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- PDB-5l6b: Yeast 20S proteasome with mouse beta5i (1-138) and mouse beta6 (9... -

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基本情報

登録情報
データベース: PDB / ID: 5l6b
タイトルYeast 20S proteasome with mouse beta5i (1-138) and mouse beta6 (97-111; 118-133) in complex with ONX 0914
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/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / Proteasome / Mutant / Inhibitor / Binding Analysis
機能・相同性
機能・相同性情報


Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 ...Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Degradation of AXIN / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity / Regulation of RAS by GAPs / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / UCH proteinases / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / Orc1 removal from chromatin / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / spermatoproteasome complex / TNFR2 non-canonical NF-kB pathway / Hedgehog ligand biogenesis / Hedgehog 'on' state / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Degradation of beta-catenin by the destruction complex / Activation of NF-kappaB in B cells / The role of GTSE1 in G2/M progression after G2 checkpoint / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Interleukin-1 signaling / Downstream TCR signaling / Separation of Sister Chromatids / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / ABC-family proteins mediated transport / Neddylation / Ub-specific processing proteases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / proteasome core complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / antigen processing and presentation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / fat cell differentiation / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / proteasome endopeptidase complex / endopeptidase activator activity / proteasome core complex, beta-subunit complex / Ub-specific processing proteases / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / Neutrophil degranulation / Neutrophil degranulation / proteolysis involved in protein catabolic process / proteasome complex / peroxisome / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 alpha5 / Proteasome subunit alpha6 / 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 alpha5 / Proteasome subunit alpha6 / 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 B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-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
1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOL / Chem-04C / Proteasome subunit beta type-1 / 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 ...1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOL / Chem-04C / Proteasome subunit beta type-1 / 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-8 / 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
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
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: 2.6 Å
データ登録者Groll, M. / Huber, E.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: EMBO J. / 年: 2016
タイトル: A humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit beta 5i.
著者: Huber, E.M. / Heinemeyer, W. / de Bruin, G. / Overkleeft, H.S. / Groll, M.
履歴
登録2016年5月28日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02016年11月9日Provider: repository / タイプ: Initial release
改定 1.12016年12月14日Group: Database references
改定 1.22016年12月21日Group: Non-polymer description
改定 1.32024年1月10日Group: Author supporting evidence / Data collection ...Author supporting evidence / 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_audit_support / 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 / _pdbx_audit_support.funding_organization / _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 1.42024年11月6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-2
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-4
K: Proteasome subunit beta type-8,Proteasome subunit beta type-5
L: Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,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-2
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-4
Y: Proteasome subunit beta type-8,Proteasome subunit beta type-5
Z: Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,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)736,02248
ポリマ－731,46728
非ポリマー4,55520
水8,053447
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)135.190, 300.840, 145.390
Angle α, β, γ (deg.)90.00, 112.94, 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(-0.999686, -0.000435, 0.025071), (-0.003897, -0.985006, -0.172477), (0.02477, -0.172521, 0.984694)67.50848, -289.39008, -26.13383

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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-2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component ...Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


分子量: 25114.459 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: 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-8,Proteasome subunit beta type-5 / Low molecular mass protein 7 / Macropain subunit C13 / Multicatalytic endopeptidase complex subunit ...Low molecular mass protein 7 / Macropain subunit C13 / Multicatalytic endopeptidase complex subunit C13 / Proteasome component C13 / Proteasome subunit beta-5i / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


分子量: 23438.480 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Mus musculus (ハツカネズミ), (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
遺伝子: Psmb8, Lmp7, Mc13, PRE2, DOA3, PRG1, YPR103W, P8283.10
発現宿主: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P28063, UniProt: P30656, proteasome endopeptidase complex
#12: タンパク質 Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Macropain subunit C5 / ...Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


分子量: 24979.010 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母), (組換発現) Mus musculus (ハツカネズミ), (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: PRE7, PRS3, PTS1, YBL041W, YBL0407, Psmb1
発現宿主: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
参照: UniProt: P23724, UniProt: O09061, 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, 467分子

#15: 化合物
ChemComp-MG / MAGNESIUM ION


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


分子量: 35.453 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cl
#17: 化合物
ChemComp-04C / 1,2,4-trideoxy-4-methyl-2-{[N-(morpholin-4-ylacetyl)-L-alanyl-O-methyl-L-tyrosyl]amino}-1-phenyl-D-xylitol


タイプ: peptide-like, Peptide-like / クラス: 阻害剤 / 分子量: 584.704 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C31H44N4O7
参照: 1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOL
#18: 化合物
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


分子量: 195.237 Da / 分子数: 4 / 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: 447 / 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
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: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2015年7月11日
放射モノクロメーター: LN2 COOLED FIXED-EXIT. SI(111) MONOCHROMATOR
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: 2.6→30 Å / Num. obs: 322154 / % possible obs: 98.6 % / 冗長度: 3.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.5
反射 シェル解像度: 2.6→2.7 Å / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.3 / % possible all: 99.3

