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- PDB-3une: Mouse constitutive 20S proteasome -

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基本情報

登録情報
データベース: PDB / ID: 3une
タイトルMouse constitutive 20S proteasome
要素
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
キーワードHYDROLASE / 20S proteasome comprises 28 subunits / Protease / Cytosol
機能・相同性
機能・相同性情報


Regulation of ornithine decarboxylase (ODC) / 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 ...Regulation of ornithine decarboxylase (ODC) / 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 / Degradation of AXIN / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / 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 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / UCH proteinases / Orc1 removal from chromatin / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / Hedgehog ligand biogenesis / TNFR2 non-canonical NF-kB pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / 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 / Interleukin-1 signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Separation of Sister Chromatids / Downstream TCR signaling / KEAP1-NFE2L2 pathway / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / ABC-family proteins mediated transport / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / proteasome core complex / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / skeletal muscle tissue development / negative regulation of inflammatory response to antigenic stimulus / : / Neutrophil degranulation / sarcomere / proteasome complex / ciliary basal body / proteolysis involved in protein catabolic process / lipopolysaccharide binding / P-body / response to virus / protein catabolic process / response to organic cyclic compound / nuclear matrix / positive regulation of NF-kappaB transcription factor activity / peptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / response to oxidative stress / postsynapse / nuclear body / ribosome / centrosome / ubiquitin protein ligase binding / synapse / mitochondrion / proteolysis / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 alpha6 / Proteasome subunit alpha5 ...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 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
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-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: 3.2 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 1.22023年9月13日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


分子量 (理論値)分子数
合計 (水以外)1,435,88856
ポリマ－1,435,88856
非ポリマー00
水11,530640
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


分子量 (理論値)分子数
合計 (水以外)717,94428
ポリマ－717,94428
非ポリマー00
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


分子量 (理論値)分子数
合計 (水以外)717,94428
ポリマ－717,94428
非ポリマー00
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)170.970, 201.300, 226.010
Angle α, β, γ (deg.)90.00, 108.07, 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(-0.998889, 0.037819, 0.028104), (0.040888, 0.992154, 0.118148), (-0.023415, 0.119166, -0.992598)31.6278, -3.75722, 49.05656
3given(0.997958, 0.061723, -0.016453), (-0.06269, 0.995797, -0.066776), (0.012262, 0.067671, 0.997632)-49.53659, 13.97071, -109.84821
4given(-0.999912, -0.010363, 0.008241), (-0.009947, 0.998752, 0.048934), (-0.008737, 0.048848, -0.998768)82.32807, -5.54937, 158.71318

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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) / 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) / 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: 27897.887 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 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) / 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) / 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) / 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) / 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) / 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) / 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) / 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) / 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) / 参照: UniProt: O09061, proteasome endopeptidase complex
#13: タンパク質
Proteasome subunit beta type-4 / Proteasome beta chain / Low molecular mass protein 3 / Macropain beta chain / Multicatalytic ...Proteasome beta chain / Low molecular mass protein 3 / Macropain beta chain / Multicatalytic endopeptidase complex 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) / 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) / 参照: UniProt: Q60692, proteasome endopeptidase complex

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非ポリマー , 1種, 640分子

#15: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 640 / 由来タイプ: 天然 / 式: H2O

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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: 2.57 Å3/Da / 溶媒含有率: 52.23 %
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 KAc, 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5月23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: 3.2→30 Å / Num. all: 236232 / Num. obs: 235050 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.9
反射 シェル解像度: 3.2→3.3 Å / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.4 / % possible all: 99.7

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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: pdb entry 1IRU

