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- PDB-3unb: Mouse constitutive 20S proteasome in complex with PR-957 -

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基本情報

登録情報
データベース: PDB / ID: 3unb
タイトルMouse constitutive 20S proteasome in complex with PR-957
要素
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
キーワードHYDROLASE/HYDROLASE INHIBITOR / 20S proteasome comprises 28 subunits / each subunit adopts the fold of an antiparallel beta-sheet flanked by helices / Protease / Regulatory complexes / Covalent binding of PR-957 to all active sites / HYDROLASE-HYDROLASE INHIBITOR complex
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 / 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 / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / skeletal muscle tissue development / proteasomal protein catabolic process / Neutrophil degranulation / proteasome complex / proteolysis involved in protein catabolic process / sarcomere / negative regulation of inflammatory response to antigenic stimulus / P-body / lipopolysaccharide binding / protein catabolic process / response to virus / nuclear matrix / peptidase activity / response to oxidative stress / ubiquitin-dependent protein catabolic process / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / nuclear body / cilium / ciliary basal body / ribosome / ubiquitin protein ligase binding / centrosome / mitochondrion / proteolysis / RNA binding / nucleoplasm / identical protein binding / cytoplasm / cytosol
類似検索 - 分子機能
Proteasome subunit alpha 1 / 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 subunit alpha 1 / 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 / Proteasome subunit beta type-5 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-7 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit alpha type-6 ...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 / Proteasome subunit beta type-5 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-7 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-7 / Proteasome subunit alpha type-5
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.9 Å
データ登録者Huber, E. / Basler, M. / Schwab, R. / Heinemeyer, W. / Kirk, C. / Groettrup, M. / Groll, M.
引用ジャーナル: Cell(Cambridge,Mass.) / 年: 2012
タイトル: Immuno- and constitutive proteasome crystal structures reveal differences in substrate and inhibitor specificity.
著者: Huber, E.M. / Basler, M. / Schwab, R. / Heinemeyer, W. / Kirk, C.J. / Groettrup, M. / Groll, M.
履歴
登録2011年11月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年2月29日Provider: repository / タイプ: Initial release
改定 1.12012年3月28日Group: Database references
改定 1.22012年12月12日Group: Other
改定 1.32013年11月13日Group: Structure summary
改定 1.42013年11月20日Group: Structure summary
改定 1.52023年9月13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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
改定 1.62024年11月27日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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-4
C: Proteasome subunit alpha type-7
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-1
F: Proteasome subunit alpha type-3
G: Proteasome subunit alpha type-6
H: Proteasome subunit beta type-7
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-2
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-1
M: Proteasome subunit beta type-4
N: Proteasome subunit beta type-6
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-4
Q: Proteasome subunit alpha type-7
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-1
T: Proteasome subunit alpha type-3
U: Proteasome subunit alpha type-6
V: Proteasome subunit beta type-7
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-2
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-1
a: Proteasome subunit beta type-4
b: Proteasome subunit beta type-6
c: Proteasome subunit alpha type-2
d: Proteasome subunit alpha type-4
e: Proteasome subunit alpha type-7
f: Proteasome subunit alpha type-5
g: Proteasome subunit alpha type-1
h: Proteasome subunit alpha type-3
i: Proteasome subunit alpha type-6
j: Proteasome subunit beta type-7
k: Proteasome subunit beta type-3
l: Proteasome subunit beta type-2
m: Proteasome subunit beta type-5
n: Proteasome subunit beta type-1
o: Proteasome subunit beta type-4
p: Proteasome subunit beta type-6
q: Proteasome subunit alpha type-2
r: Proteasome subunit alpha type-4
s: Proteasome subunit alpha type-7
t: Proteasome subunit alpha type-5
u: Proteasome subunit alpha type-1
v: Proteasome subunit alpha type-3
w: Proteasome subunit alpha type-6
x: Proteasome subunit beta type-7
y: Proteasome subunit beta type-3
z: Proteasome subunit beta type-2
1: Proteasome subunit beta type-5
2: Proteasome subunit beta type-1
3: Proteasome subunit beta type-4
4: Proteasome subunit beta type-6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,442,67268
ポリマ－1,435,65656
非ポリマー7,01612
水26,6621480
1
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-4
C: Proteasome subunit alpha type-7
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-1
F: Proteasome subunit alpha type-3
G: Proteasome subunit alpha type-6
H: Proteasome subunit beta type-7
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-2
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-1
M: Proteasome subunit beta type-4
N: Proteasome subunit beta type-6
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-4
Q: Proteasome subunit alpha type-7
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-1
T: Proteasome subunit alpha type-3
U: Proteasome subunit alpha type-6
V: Proteasome subunit beta type-7
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-2
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-1
a: Proteasome subunit beta type-4
b: Proteasome subunit beta type-6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)721,33634
ポリマ－717,82828
非ポリマー3,5086
水50428
タイプ名称対称操作数
identity operation1_555x,y,z1
2
c: Proteasome subunit alpha type-2
d: Proteasome subunit alpha type-4
e: Proteasome subunit alpha type-7
f: Proteasome subunit alpha type-5
g: Proteasome subunit alpha type-1
h: Proteasome subunit alpha type-3
i: Proteasome subunit alpha type-6
j: Proteasome subunit beta type-7
k: Proteasome subunit beta type-3
l: Proteasome subunit beta type-2
m: Proteasome subunit beta type-5
n: Proteasome subunit beta type-1
o: Proteasome subunit beta type-4
p: Proteasome subunit beta type-6
q: Proteasome subunit alpha type-2
r: Proteasome subunit alpha type-4
s: Proteasome subunit alpha type-7
t: Proteasome subunit alpha type-5
u: Proteasome subunit alpha type-1
v: Proteasome subunit alpha type-3
w: Proteasome subunit alpha type-6
x: Proteasome subunit beta type-7
y: Proteasome subunit beta type-3
z: Proteasome subunit beta type-2
1: Proteasome subunit beta type-5
2: Proteasome subunit beta type-1
3: Proteasome subunit beta type-4
4: Proteasome subunit beta type-6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)721,33634
ポリマ－717,82828
非ポリマー3,5086
水50428
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)171.720, 198.590, 226.750
Angle α, β, γ (deg.)90.00, 106.59, 90.00
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCS oper:
IDCodeMatrixベクター
1given(1), (1), (1)
2given(-0.997819, 0.065268, 0.009896), (0.066014, 0.986049, 0.152808), (0.000216, 0.153128, -0.988206)31.33581, -4.43493, 45.32309
3given(1, -0.000242, -0.000708), (0.000241, 0.999999, -0.001238), (0.000708, 0.001238, 0.999999)-53.35929, 0.17881, -108.78284
4given(-0.997786, 0.065734, 0.010155), (0.066514, 0.986102, 0.152243), (-6.0E-6, 0.152581, -0.988291)83.55444, -24.55868, 152.83635