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解析

ソフトウェア
名称バージョン分類
REFMAC5.7.0032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: 2.6→15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 21.186 / SU ML: 0.193 / 交差検証法: THROUGHOUT / ESU R Free: 0.238 / 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
Rfree0.22091 16108 5 %RANDOM
Rwork0.19583 ---
obs0.19708 306046 98.68 %-
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: 64.387 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å2-1.03 Å2
2---4.51 Å2-0 Å2
3---1.08 Å2
精密化ステップサイクル: LAST / 解像度: 2.6→15 Å
タンパク質核酸リガンド溶媒全体
原子数49392 0 310 447 50149
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01950621
X-RAY DIFFRACTIONr_bond_other_d0.0020.0248352
X-RAY DIFFRACTIONr_angle_refined_deg0.9271.97168491
X-RAY DIFFRACTIONr_angle_other_deg0.8023.003111349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.93656314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46524.3912257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51158773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.24215289
X-RAY DIFFRACTIONr_chiral_restr0.0510.27689
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257342
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211355
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_it2.3625.47925340
X-RAY DIFFRACTIONr_mcbond_other2.3625.47925339
X-RAY DIFFRACTIONr_mcangle_it3.1248.20231623
X-RAY DIFFRACTIONr_mcangle_other3.1248.20231624
X-RAY DIFFRACTIONr_scbond_it2.3145.91425281
X-RAY DIFFRACTIONr_scbond_other2.3145.91325281
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8148.70136868
X-RAY DIFFRACTIONr_long_range_B_refined3.56142.92454310
X-RAY DIFFRACTIONr_long_range_B_other3.56142.92454310
X-RAY DIFFRACTIONr_rigid_bond_restr1.021398973
X-RAY DIFFRACTIONr_sphericity_free32.8515289
X-RAY DIFFRACTIONr_sphericity_bonded15.217598220
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-ID数タイプRms dev position (Å)Weight position
1A3099TIGHT POSITIONAL0.020.05
1A3277TIGHT POSITIONAL00.05
1A3449TIGHT POSITIONAL0.010.05
1A3598TIGHT POSITIONAL00.05
1A3032TIGHT POSITIONAL00.05
1A3795TIGHT THERMAL4.540.5
2B3756TIGHT THERMAL3.980.5
3C3729TIGHT THERMAL7.650.5
4D3578TIGHT THERMAL7.810.5
5E3509TIGHT THERMAL6.070.5
6F3749TIGHT THERMAL5.920.5
7G3770TIGHT THERMAL4.020.5
8H3486TIGHT THERMAL3.450.5
9I3119TIGHT THERMAL2.610.5
10J3099TIGHT THERMAL3.130.5
11K3277TIGHT THERMAL3.090.5
12L3449TIGHT THERMAL3.550.5
13M3598TIGHT THERMAL3.240.5
14N3032TIGHT THERMAL2.250.5
LS精密化 シェル解像度: 2.6→2.665 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.376 1160 -
Rwork0.331 22037 -
obs--99.42 %
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)
10.01440.00670.00790.00430.00560.01090.00230.0183-0.0075-0.00320.0081-0.0137-0.0126-0.0028-0.01040.1163-0.00890.00040.06260.00050.114966.967-92.222546.2163
20.00720.00220.0070.00190.00250.0082-0.00790.00230.0005-0.0103-0.00040.0072-0.0030.0090.00830.1181-0.00660.01360.06770.00350.10759.702-88.090816.5181
30.00010-0.00020.000400.00110.0013-0.0021-0.00120.00710.00140.0012-0.00050.0082-0.00270.12780.00030.00110.07050.00680.101832.3757-87.68561.2221
40.0073-0.00780.00550.0178-0.02030.0532-0.0069-0.01340.002-0.00090.00760.0223-0.00940.0158-0.00070.10760.0133-0.00760.04180.01470.12163.1716-90.041613.7799
50.03490.01840.01570.01240.00620.0471-00.01060.0087-0.00850.01020.0199-0.0001-0.0009-0.01020.10470.00410.00960.06260.0040.1246-3.1181-94.453945.7078
60.01540.0085-0.01390.006-0.00550.01590.0038-0.00440.00260.0139-0.00470.00380.0170.00360.00080.1210.00230.02340.0558-0.01070.096215.2577-95.037669.9656
70.00380.00760.00090.04530.010.00420.01070.0045-0.00450.0271-0.019-0.0150.0036-0.00760.00830.13990.00460.0020.0303-0.01330.104647.6996-93.485171.2797
