROSCOPY20chain 'E' and (resid 52 through 81 )
21ELECTRON MICROSCOPY21chain 'E' and (resid 82 through 96 )
22ELECTRON MICROSCOPY22chain 'E' and (resid 97 through 114 )
23ELECTRON MICROSCOPY23chain 'F' and (resid 53 through 84 )
24ELECTRON MICROSCOPY24chain 'F' and (resid 85 through 94 )
25ELECTRON MICROSCOPY25chain 'F' and (resid 95 through 121 )
26ELECTRON MICROSCOPY26chain 'F' and (resid 122 through 134 )
27ELECTRON MICROSCOPY27chain 'F' and (resid 135 through 144 )
28ELECTRON MICROSCOPY28chain 'F' and (resid 145 through 154 )
29ELECTRON MICROSCOPY29chain 'F' and (resid 155 through 159 )
30ELECTRON MICROSCOPY30chain 'F' and (resid 160 through 167 )
31ELECTRON MICROSCOPY31chain 'U' and (resid 1 through 71 )
32ELECTRON MICROSCOPY32chain 'U' and (resid 72 through 172 )
33ELECTRON MICROSCOPY33chain 'U' and (resid 173 through 254 )
34ELECTRON MICROSCOPY34chain 'U' and (resid 255 through 426 )
35ELECTRON MICROSCOPY35chain 'U' and (resid 427 through 838 )
36ELECTRON MICROSCOPY36chain 'U' and (resid 839 through 935 )
37ELECTRON MICROSCOPY37chain 'V' and (resid 18 through 104 )
38ELECTRON MICROSCOPY38chain 'V' and (resid 105 through 371 )
39ELECTRON MICROSCOPY39chain 'V' and (resid 372 through 505 )
40ELECTRON MICROSCOPY40chain 'W' and (resid 1 through 93 )
41ELECTRON MICROSCOPY41chain 'W' and (resid 94 through 134 )
42ELECTRON MICROSCOPY42chain 'W' and (resid 135 through 221 )
43ELECTRON MICROSCOPY43chain 'W' and (resid 222 through 343 )
44ELECTRON MICROSCOPY44chain 'W' and (resid 344 through 399 )
45ELECTRON MICROSCOPY45chain 'W' and (resid 400 through 423 )
46ELECTRON MICROSCOPY46chain 'W' and (resid 424 through 456 )
47ELECTRON MICROSCOPY47chain 'X' and (resid 38 through 81 )
48ELECTRON MICROSCOPY48chain 'X' and (resid 82 through 220 )
49ELECTRON MICROSCOPY49chain 'X' and (resid 221 through 317 )
50ELECTRON MICROSCOPY50chain 'X' and (resid 318 through 393 )
51ELECTRON MICROSCOPY51chain 'X' and (resid 394 through 422 )
52ELECTRON MICROSCOPY52chain 'Y' and (resid 12 through 113 )
53ELECTRON MICROSCOPY53chain 'Y' and (resid 114 through 245 )
54ELECTRON MICROSCOPY54chain 'Y' and (resid 246 through 389 )
55ELECTRON MICROSCOPY55chain 'Z' and (resid 5 through 115 )
56ELECTRON MICROSCOPY56chain 'Z' and (resid 116 through 185 )
57ELECTRON MICROSCOPY57chain 'Z' and (resid 186 through 290 )
58ELECTRON MICROSCOPY58chain 'a' and (resid 3 through 149 )
59ELECTRON MICROSCOPY59chain 'a' and (resid 150 through 242 )
60ELECTRON MICROSCOPY60chain 'a' and (resid 243 through 376 )
61ELECTRON MICROSCOPY61chain 'b' and (resid 1 through 24 )
62ELECTRON MICROSCOPY62chain 'b' and (resid 25 through 62 )
63ELECTRON MICROSCOPY63chain 'b' and (resid 63 through 113 )
64ELECTRON MICROSCOPY64chain 'b' and (resid 114 through 133 )
65ELECTRON MICROSCOPY65chain 'b' and (resid 134 through 169 )
66ELECTRON MICROSCOPY66chain 'b' and (resid 170 through 191 )
67ELECTRON MICROSCOPY67chain 'c' and (resid 24 through 47 )
68ELECTRON MICROSCOPY68chain 'c' and (resid 48 through 74 )
69ELECTRON MICROSCOPY69chain 'c' and (resid 75 through 125 )
70ELECTRON MICROSCOPY70chain 'c' and (resid 126 through 185 )
71ELECTRON MICROSCOPY71chain 'c' and (resid 186 through 210 )
72ELECTRON MICROSCOPY72chain 'c' and (resid 211 through 225 )
73ELECTRON MICROSCOPY73chain 'c' and (resid 226 through 243 )
74ELECTRON MICROSCOPY74chain 'c' and (resid 244 through 273 )
75ELECTRON MICROSCOPY75chain 'c' and (resid 274 through 310 )
76ELECTRON MICROSCOPY76chain 'd' and (resid 1 through 15 )
77ELECTRON MICROSCOPY77chain 'd' and (resid 16 through 64 )
78ELECTRON MICROSCOPY78chain 'd' and (resid 65 through 108 )
79ELECTRON MICROSCOPY79chain 'd' and (resid 109 through 145 )
80ELECTRON MICROSCOPY80chain 'd' and (resid 146 through 182 )
81ELECTRON MICROSCOPY81chain 'd' and (resid 183 through 218 )
82ELECTRON MICROSCOPY82chain 'd' and (resid 219 through 236 )
83ELECTRON MICROSCOPY83chain 'd' and (resid 237 through 257 )
84ELECTRON MICROSCOPY84chain 'e' and (resid 1 through 19 )
85ELECTRON MICROSCOPY85chain 'e' and (resid 20 through 32 )
86ELECTRON MICROSCOPY86chain 'e' and (resid 33 through 38 )
87ELECTRON MICROSCOPY87chain 'e' and (resid 39 through 62 )
88ELECTRON MICROSCOPY88chain 'e' and (resid 63 through 70 )

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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://pdbjlvh1.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