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要素

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Proteasome subunit alpha type- ... , 7種, 28分子 AOcqBPdrCQesDRftESguFThvGUiw

#1: タンパク質
Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


分子量: 25955.613 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: P49722, proteasome endopeptidase complex
#2: タンパク質
Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


分子量: 29512.807 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: Q9R1P0, proteasome endopeptidase complex
#3: タンパク質
Proteasome subunit alpha type-7 / Proteasome subunit RC6-1


分子量: 27839.852 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: Q9Z2U0, proteasome endopeptidase complex
#4: タンパク質
Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


分子量: 26435.977 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: Q9Z2U1, proteasome endopeptidase complex
#5: タンパク質
Proteasome subunit alpha type-1 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / ...Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


分子量: 29586.576 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: Q9R1P4, proteasome endopeptidase complex
#6: タンパク質
Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8 / ...Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8 / Proteasome subunit K


分子量: 28442.248 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: O70435, proteasome endopeptidase complex
#7: タンパク質
Proteasome subunit alpha type-6 / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


分子量: 27405.434 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: Q9QUM9, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7種, 28分子 HVjxIWkyJXlzKYm1LZn2Mao3Nbp4

#8: タンパク質
Proteasome subunit beta type-7 / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


分子量: 25280.010 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: P70195, proteasome endopeptidase complex
#9: タンパク質
Proteasome subunit beta type-3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


分子量: 22988.895 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: Q9R1P1, proteasome endopeptidase complex
#10: タンパク質
Proteasome subunit beta type-2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


分子量: 22935.377 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: Q9R1P3, proteasome endopeptidase complex
#11: タンパク質
Proteasome subunit beta type-5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / ...Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit X


