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- PDB-6hvw: Yeast 20S proteasome with human beta2i (1-53) in complex with 43 -

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基本情報

登録情報
データベース: PDB / ID: 6hvw
タイトルYeast 20S proteasome with human beta2i (1-53) in complex with 43
要素
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
キーワードHYDROLASE / Proteasome / Mutant / Inhibitor / Binding Analysis
機能・相同性
機能・相同性情報


spermatoproteasome complex / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process ...spermatoproteasome complex / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / humoral immune response / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / Ub-specific processing proteases / threonine-type endopeptidase activity / T cell proliferation / Neutrophil degranulation / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / 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 / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / G2/M Checkpoints / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / cell morphogenesis / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / 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 / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / peroxisome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / Ub-specific processing proteases / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleoplasm / nucleus / cytosol
類似検索 - 分子機能
Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. ...Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Chem-GVW / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 ...Chem-GVW / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / Proteasome subunit beta type-10
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Saccharomyces cerevisiae (パン酵母)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3 Å
データ登録者Huber, E.M. / Groll, M.
資金援助 ドイツ, 1件
組織認可番号国
German Research FoundationGR1861/10-1 ドイツ
引用ジャーナル: J.Med.Chem. / 年: 2019
タイトル: Structure-Based Design of Inhibitors Selective for Human Proteasome beta 2c or beta 2i Subunits.
著者: Xin, B.T. / Huber, E.M. / de Bruin, G. / Heinemeyer, W. / Maurits, E. / Espinal, C. / Du, Y. / Janssens, M. / Weyburne, E.S. / Kisselev, A.F. / Florea, B.I. / Driessen, C. / van der Marel, G. ...著者: Xin, B.T. / Huber, E.M. / de Bruin, G. / Heinemeyer, W. / Maurits, E. / Espinal, C. / Du, Y. / Janssens, M. / Weyburne, E.S. / Kisselev, A.F. / Florea, B.I. / Driessen, C. / van der Marel, G.A. / Groll, M. / Overkleeft, H.S.
履歴
登録2018年10月11日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年1月30日Provider: repository / タイプ: Initial release
改定 1.12019年4月24日Group: Data collection / Database references
カテゴリ: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
改定 1.22024年1月24日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
改定 1.32024年10月16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: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-3
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-6
F: Probable proteasome subunit alpha type-7
G: Proteasome subunit alpha type-1
H: Proteasome subunit beta type-10,Proteasome subunit beta type-2
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-4
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-6
M: Proteasome subunit beta type-7
N: Proteasome subunit beta type-1
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-3
Q: Proteasome subunit alpha type-4
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-6
T: Probable proteasome subunit alpha type-7
U: Proteasome subunit alpha type-1
V: Proteasome subunit beta type-10,Proteasome subunit beta type-2
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-4
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-6
a: Proteasome subunit beta type-7
b: Proteasome subunit beta type-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)733,72548
ポリマ－729,70928
非ポリマー4,01620
水3,567198
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
単位格子
Length a, b, c (Å)134.240, 299.900, 143.250
Angle α, β, γ (deg.)90.00, 112.50, 90.00
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21O
12B
22P
13C
23Q
14D
24R
15E
25S
16F
26T
17G
27U
18H
28V
19I
29W
110J
210X
111K
211Y
112L
212Z
113M
213a
114N
214b

NCSドメイン領域:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 300
2111O1 - 300
1121B1 - 300
2121P1 - 300
1131C1 - 300
2131Q1 - 300
1141D1 - 300
2141R1 - 300
1151E1 - 300
2151S1 - 300
1161F1 - 300
2161T1 - 300
1171G1 - 300
2171U1 - 300
1181H1 - 300
2181V1 - 300
1191I1 - 300
2191W1 - 300
11101J1 - 300
21101X1 - 300
11111K1 - 300
21111Y1 - 300
11121L1 - 300
21121Z1 - 300
11131M1 - 300
21131a1 - 300
11141N1 - 300
21141b1 - 300

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

NCS oper:
IDCodeMatrixベクター
1given(1), (1), (1)
2given(-0.999174, -0.007569, 0.039931), (0.000606, -0.985172, -0.171568), (0.040638, -0.171402, 0.984363)66.25985, -288.36252, -25.60985

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要素

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Proteasome subunit alpha type- ... , 6種, 12分子 AOBPCQDRESGU

#1: タンパク質 Proteasome subunit alpha type-2 / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / ...Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


分子量: 27191.828 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P23639, proteasome endopeptidase complex
#2: タンパク質 Proteasome subunit alpha type-3 / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 ...Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


分子量: 28748.230 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P23638, proteasome endopeptidase complex
#3: タンパク質 Proteasome subunit alpha type-4 / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component ...Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