1iru


解像度: 3.2→15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.921 / SU B: 61.794 / SU ML: 0.458 / 交差検証法: THROUGHOUT / ESU R Free: 0.535 / 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
Rfree0.24636 11752 5 %RANDOM
Rwork0.22044 ---
obs0.22174 223279 98.14 %-
all-235031 --
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: 78.682 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-3.82 Å2
2--2.37 Å20 Å2
3----4.16 Å2
精密化ステップサイクル: LAST / 解像度: 3.2→15 Å
タンパク質核酸リガンド溶媒全体
原子数97316 0 0 640 97956
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0299076
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7531.965133844
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.411512468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9623.8224364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.391517400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.05315684
X-RAY DIFFRACTIONr_chiral_restr0.0480.215024
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02174248
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_restr0.442399076
X-RAY DIFFRACTIONr_sphericity_free27.4255367
X-RAY DIFFRACTIONr_sphericity_bonded3.628597593
LS精密化 シェル解像度: 3.2→3.279 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.353 669 -
Rwork0.316 12771 -
obs--80.74 %
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)
10.10830.16970.20241.086-0.02840.64090.0001-0.03150.1286-0.0849-0.10690.5388-0.1045-0.12550.10690.17040.0136-0.09920.3834-0.020.7874-48.558755.834737.9839
20.3383-0.03170.06890.41310.20150.4912-0.0485-0.07030.0699-0.01210.02330.16330.147-0.13230.02520.2839-0.1556-0.02230.3439-0.02970.6636-46.507224.314741.4507
30.6443-0.17060.75570.1003-0.23610.91410.2965-0.0845-0.1424-0.124-0.05050.16880.4131-0.0474-0.2460.5972-0.12950.03380.2366-0.01740.5843-28.17347.452861.8314
41.0744-0.2772-0.16180.4946-0.09720.4470.0632-0.2474-0.10950.1236-0.09880.21670.0950.12620.03560.472-0.08650.11340.3780.07410.3382-9.208420.108783.3811
51.16680.03170.18040.459-0.11980.1830.0607-0.41670.06230.10190.00260.1772-0.05890.1611-0.06330.3549-0.08180.14440.6028-0.12070.2674-3.826550.242690.9904
60.5391-0.00410.31040.5834-0.14840.8181-0.0235-0.25710.3170.123-0.08290.1649-0.09620.04660.10630.3163-0.07620.17940.3195-0.28110.6169-16.19775.980278.9148
70.6650.3757-0.00970.3011-0.20610.79120.04410.03350.2480.0809-0.03510.2185-0.1242-0.1532-0.00890.21330.05070.11970.2475-0.05760.8293-37.253278.542554.8489
80.2956-0.1425-0.17880.24850.20550.2430.0730.19550.15940.04710.00990.08590.1268-0.1303-0.08290.2961-0.0079-0.17470.44140.15860.6075-18.773162.136613.5114
91.3023-0.093-0.40030.1420.15670.25390.05150.27210.09540.1432-0.04370.05770.1532-0.153-0.00780.3517-0.1104-0.14050.4380.02020.4304-20.047934.02211.3323