分子量: 22554.545 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: O55234, proteasome endopeptidase complex
#12: タンパク質
Proteasome subunit beta type-1 / 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


分子量: 23576.969 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: O09061, proteasome endopeptidase complex
#13: タンパク質
Proteasome subunit beta type-4 / Low molecular mass protein 3 / Macropain beta chain / Multicatalytic endopeptidase complex beta ...Low molecular mass protein 3 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3


分子量: 24384.715 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: P99026, proteasome endopeptidase complex
#14: タンパク質
Proteasome subunit beta type-6 / Low molecular mass protein 19 / Macropain delta chain / Multicatalytic endopeptidase complex delta ...Low molecular mass protein 19 / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / Proteasome subunit Y


分子量: 22014.920 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 属: 10090 / 参照: UniProt: Q60692, proteasome endopeptidase complex

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非ポリマー , 2種, 1492分子

#15: 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: 12 / 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
#16: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1480 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY
配列の詳細THE STARTING EPOXIDE RING OF AN EPOXOMICIN-LIKE INHIBITOR UNDERGOES RE-CYCLIZATION REACTION WITH ...THE STARTING EPOXIDE RING OF AN EPOXOMICIN-LIKE INHIBITOR UNDERGOES RE-CYCLIZATION REACTION WITH THE SIDE CHAIN OF N-TERMINAL RESIDUE THR-1 (CHAINS V,4,j,N,p,m,x,H,1,Y, b, AND k) AND THE FINAL PRODUCT 04C IS OBSERVED. SEE ALSO LINK RECORDS AND REMARK 630.

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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: 2.58 Å3/Da / 溶媒含有率: 52.33 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.4
詳細: 0.2 M Sodium formate, 40% MPD , pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: 2011年8月8日
放射モノクロメーター: double-crystal fixed-exit 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: 2.9→30 Å / Num. all: 321807 / Num. obs: 308934 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.4
反射 シェル解像度: 2.9→3 Å / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2 / % possible all: 96.7

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解析

ソフトウェア
名称バージョン分類
XDSデータスケーリング
PHASER位相決定
REFMAC5.6.0119精密化
XDSデータ削減
XSCALEデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 1IRU