分子量: 28478.111 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P40303, proteasome endopeptidase complex
#4: タンパク質 Proteasome subunit alpha type-5 / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component ...Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


分子量: 28649.086 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P32379, proteasome endopeptidase complex
#5: タンパク質 Proteasome subunit alpha type-6 / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component ...Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


分子量: 25634.000 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P40302, proteasome endopeptidase complex
#7: タンパク質 Proteasome subunit alpha type-1 / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


分子量: 28033.830 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P21243, proteasome endopeptidase complex

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タンパク質 , 1種, 2分子 FT

#6: タンパク質 Probable proteasome subunit alpha type-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / ...Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


分子量: 31575.068 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P21242, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7種, 14分子 HVIWJXKYLZMaNb

#8: タンパク質 Proteasome subunit beta type-10,Proteasome subunit beta type-2 / Low molecular mass protein 10 / Macropain subunit MECl-1 / Multicatalytic endopeptidase complex ...Low molecular mass protein 10 / Macropain subunit MECl-1 / Multicatalytic endopeptidase complex subunit MECl-1 / Proteasome MECl-1 / Proteasome subunit beta-2i / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


分子量: 24443.674 Da / 分子数: 2
Mutation: Chimera: 1-53 Homo sapiens,Chimera: 1-53 Homo sapiens,Chimera: 1-53 Homo sapiens,Chimera: 1-53 Homo sapiens
由来タイプ: 組換発現
由来: (組換発現) Homo sapiens (ヒト), (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
遺伝子: PSMB10, LMP10, MECL1, PUP1, YOR157C / 発現宿主: Saccharomyces cerevisiae S288c (パン酵母)
参照: UniProt: P40306, UniProt: P25043, proteasome endopeptidase complex
#9: タンパク質 Proteasome subunit beta type-3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


分子量: 22627.842 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P25451, proteasome endopeptidase complex
#10: タンパク質 Proteasome subunit beta type-4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 ...Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


分子量: 22545.676 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P22141, proteasome endopeptidase complex
#11: タンパク質 Proteasome subunit beta type-5 / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component ...Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


分子量: 23325.248 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P30656, proteasome endopeptidase complex
#12: タンパク質 Proteasome subunit beta type-6 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


分子量: 24883.928 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P23724, proteasome endopeptidase complex
#13: タンパク質 Proteasome subunit beta type-7 / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component ...Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component PRE4 / Proteinase YSCE subunit PRE4


分子量: 27200.893 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P30657, proteasome endopeptidase complex
#14: タンパク質 Proteasome subunit beta type-1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component ...Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


分子量: 21517.186 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P38624, proteasome endopeptidase complex

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非ポリマー , 5種, 218分子

#15: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Mg
#16: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cl
#17: 化合物
ChemComp-GVW / (2~{S})-~{N}-[(2~{S},3~{R})-1-[(4~{a}~{S},8~{a}~{S})-1,2,3,4,4~{a},5,6,7,8,8~{a}-decahydronaphthalen-2-yl]-4-methyl-3,4-bis(oxidanyl)pentan-2-yl]-3-(4-methoxyphenyl)-2-[[(2~{S})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide


分子量: 644.842 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C35H56N4O7
#18: 化合物
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / 2-モルホリノエタンスルホン酸


分子量: 195.237 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C6H13NO4S / コメント: pH緩衝剤*YM
#19: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 198 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 3.67 Å3/Da / 溶媒含有率: 66.52 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.8 / 詳細: 20 mM MgAC2, 13% MPD, 0.1 M MES / PH範囲: 6.8

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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: SLS / ビームライン: X06SA / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2016年11月20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: 1 Å / 相対比: 1
反射解像度: 3→50 Å / Num. obs: 204830 / % possible obs: 98.2 % / 冗長度: 3.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.8
反射 シェル解像度: 3→3.1 Å / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.2 / % possible all: 99.2

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0158精密化
XDSデータ削減
XSCALEデータスケーリング
REFMAC位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5CZ4