100.5111-0.0227-0.13950.30160.03890.5026-0.15980.1034-0.07710.11220.04590.02210.1822-0.04430.11390.5045-0.0797-0.0340.1945-0.04250.4634-5.044410.608327.7333
111.53810.3574-0.28230.33310.17790.6018-0.0946-0.1057-0.13360.0367-0.02380.02410.14120.01590.11830.50990.002-0.02760.2560.09480.370217.153912.723552.2508
120.27990.0732-0.32630.4964-0.54130.89450.0427-0.17520.09920.0076-0.00060.03520.0770.1195-0.04210.3819-0.0078-0.03390.4609-0.04160.297128.684338.784964.8426
130.29790.0053-0.3360.1836-0.05430.86820.1226-0.23680.2702-0.0716-0.03360.14930.05080.1913-0.0890.3351-0.0990.06230.397-0.210.539122.178570.648857.3092
140.62490.1714-0.37531.2063-0.16940.95060.19830.04850.2319-0.0108-0.01180.16890.0043-0.0565-0.18650.24850.02-0.03370.2064-0.01080.67120.655182.917835.7554
150.412-0.21670.23481.1299-0.10830.3737-0.0281-0.05090.18480.03370.0375-0.24250.05460.1863-0.00930.26110.01610.00230.4527-0.11080.475482.795354.773315.7767
160.38980.0132-0.18450.5386-0.1010.2282-0.07690.0366-0.0659-0.02790.099-0.15150.08940.0727-0.02210.36690.11850.05140.366-0.08690.441679.497224.00269.1941
170.632-0.49380.52111.4708-0.21071.07980.1030.0434-0.1363-0.13670.0349-0.07540.30120.0063-0.13790.55810.06250.04770.297-0.16210.378460.518410.2727-12.9124
180.55420.0990.11280.6608-0.12450.09430.02840.2926-0.0784-0.1654-0.0156-0.08630.1015-0.0309-0.01290.5798-0.010.01440.5143-0.13230.188442.281526.0612-32.9965
190.19230.30280.21580.75720.51250.3718-0.00440.2261-0.018-0.21210.0864-0.0374-0.0760.0301-0.0820.51810.0380.00440.67020.11650.206737.803256.7952-37.0288
200.9693-0.07670.32480.2875-0.1880.91550.03590.16570.2695-0.16930.01180.0339-0.08360.056-0.04780.450.00230.09310.32110.18090.446550.898780.6287-22.1231
210.27520.26030.21881.393-0.10370.33670.04550.02090.1225-0.1019-0.0180.0179-0.02960.1228-0.02750.3336-0.0840.17450.3172-0.00660.544272.016979.70382.1219
220.34350.2482-0.06610.4625-0.18720.14120.0806-0.19920.1173-0.0343-0.0439-0.0240.06370.1029-0.03680.2985-0.0401-0.00960.4228-0.1070.45252.892659.41741.2174
230.63340.2573-0.28120.3951-0.44760.5740.0836-0.09470.029-0.0532-0.03020.06210.11560.1973-0.05340.3970.1046-0.00120.4057-0.03330.3653.332331.268340.1579
240.75440.2518-0.31120.16980.09920.6508-0.11580.1115-0.1229-0.05560.0487-0.0140.14760.00850.06710.54560.0302-0.02960.1978-0.05710.411937.566610.316121.3058
251.3206-0.1999-0.31370.3392-0.21570.3163-0.1310.2119-0.0803-0.15020.04390.00470.1387-0.08320.08710.5096-0.0959-0.07150.3763-0.15120.337515.512915.7781-2.8458
260.7138-0.2632-0.70080.32530.48880.954500.31060.0733-0.02820.0052-0.0638-0.0202-0.2214-0.00520.3717-0.0492-0.13990.5790.04030.28854.829643.5008-12.3519