1iru


解像度: 2.9→15 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 45.959 / SU ML: 0.36 / 交差検証法: THROUGHOUT / ESU R Free: 0.474 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor反射数%反射Selection details
Rfree0.27259 15447 5 %RANDOM
Rwork0.22966 ---
obs0.23178 293487 96.03 %-
all-308934 --
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: 67.88 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å20 Å2-0.13 Å2
2---1.39 Å20 Å2
3---4.14 Å2
精密化ステップサイクル: LAST / 解像度: 2.9→15 Å
タンパク質核酸リガンド溶媒全体
原子数97252 0 504 1480 99236
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0299564
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8851.967134532
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.55512444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16723.8224364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7571517388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.95215684
X-RAY DIFFRACTIONr_chiral_restr0.0590.215156
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02174136
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr4.015399564
X-RAY DIFFRACTIONr_sphericity_free24.8685719
X-RAY DIFFRACTIONr_sphericity_bonded5.718598521
LS精密化 シェル解像度: 2.9→2.972 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.436 1096 -
Rwork0.411 20695 -
obs--96.55 %
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)
10.0595-0.0617-0.03350.3823-0.07550.15470.0031-0.01440.0093-0.0255-0.01570.0738-0.01810.00560.01260.1320.0298-0.00630.30560.00240.2814-47.9255.36737.467
20.1405-0.08210.10.46250.09190.163-0.0559-0.0516-0.1056-0.01610.04530.0695-0.0375-0.03430.01060.1568-0.05530.02680.2599-0.0010.3172-46.22724.18239.914
30.1245-0.00440.29110.04440.03680.7580.0764-0.0602-0.0439-0.08590.05310.01830.1017-0.0599-0.12950.2575-0.04490.00580.19150.11620.3239-28.0386.84359.842
40.10770.0821-0.03050.38250.02740.0223-0.0442-0.167-0.0658-0.11420.0030.08680.03020.06150.04120.2320.0230.04980.33370.1930.1881-9.30618.76181.895
50.0778-0.14280.02690.5453-0.04380.0196-0.0481-0.1442-0.03550.02010.06610.032-0.0538-0.0144-0.0180.1718-0.00580.04330.55590.07360.0217-3.49848.26290.269
60.5513-0.17650.3060.215-0.11920.176-0.0764-0.18280.1689-0.0293-0.0125-0.0227-0.008-0.08940.08890.21210.0360.06540.352-0.17360.1716-15.44774.16178.828
70.0208-0.03020.04560.20680.11690.3716-0.0249-0.05050.0189-0.01970.0855-0.0585-0.044-0.0731-0.06060.18290.06320.04350.2468-0.05440.3089-36.40577.42554.713
80.0886-0.0897-0.07440.28430.02960.13770.03710.01660.0579-0.0465-0.00240.06390.0436-0.064-0.03470.18010.0381-0.02830.2814-0.0010.2786-18.07761.88313.172
90.5799-0.0125-0.26020.34750.14630.2111-0.00970.09070.02160.07890.0037-0.020.0889-0.11170.0060.1834-0.0192-0.04740.258-0.04140.2609-19.55834.15310.192
100.4556-0.1019-0.16580.10110.19360.3938-0.1148-0.0497-0.08190.00360.02530.04640.04120.00580.08950.2773-0.0065-0.00260.11920.0080.3191-5.20810.36926.311
110.6610.2151-0.1810.4180.08380.2306-0.0411-0.1037-0.01340.0197-0.0236-0.03130.056-0.0080.06470.2760.0352-0.01080.16550.11690.238416.89311.05751.178
120.10450.1596-0.10650.3539-0.17240.2067-0.0205-0.09090.00770.0191-0.0048-0.01310.00690.01270.02530.20020.0429-0.0230.32910.01410.191229.0237.05564.337
130.59230.1121-0.24160.0739-0.16610.38640.1219-0.08490.1220.0159-0.02080.0420.02050.0431-0.10110.2519-0.0047-0.00090.2663-0.08180.187222.97968.78757.275