80.00170.0041-0.00190.02770.00520.00820.01540.00330.00120.0454-0.0035-0.028-0.004-0.0149-0.01190.1101-0.00240.00240.0435-0.00820.11167.5004-129.79147.5305
90.0008-0.0008-0.00040.0704-0.05970.0530.00530.0069-0.00240.017-0.0205-0.0159-0.02860.01380.01520.10470.00040.02250.0728-0.00120.103468.4507-127.64721.1042
100.00780.01570.00350.06280.01390.00530.0079-0.00820.0036-0.02040.0029-0.01540.00730.0091-0.01080.1367-0.00160.01380.06830.00160.102144.5439-126.8031-0.1998
110.00150.001-0.00090.0019-0.00020.0007-0.009-0.00530.0023-0.01320.00390.01010.00590.00450.00510.12950.0053-0.0180.0470.01170.131710.7302-131.05153.1084
120.00790.01470.01920.03450.03610.0534-0.00490.0064-0.0001-0.01050.00230.0212-0.02770.02050.00260.09480.0139-0.0010.0490.01690.1132-4.4145-134.401528.6444
130.0092-0.0295-0.00740.17370.04560.01280.00260.01040.01120.0458-0.00650.01890.00670.00410.00380.1207-0.0030.02240.0574-0.00110.10537.7819-137.925360.5129
140.06190.0605-0.02150.0839-0.01840.00950.0123-0.0092-0.00220.0443-0.00550.00470.0058-0.0029-0.00680.1365-0.00550.00620.0606-0.0040.094839.8825-134.246770.777
150.0139-0.0051-0.0160.00350.00610.0234-0.00420.01190.0064-0.0084-0.00260.00710.0167-0.00230.00680.1237-0.0098-0.00730.06430.0040.11471.5651-206.692437.2217
160.04840.02390.01580.01230.00790.0058-0.00320.00260.0003-0.0036-0.00250.00570.00510.0020.00570.1259-0.0017-0.0110.0622-0.00270.1118.1262-205.76047.0558
170.00320.0002-0.0010.0009-0.00090.00270.006-0.0133-0.0042-0.00620.00210.007-0.00590.0067-0.00810.13120.0064-0.00110.06-0.00330.099135.195-203.7395-8.6474
180.0108-0.01860.0180.0374-0.03810.04250.0012-0.00640.022-0.0219-0.0102-0.03310.0190.00370.00910.08860.01580.02430.0312-0.02110.096664.6621-203.44013.5281
190.01890.0242-0.01060.0465-0.00580.01010.01210.004-0.00520.0475-0.0015-0.03110.0046-0.0024-0.01060.07830.0182-0.00730.0573-0.01190.133971.6617-204.406835.589
200.02480.01430.00770.01040.00440.00250.0302-0.0166-0.02670.0179-0.0168-0.02720.0102-0.007-0.01340.14070.0075-0.02960.03940.01050.100753.7908-207.929959.9452
210.0052-0.00220.0030.002-0.00140.0022-0.00570.00170.00790.01160.00330.0026-0.00540.00520.00250.15320.0007-0.00670.05880.00280.104721.4182-209.892861.5907
220.01020.0107-0.01170.0256-0.00860.01610.0005-0.0099-0.00150.0282-0.00030.01940.02020.0111-0.00020.1118-0.00640.00540.05490.00660.11181.2278-169.94844.8707
230.00740.0185-0.00580.0504-0.0160.00550.005-0.00270.0076-0.0111-0.00860.00820.0029-0.00010.00370.1147-0.0014-0.00010.06780.00420.1106-0.3073-167.615418.3942
240.01-0.01050.00490.0141-0.0070.00630.012-0.0137-0.0131-0.01560.00340.0112-0.0091-0.003-0.01540.13740.003-0.00260.0574-0.00150.095523.1228-164.8321-3.2363
250.00080.00010.00070.00420.00060.0011-0.0016-0.0034-0.0072-0.01770.0108-0.0105-0.00060.0012-0.00930.12120.0030.03580.0577-0.01450.120657.0246-161.19540.0348
260.02210.042-0.00750.0861-0.01150.00950.01510.0059-0.01040.0279-0.0058-0.03290.0088-0.0118-0.00930.10920.00660.01330.0455-0.01140.107472.6882-162.163125.4654
270.0165-0.0347-0.00920.13490.02890.00770.01430.0185-0.01190.0273-0.0175-0.02340.0095-0.01250.00310.12230.0044-0.00780.04690.00410.112861.2115-164.039257.7309
280.0182-0.03760.01620.1009-0.03590.01520.0027-0.0066-0.01610.03480.01350.0045-0.0082-0.0034-0.01620.1371-0.00520.0070.06020.00420.099329.3682-169.427167.953
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 - 211
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 - 226
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 195
25X-RAY DIFFRACTION25Y1 - 211
26X-RAY DIFFRACTION26Z1 - 222
27X-RAY DIFFRACTION27a1 - 233
28X-RAY DIFFRACTION28b1 - 196

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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://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

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