270.9324-0.3226-0.62630.18470.14020.86670.0780.23890.3376-0.04690.0113-0.0274-0.0604-0.0968-0.08920.3950.0344-0.05470.33860.19580.497312.272674.118-1.2792
280.8766-0.09430.03480.58340.25820.66630.0555-0.06060.1895-0.050.04250.0201-0.0308-0.0111-0.0980.3613-0.05160.02280.2189-0.0320.557334.115383.143321.4791
290.41660.5634-0.18371.2629-0.18090.77690.05870.04770.1363-0.05880.04440.39490.0247-0.2707-0.10310.17430.0702-0.03250.59350.10520.50210.162751.7514144.6672
300.32630.0634-0.18570.7804-0.27310.6818-0.016-0.0245-0.088-0.00070.04020.2820.2413-0.1723-0.02420.3378-0.1508-0.05510.49340.02430.41714.123320.8008150.0198
310.64380.18260.26211.77560.00170.6870.1049-0.1215-0.09490.0737-0.06690.30160.38720.1452-0.03790.5724-0.0102-0.00890.4390.12770.288323.51816.4475171.259
321.23360.0330.39140.01370.01310.21490.0539-0.5023-0.06110.0741-0.0658-0.00710.13520.0560.0120.51880.0330.04210.83560.1840.099441.553121.539192.084
330.5377-0.33120.08150.682-0.10950.0661-0.0363-0.2725-0.10690.23890.14550.1155-0.11690.1232-0.10920.4452-0.09070.11340.9725-0.21140.120645.117752.4968197.697
340.81770.33190.66160.57210.14790.66770.0253-0.24160.24540.1615-0.02740.1413-0.1506-0.03730.00210.421-0.05360.28410.5736-0.36050.423631.332576.657183.8089
350.03080.06280.09680.17660.21540.95160.0119-0.03460.10550.00310.05910.2289-0.2499-0.1055-0.0710.29980.15860.21910.449-0.02270.646110.123476.2208159.7558
360.29690.1689-0.02660.71950.44120.41020.07260.14180.1105-0.0036-0.00550.1210.0513-0.1959-0.06710.30840.0965-0.11440.50730.10020.449129.661458.177119.6123
370.75910.0655-0.50940.30710.26140.77120.09590.12830.06560.08690.0593-0.04690.1686-0.2341-0.15520.4471-0.0327-0.13250.48160.01870.29329.978129.9302119.3297
381.38560.1442-0.57470.0254-0.0170.6893-0.1477-0.0828-0.12390.03170.0279-0.02650.2754-0.01410.11970.62060.043-0.10980.28620.04520.345546.26528.6066137.1256
391.54240.2019-0.57310.3324-0.00860.2859-0.1424-0.2942-0.12060.1273-0.04160.00480.03160.14550.1840.54580.1482-0.13260.55730.17560.273968.256913.5416161.3968
400.60080.2411-0.66530.3025-0.60971.33130.1465-0.43830.124-0.0643-0.04420.07820.03570.3103-0.10240.36410.0317-0.10140.9356-0.13250.150578.260940.9746172.2485
410.66740.0162-0.09190.23960.06940.79840.1552-0.37480.3244-0.0491-0.04720.08790.00290.1606-0.10810.3808-0.08140.05480.5534-0.3090.330169.979171.9644162.687
421.2221-0.4265-0.40740.65490.32871.02910.0933-0.0880.3583-0.08330.03190.12830.0407-0.0107-0.12520.32530.06280.06580.3188-0.11330.488147.799581.5522140.404
430.23830.02140.06241.045-0.17490.78240.1351-0.03980.10450.0958-0.0746-0.3185-0.02140.0757-0.06050.2480.0681-0.03550.6029-0.16690.4285131.321256.7656122.5043