5cz4


解像度: 3→15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 36.941 / SU ML: 0.273 / 交差検証法: THROUGHOUT / ESU R Free: 0.316 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.20199 10161 5 %RANDOM
Rwork0.16461 ---
obs0.16648 193054 97.58 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 75.079 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å2-0 Å2-1.82 Å2
2---3.11 Å2-0 Å2
3---1.88 Å2
精密化ステップサイクル: LAST / 解像度: 3→15 Å
タンパク質核酸リガンド溶媒全体
原子数49340 0 266 198 49804
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01950512
X-RAY DIFFRACTIONr_bond_other_d0.0020.0247108
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.96968348
X-RAY DIFFRACTIONr_angle_other_deg0.9883.002109349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93256311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40824.4292251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.654158742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.14615282
X-RAY DIFFRACTIONr_chiral_restr0.1010.27701
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0256221
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0210101
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6746.14825334
X-RAY DIFFRACTIONr_mcbond_other3.6746.14825333
X-RAY DIFFRACTIONr_mcangle_it5.0989.2131615
X-RAY DIFFRACTIONr_mcangle_other5.0989.2131616
X-RAY DIFFRACTIONr_scbond_it3.4176.50925178
X-RAY DIFFRACTIONr_scbond_other3.4176.50925178
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4279.62636734
X-RAY DIFFRACTIONr_long_range_B_refined5.76970.96653446
X-RAY DIFFRACTIONr_long_range_B_other5.7670.96753425
X-RAY DIFFRACTIONr_rigid_bond_restr1.441397620
X-RAY DIFFRACTIONr_sphericity_free34.025180
X-RAY DIFFRACTIONr_sphericity_bonded25.818596732
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-ID数タイプRms dev position (Å)Weight position
1010A3063tight positional0.010.05
1111A3262tight positional0.040.05
1212A3389tight positional0.010.05
1313A3564tight positional0.010.05
1414A2919tight positional0.010.05
11A3765tight thermal8.280.5
22B3714tight thermal6.880.5
33C3685tight thermal16.220.5
44D3538tight thermal9.170.5
55E3459tight thermal10.860.5
66F3693tight thermal10.860.5
77G3724tight thermal8.170.5
88H3388tight thermal5.540.5
99I3091tight thermal3.80.5
1010J3063tight thermal3.890.5
1111K3262tight thermal4.060.5
1212L3389tight thermal4.120.5
1313M3564tight thermal3.980.5
1414N2919tight thermal4.250.5
LS精密化 シェル解像度: 3→3.075 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.351 735 -
Rwork0.318 13955 -
obs--99.17 %
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)
10.00250.00050.00110.00010.00030.001-0.00170.01070.0059-0.00140.00270.0016-0.01020.0056-0.0010.2335-0.0079-0.04160.0509-0.00420.238966.8499-91.645.5504
20.0019-0.00120.00470.0046-0.00880.0226-0.0026-0.00640.0015-0.0052-0.00320.0116-0.00530.00040.00590.2337-0.0035-0.03910.04690.00180.240359.3256-87.373316.1181
30.03690.0269-0.02370.0204-0.01810.0183-0.00730.01410.00360.0050.01050.00180.0050.0016-0.00320.23750.0043-0.04410.04350.00520.225831.9623-87.06970.9034
40.0284-0.0330.0050.0405-0.00730.0089-0.0047-0.001-0.00140.0023-0.00270.02-0.0180.01470.00740.21890.0088-0.04170.0367-0.00140.23362.9546-89.745213.6621
50.04480.01120.03860.00290.00980.0336-0.001-0.0166-0.0052-0.0023-0.0013-0.0013-0.0075-0.01170.00230.22650.0014-0.03940.04140.00680.2413-3.2459-94.167745.5222
60.00020.00040.00110.00070.00180.00530.0016-0.0009-0.0021-0.004-0.0011-0.0006-0.0034-0.006-0.00050.23470.0018-0.03450.04440.00450.238315.4022-94.784269.5768
70.00530.006-0.00380.0092-0.00410.0030.00320.00630.00380.0018-0.00120.01640.0039-0.0054-0.0020.2498-0.003-0.04230.0355-0.01030.223447.756-93.088170.7405
80.0023-0.0028-0.00180.01540.00730.00460.01670.0070.00640.0246-0.0067-0.0420.0044-0.0052-0.01010.2384-0.0032-0.03820.0395-0.00080.21367.7142-129.090246.9059
90.01760.02820.01450.05030.02430.0148-0.00060.0073-0.00350.0103-0.0038-0.0186-0.0195-0.0010.00440.2325-0.0027-0.04570.0502-0.00080.23568.259-126.852520.3804
100.0015-0.0019-0.00150.00280.00250.00240.0055-0.00130.0161-0.01490.0045-0.0148-0.0160.0054-0.010.2375-0.0003-0.04630.0488-0.00160.228544.561-126.084-0.9994