140.3558-0.0066-0.23080.0712-0.1450.59910.09270.0168-0.02520.00380.0186-0.021-0.0808-0.0916-0.11130.23040.04120.04060.1833-0.04250.28431.55481.76835.965
150.1817-0.01440.18330.59270.08030.21320.02990.0224-0.01040.03380.0281-0.02220.0270.0765-0.0580.12290.0642-0.00550.3275-0.1140.271783.03552.59516.104
160.1176-0.0030.10630.14330.0610.4582-0.0617-0.0203-0.00090.01470.0616-0.06650.0431-0.00010.00010.18840.12970.0210.2294-0.05170.281679.27822.3049.122
170.2866-0.05150.21990.46890.03530.19090.07660.006-0.11170.04430.021-0.07740.0197-0.0229-0.09770.27180.1101-0.01080.1578-0.09680.304560.2169.507-13.399
180.2621-0.05790.05410.1999-0.14580.10990.15440.086-0.0578-0.0106-0.09420.06420.01390.0606-0.06020.29480.0922-0.01920.2446-0.15870.19442.31425.886-33.24
190.39760.12010.3350.28710.09650.30160.04330.1147-0.049-0.03150.03130.01240.0530.0476-0.07470.27320.068-0.01620.3264-0.02730.135138.47456.491-36.89
200.1445-0.12990.10590.2730.06090.46920.00380.01780.127-0.0276-0.0128-0.0390.02440.00990.0090.19510.00750.04710.23140.03210.290352.05879.544-21.643
210.0517-0.08980.04780.321-0.05220.15230.02760.03690.03560.01720.03180.029-0.02760.1172-0.05940.1579-0.04530.07270.2508-0.04410.312373.02577.7152.631
220.1210.0972-0.03370.1583-0.02290.01180.0327-0.10050.01840.001-0.0115-0.08530.00680.0325-0.02120.2356-0.0083-0.02110.3178-0.04230.188853.46857.36141.267
230.1950.2102-0.10560.3848-0.1840.09030.048-0.045-0.0467-0.0678-0.0562-0.02810.04010.04510.00810.25640.10610.00670.31070.01650.170253.1529.42639.996
240.58280.3044-0.08350.1619-0.03420.43-0.0570.0469-0.0989-0.02860.0393-0.03170.0344-0.00840.01770.26580.0855-0.01430.1167-0.01230.322537.3359.39720.475
250.9069-0.0515-0.11840.0907-0.10050.153-0.01530.11780.0005-0.03210.00480.0230.0463-0.02520.01050.27670.0059-0.0440.1597-0.09150.275315.47515.357-3.895
260.02830.00490.00640.01610.00330.03950.00420.0195-0.0167-0.00770.0180.0324-0.00760.0125-0.02220.2720.0340.02310.2251-0.01770.121525.37145.16829.652
270.1222-0.1583-0.18740.23660.21860.6040.02120.00640.07320.00060.034-0.03690.0067-0.0126-0.05520.24780.04050.02410.2180.03520.221313.15173.599-1.096
280.3772-0.0863-0.40060.2960.01550.44970.0367-0.05210.0491-0.02010.00040.0185-0.01990.0631-0.03710.2211-0.00580.00920.1925-0.04780.282835.28881.70721.815
290.0644-0.1458-0.01780.36160.00210.1035-0.0002-0.01-0.027-0.0208-0.03110.0311-0.03120.01460.03120.11810.0283-0.02670.28510.00720.33665.56355.367146.185
300.0815-0.06720.03410.28050.03730.1164-0.0615-0.0432-0.1022-0.00730.04620.0148-0.0365-0.06490.01530.1447-0.05540.00660.24110.00760.3687.26124.169148.629
310.15620.00440.33640.05810.03680.76680.0636-0.0605-0.0325-0.10550.03570.01060.1076-0.0742-0.09920.2504-0.0378-0.01160.16420.11090.33325.4286.828168.582
320.1735-0.0291-0.14660.17020.01050.1516-0.0281-0.1505-0.0128-0.12520.02550.03460.05890.08290.00260.21050.00950.01710.29190.16970.260944.16818.759190.613
330.1121-0.11170.07360.460.01990.0934-0.0271-0.1457-0.04220.03020.05250.0208-0.0178-0.0453-0.02530.1528-0.00940.00480.51110.06880.083249.97648.261198.992
340.5024-0.25150.23950.1867-0.12550.1151-0.0679-0.17010.1512-0.0472-0.0005-0.0437-0.0198-0.08060.06840.19510.03070.03620.3225-0.18060.225638.05574.173187.524
350.03430.04220.10860.18310.00040.5668-0.0179-0.0209-0.0041-0.00140.0719-0.0338-0.0907-0.0576-0.0540.17090.06610.03580.2312-0.05820.318617.05677.436163.427
360.20140.0018-0.06450.2630.10660.10430.08340.01870.0015-0.0476-0.02330.0196-0.0126-0.0769-0.06010.16190.0495-0.05770.2431-0.00710.336535.37161.803121.993