440.0224-0.09640.06410.5276-0.24480.20410.0014-0.018-0.0108-0.08390.1079-0.17690.06150.0387-0.10940.29250.23030.02110.6053-0.10630.4666129.779925.4653117.726
451.0032-0.380.56020.3362-0.02920.66440.1884-0.0628-0.1954-0.05460.0132-0.16420.2367-0.0546-0.20160.55390.23920.03910.4365-0.12420.5126112.0429.421596.203
461.1742-0.1180.14470.1981-0.09810.0716-0.01360.2212-0.181-0.23350.0539-0.02520.06760.0307-0.04040.70070.15450.04510.5168-0.21350.204392.809622.739275.4534
471.18680.35610.11990.42430.03520.03-0.0430.3163-0.0177-0.18060.111-0.0587-0.0540.0551-0.0680.58110.04320.04620.6360.01210.15186.482652.799469.5059
480.4302-0.18280.42080.2273-0.20030.4404-0.09580.11660.1679-0.20660.0156-0.0692-0.07910.14080.08020.56140.00310.13130.42830.07620.352298.168978.293782.8738
490.0451-0.06910.01710.6371-0.07510.84720.0428-0.05980.1345-0.15710.0973-0.1178-0.12940.1132-0.14020.3223-0.02340.18970.4892-0.14190.4699119.493280.14106.9332
500.3045-0.0573-0.16020.9587-0.21940.17880.1569-0.42870.1067-0.0408-0.0648-0.10110.00180.3249-0.09210.2923-0.0448-0.09310.7563-0.23930.3223101.257561.4217147.3287
511.73690.4907-0.67230.2833-0.26740.34620.1399-0.54270.0015-0.181-0.1018-0.01270.14130.3287-0.03810.44240.1818-0.0610.7708-0.05020.2478103.260133.2708148.0765
521.12520.2258-0.83260.62520.29481.4722-0.2819-0.1488-0.1682-0.06890.2180.02130.23780.17360.06390.49230.2121-0.09130.33150.03850.322688.772410.3309130.6333
531.06460.0565-0.37370.4273-0.31740.3535-0.09570.085-0.1243-0.04120.069-0.04070.1437-0.04850.02680.67470.0719-0.12110.3376-0.11220.23866.62712.9758106.3116
540.37210.2739-0.16040.91070.40110.4497-0.08970.09540.0253-0.06750.11280.01020.0315-0.0228-0.02310.48920.0354-0.15340.49590.03760.198154.375439.185495.0452
550.6378-0.2041-0.35970.10780.30231.4640.15460.11810.3311-0.04-0.0021-0.04970.0204-0.0716-0.15250.45660.1008-0.02770.34940.11890.379359.991570.9682104.0562
560.79030.14560.23080.3765-0.07231.40.2068-0.13150.2774-0.03550.05840.0821-0.01120.0768-0.26520.3794-0.04320.10160.2922-0.12520.447381.248582.8135126.1074
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 233
2X-RAY DIFFRACTION1A301 - 312
3X-RAY DIFFRACTION2B2 - 249
4X-RAY DIFFRACTION2B301 - 311
5X-RAY DIFFRACTION3C2 - 240
6X-RAY DIFFRACTION3C301 - 307
7X-RAY DIFFRACTION4D9 - 241
8X-RAY DIFFRACTION4D301 - 305
9X-RAY DIFFRACTION5E4 - 241
10X-RAY DIFFRACTION5E301 - 308
11X-RAY DIFFRACTION6F1 - 244
12X-RAY DIFFRACTION6F301 - 311
13X-RAY DIFFRACTION7G2 - 245
14X-RAY DIFFRACTION7G301 - 311
15X-RAY DIFFRACTION8H1 - 220
16X-RAY DIFFRACTION8H301 - 317
17X-RAY DIFFRACTION9I1 - 204
18X-RAY DIFFRACTION9I301 - 312
19X-RAY DIFFRACTION10J1 - 196
20X-RAY DIFFRACTION10J301 - 313
21X-RAY DIFFRACTION11K1 - 201
22X-RAY DIFFRACTION11K301 - 311
23X-RAY DIFFRACTION12L1 - 213