110.0135-0.00030.02540.11610.02070.0536-0.00560.0016-0.0034-0.02790.0216-0.0001-0.02360.0105-0.0160.21940.0065-0.03770.03080.00770.214710.8285-130.45212.4294
120.0182-0.0030.03050.0017-0.00930.07290.02050.00030.00530.01130.0024-0.0006-0.01970.0061-0.02290.2180.0022-0.04420.0450.00370.2251-4.4197-134.063728.4858
130.0017-0.00430.00380.0619-0.03870.02560.0039-0.00660.0003-0.0132-0.0074-0.01560.0011-0.00080.00350.22760.0011-0.03580.0493-0.00320.23517.9895-137.636260.1973
140.0407-0.0333-0.00470.05120.010.00330.0136-0.0079-0.01410.00690.0016-0.00720.012-0.0037-0.01510.2317-0.0018-0.03770.04910.00050.229240.0413-133.631670.5908
150.01140.0064-0.02730.0057-0.01520.06580.00180.00880.0057-0.02060.00630.0007-0.0037-0.016-0.00810.2312-0.0111-0.04930.04260.00730.24382.4186-206.044836.3112
160.0007-0.00090.00060.0012-0.00070.00050.00480.00220.0067-0.0083-0.0072-0.00710.00590.0020.00240.238-0.0053-0.0490.0425-0.00260.2368.7149-204.80186.3357
170.000600.0010.00030.00080.0038-0.0103-0.00180.0006-0.00210.00360.0003-0.02320.00390.00670.22820.0237-0.02860.0329-0.01510.21935.8148-202.4979-9.6616
180.0232-0.0298-0.0160.04090.01850.0127-0.0056-0.0062-0.0079-0.0132-0.0024-0.00090.01350.00820.00790.18570.0241-0.03320.0287-0.00910.220865.1965-202.02252.6901
190.0008-00.00070.00250.00020.00190.0039-0.00260.00770.0153-0.0031-0.0198-0.0011-0.0071-0.00080.21410.0104-0.03950.0266-0.01290.233672.4284-203.190834.3551
200.0027-0.00030.00190.00080.00010.00490.0124-0.00020.00630.0023-0.0101-0.01310.006-0.0061-0.00230.2190.0061-0.04290.01050.00950.219554.6256-206.986158.6783
210.01330.01590.00010.0214-0.00370.01960.0110.0033-0.00720.00590.00030.0021-0.0167-0.0038-0.01120.237-0.0047-0.04010.03020.01060.217322.3836-209.085660.559
220.00180.00080.00130.0036-0.00040.00110.0169-0.0019-0.00590.0103-0.00350.02120.0129-0.0014-0.01350.2101-0.0158-0.04540.02130.02090.20361.81-169.129544.9545
230.00120.00160.00210.00380.00370.0041-0.00110.0063-0.00650.01260.00930.00130.00780.0117-0.00820.2256-0.0081-0.04150.03980.00310.23760.2258-166.834117.8883
240.0011-0.0008-0.00010.0055-0.00260.00150.00840.0017-0.0144-0.0137-0.0156-0.00090.00420.00770.00720.235-0.0008-0.04330.05380.00030.228823.1985-163.729-4.0897
250.0380.04160.01830.05290.01780.0121-0.00030.01140.0033-0.00880.0147-0.0037-0.00870.0033-0.01440.23230.007-0.03940.04390.00070.228157.0769-159.9517-0.9897
260.0021-0.0007-0.00090.03920.03470.0320.02180.0032-0.01130.030.0032-0.02170.018-0.0048-0.0250.21630.0026-0.02980.0485-0.00850.222773.1599-160.978524.7659
270.000200.00010.00360.00460.0088-0.00230.00060.0068-0.0171-0.00940.0011-0.0046-0.01740.01170.23090.002-0.04880.03810.00550.243761.8271-163.125756.9899
280.0024-0.00520.00490.0136-0.0150.01980.0044-0.0020.00420.00170.0131-0.0047-0.0106-0.017-0.01750.2276-0.008-0.03960.049-0.00160.228930.1327-169.03767.5613
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION2B1 - 244
3X-RAY DIFFRACTION3C1 - 240
4X-RAY DIFFRACTION4D1 - 242
5X-RAY DIFFRACTION5E3 - 233
6X-RAY DIFFRACTION6F2 - 244
7X-RAY DIFFRACTION7G2 - 242
8X-RAY DIFFRACTION8H1 - 226
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 195
11X-RAY DIFFRACTION11K1 - 212
12X-RAY DIFFRACTION12L1 - 222
13X-RAY DIFFRACTION13M1 - 233
14X-RAY DIFFRACTION14N1 - 196
15X-RAY DIFFRACTION15O1 - 250
16X-RAY DIFFRACTION16P1 - 244
17X-RAY DIFFRACTION17Q1 - 240
18X-RAY DIFFRACTION18R1 - 242
19X-RAY DIFFRACTION19S3 - 233
20X-RAY DIFFRACTION20T2 - 244
21X-RAY DIFFRACTION21U2 - 242
22X-RAY DIFFRACTION22V1 - 223
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 195
25X-RAY DIFFRACTION25Y1 - 212
26X-RAY DIFFRACTION26Z1 - 222
27X-RAY DIFFRACTION27a1 - 233
28X-RAY DIFFRACTION28b1 - 196

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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。
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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

  • 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

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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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