370.35040.0358-0.25380.45910.22080.3223-0.01420.0763-0.03740.0534-0.00480.00210.0521-0.09040.0190.1585-0.0139-0.07060.236-0.04320.310933.92734.145118.912
380.472-0.1001-0.13210.28310.1650.3094-0.1028-0.0354-0.0872-0.0010.02910.01990.0345-0.01150.07380.2623-0.0113-0.0060.1080.02010.335748.28210.37135.014
390.72030.1159-0.19050.44840.05290.3318-0.034-0.11940.0089-0.0149-0.0221-0.01250.06320.01510.0560.26390.0341-0.02510.13420.11320.28670.35811.062159.878
400.115-0.0315-0.11560.2056-0.11270.3069-0.0362-0.09860.04720.01440.0190.02060.02610.03340.01710.20440.0382-0.03010.31120.01630.226582.49437.045173.089
410.52350.2063-0.27870.1073-0.20060.47260.1216-0.07190.11020.0353-0.02830.04340.00660.0315-0.09330.2256-0.0006-0.02370.2195-0.07540.282376.44968.788165.99
420.35030.1082-0.38930.0604-0.120.55920.08970.01250.03330.02180.045-0.0429-0.0484-0.0927-0.13470.21640.04810.01880.1745-0.04920.319655.02881.767144.692
430.1124-0.00020.14610.49940.02720.21830.04360.0167-0.00910.03890.0252-0.01230.04430.0923-0.06890.11590.0683-0.02780.3121-0.13060.3022136.51152.569124.849
440.0603-0.0036-0.04890.11660.10280.311-0.0791-0.0385-0.0165-0.01010.0896-0.03670.03030.0081-0.01050.18790.12820.0050.2181-0.06010.3122132.80122.323117.824
450.34-0.17530.23280.5459-0.04590.17340.0536-0.0118-0.09740.02930.0282-0.0910.0294-0.02-0.08180.25360.1076-0.01730.1306-0.1010.3193113.6719.50595.323
460.307-0.23040.11350.337-0.15510.07290.13550.0627-0.0675-0.0396-0.08950.06040.01840.0465-0.0460.30350.0915-0.02830.2314-0.1660.209795.79525.91275.487
470.33140.07430.23890.2850.05210.18450.04350.0953-0.0423-0.04740.02570.05150.0550.0679-0.06920.27040.06-0.02450.3233-0.03360.15891.95356.49371.814
480.1562-0.02090.18290.25940.15220.3904-0.00130.0180.0996-0.0395-0.0019-0.0280.00850.01540.00310.19120.00760.04820.2150.02730.3193105.5279.54987.092
490.0179-0.03190.03420.4554-0.00950.21210.03180.02620.01530.02040.00810.0136-0.0280.0893-0.03990.1664-0.04140.06570.2425-0.05010.3287126.48677.716111.325
500.16050.1539-0.05310.3483-0.04160.02710.0169-0.1080.0774-0.01680.0288-0.0650.03270.0564-0.04580.18510.0055-0.07710.2555-0.05950.318106.93257.354149.998
510.17480.2441-0.08680.5046-0.16630.07650.0577-0.0644-0.0373-0.049-0.07520.04570.05370.09490.01750.20620.1189-0.04360.25250.00820.2967106.62929.4148.759
520.56020.2108-0.21930.0838-0.09620.5778-0.05690.0383-0.0477-0.0190.0347-0.0040.05770.0270.02220.25090.0811-0.02530.1018-0.01350.351590.8199.405129.197
530.6328-0.2039-0.04150.1131-0.05230.12250.00570.09840.0071-0.0058-0.02330.03170.0372-0.01090.01760.28310.0027-0.06180.1531-0.08680.293768.95315.347104.855
540.12580.088-0.04750.31080.26310.4352-0.0136-0.00890.0388-0.08550.0368-0.019-0.0227-0.0305-0.02320.23670.0175-0.06030.2143-0.02120.287758.61943.74195.831
550.0857-0.1265-0.12610.23110.25380.42930.02470.01160.07750.0060.0266-0.04270.0127-0.0207-0.05130.21780.0461-0.00360.1730.02620.313166.63273.596107.648
560.259-0.0339-0.28430.3461-0.00240.37110.0423-0.04150.0343-0.0198-0.01620.0044-0.0290.0648-0.02610.215-0.0036-0.01630.1742-0.05080.32588.76581.709130.584
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 231
2X-RAY DIFFRACTION2B1 - 248
3X-RAY DIFFRACTION3C1 - 239
4X-RAY DIFFRACTION4D1 - 233
5X-RAY DIFFRACTION5E1 - 238
6X-RAY DIFFRACTION6F1 - 244
7X-RAY DIFFRACTION7G1 - 243
8X-RAY DIFFRACTION8H2 - 220
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 196
11X-RAY DIFFRACTION11K2 - 201
12X-RAY DIFFRACTION12L1 - 213
13X-RAY DIFFRACTION13M1 - 216
14X-RAY DIFFRACTION14N2 - 202
15X-RAY DIFFRACTION15O1 - 231
16X-RAY DIFFRACTION16P1 - 248
17X-RAY DIFFRACTION17Q1 - 239
18X-RAY DIFFRACTION18R1 - 233
19X-RAY DIFFRACTION19S1 - 238
20X-RAY DIFFRACTION20T1 - 244
21X-RAY DIFFRACTION21U1 - 243
22X-RAY DIFFRACTION22V2 - 220
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 196
25X-RAY DIFFRACTION25Y2 - 201
26X-RAY DIFFRACTION261401 - 427
27X-RAY DIFFRACTION262301 - 333
28X-RAY DIFFRACTION263301 - 337
29X-RAY DIFFRACTION264401 - 430
30X-RAY DIFFRACTION26A301 - 319
31X-RAY DIFFRACTION26B301 - 324
32X-RAY DIFFRACTION26C301 - 313
33X-RAY DIFFRACTION26D301 - 316
34X-RAY DIFFRACTION26E301 - 321
35X-RAY DIFFRACTION26F301 - 320
36X-RAY DIFFRACTION26G301 - 322
37X-RAY DIFFRACTION26H401 - 431
38X-RAY DIFFRACTION26I301 - 332
39X-RAY DIFFRACTION26J301 - 325
40X-RAY DIFFRACTION26K401 - 428
41X-RAY DIFFRACTION26L301 - 323
42X-RAY DIFFRACTION26M301 - 327
43X-RAY DIFFRACTION26N401 - 433
44X-RAY DIFFRACTION26O301 - 333
45X-RAY DIFFRACTION26P301 - 338
46X-RAY DIFFRACTION26Q301 - 316
47X-RAY DIFFRACTION26R301 - 319
48X-RAY DIFFRACTION26S301 - 325
49X-RAY DIFFRACTION26T301 - 325
50X-RAY DIFFRACTION26U301 - 337
51X-RAY DIFFRACTION26V401 - 435
52X-RAY DIFFRACTION26W301 - 337
53X-RAY DIFFRACTION26X301 - 333
54X-RAY DIFFRACTION26Y401 - 416
55X-RAY DIFFRACTION26Z301 - 332
56X-RAY DIFFRACTION26a301 - 333
57X-RAY DIFFRACTION26b401 - 440
58X-RAY DIFFRACTION26c301 - 321
59X-RAY DIFFRACTION26d301 - 319
60X-RAY DIFFRACTION26e301 - 314
61X-RAY DIFFRACTION26f301 - 313
62X-RAY DIFFRACTION26g301 - 315
63X-RAY DIFFRACTION26h301 - 319
64X-RAY DIFFRACTION26i301 - 329
65X-RAY DIFFRACTION26j401 - 425
66X-RAY DIFFRACTION26k301 - 330
67X-RAY DIFFRACTION26l301 - 322
68X-RAY DIFFRACTION26m401 - 420
69X-RAY DIFFRACTION26n301 - 329
70X-RAY DIFFRACTION26o301 - 327
71X-RAY DIFFRACTION26p401 - 432
72X-RAY DIFFRACTION26q301 - 326
73X-RAY DIFFRACTION26r301 - 334
74X-RAY DIFFRACTION26s301 - 319
75X-RAY DIFFRACTION26t301 - 317
76X-RAY DIFFRACTION26u301 - 327
77X-RAY DIFFRACTION26v301 - 331
78X-RAY DIFFRACTION26w301 - 327
79X-RAY DIFFRACTION26x401 - 434
80X-RAY DIFFRACTION26y301 - 332
81X-RAY DIFFRACTION26z301 - 338
82X-RAY DIFFRACTION27a1 - 216
83X-RAY DIFFRACTION28b2 - 202
84X-RAY DIFFRACTION29c1 - 231
85X-RAY DIFFRACTION30d1 - 248
86X-RAY DIFFRACTION31e1 - 239
87X-RAY DIFFRACTION32f1 - 233
88X-RAY DIFFRACTION33g1 - 238
89X-RAY DIFFRACTION34h1 - 244
90X-RAY DIFFRACTION35i1 - 243
91X-RAY DIFFRACTION36j2 - 220
92X-RAY DIFFRACTION37k1 - 204
93X-RAY DIFFRACTION38l1 - 196
94X-RAY DIFFRACTION39m2 - 201
95X-RAY DIFFRACTION40n1 - 213
96X-RAY DIFFRACTION41o1 - 216
97X-RAY DIFFRACTION42p2 - 202
98X-RAY DIFFRACTION43q1 - 231
99X-RAY DIFFRACTION44r1 - 248
100X-RAY DIFFRACTION45s1 - 239
101X-RAY DIFFRACTION46t1 - 233
102X-RAY DIFFRACTION47u1 - 238
103X-RAY DIFFRACTION48v1 - 244
104X-RAY DIFFRACTION49w1 - 243
105X-RAY DIFFRACTION50x2 - 220
106X-RAY DIFFRACTION51y1 - 204
107X-RAY DIFFRACTION52z1 - 196
108X-RAY DIFFRACTION5312 - 201
109X-RAY DIFFRACTION5421 - 213
110X-RAY DIFFRACTION5531 - 216
111X-RAY DIFFRACTION5642 - 202

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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

-
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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