24X-RAY DIFFRACTION12L301 - 318
25X-RAY DIFFRACTION13M1 - 216
26X-RAY DIFFRACTION13M301 - 315
27X-RAY DIFFRACTION14N1 - 202
28X-RAY DIFFRACTION14N301 - 313
29X-RAY DIFFRACTION15O1 - 233
30X-RAY DIFFRACTION15O301 - 318
31X-RAY DIFFRACTION16P2 - 249
32X-RAY DIFFRACTION16P301 - 324
33X-RAY DIFFRACTION17Q2 - 240
34X-RAY DIFFRACTION17Q301 - 312
35X-RAY DIFFRACTION18R9 - 241
36X-RAY DIFFRACTION18R301 - 312
37X-RAY DIFFRACTION19S4 - 241
38X-RAY DIFFRACTION19S301 - 319
39X-RAY DIFFRACTION20T1 - 244
40X-RAY DIFFRACTION20T301 - 313
41X-RAY DIFFRACTION21U2 - 245
42X-RAY DIFFRACTION21U301 - 321
43X-RAY DIFFRACTION22V1 - 220
44X-RAY DIFFRACTION22V301 - 319
45X-RAY DIFFRACTION23W1 - 204
46X-RAY DIFFRACTION23W301 - 321
47X-RAY DIFFRACTION24X1 - 196
48X-RAY DIFFRACTION24X301 - 308
49X-RAY DIFFRACTION25Y1 - 201
50X-RAY DIFFRACTION25Y301 - 308
51X-RAY DIFFRACTION26Z1 - 213
52X-RAY DIFFRACTION26Z301 - 316
53X-RAY DIFFRACTION27a1 - 216
54X-RAY DIFFRACTION27a301 - 316
55X-RAY DIFFRACTION28b1 - 202
56X-RAY DIFFRACTION28b301 - 320
57X-RAY DIFFRACTION29c1 - 233
58X-RAY DIFFRACTION29c301 - 315
59X-RAY DIFFRACTION30d2 - 249
60X-RAY DIFFRACTION30d301 - 309
61X-RAY DIFFRACTION31e2 - 240
62X-RAY DIFFRACTION31e301 - 303
63X-RAY DIFFRACTION32f9 - 241
64X-RAY DIFFRACTION32f301 - 303
65X-RAY DIFFRACTION33g4 - 241
66X-RAY DIFFRACTION33g301 - 307
67X-RAY DIFFRACTION34h1 - 244
68X-RAY DIFFRACTION34h301 - 307
69X-RAY DIFFRACTION35i2 - 245
70X-RAY DIFFRACTION35i301 - 310
71X-RAY DIFFRACTION36j1 - 220
72X-RAY DIFFRACTION36j301 - 313
73X-RAY DIFFRACTION37k1 - 204
74X-RAY DIFFRACTION37k301 - 311
75X-RAY DIFFRACTION38l1 - 196
76X-RAY DIFFRACTION38l301 - 308
77X-RAY DIFFRACTION39m1 - 201
78X-RAY DIFFRACTION39m301 - 311
79X-RAY DIFFRACTION40n1 - 213
80X-RAY DIFFRACTION40n301 - 313
81X-RAY DIFFRACTION41o1 - 216
82X-RAY DIFFRACTION41o301 - 311
83X-RAY DIFFRACTION42p1 - 202
84X-RAY DIFFRACTION42p301 - 306
85X-RAY DIFFRACTION43q1 - 233
86X-RAY DIFFRACTION43q301 - 303
87X-RAY DIFFRACTION44r2 - 249
88X-RAY DIFFRACTION44r301 - 310
89X-RAY DIFFRACTION45s2 - 240
90X-RAY DIFFRACTION45s301 - 307
91X-RAY DIFFRACTION46t9 - 241
92X-RAY DIFFRACTION46t301 - 306
93X-RAY DIFFRACTION47u4 - 241
94X-RAY DIFFRACTION47u301 - 307
95X-RAY DIFFRACTION48v1 - 244
96X-RAY DIFFRACTION48v301 - 311
97X-RAY DIFFRACTION49w2 - 245
98X-RAY DIFFRACTION49w301 - 310
99X-RAY DIFFRACTION50x1 - 220
100X-RAY DIFFRACTION50x301 - 306
101X-RAY DIFFRACTION51y1 - 204
102X-RAY DIFFRACTION51y301 - 310
103X-RAY DIFFRACTION52z1 - 196
104X-RAY DIFFRACTION52z301 - 306
105X-RAY DIFFRACTION5311 - 201
106X-RAY DIFFRACTION531301 - 312
107X-RAY DIFFRACTION5421 - 213
108X-RAY DIFFRACTION542301 - 317
109X-RAY DIFFRACTION5531 - 216
110X-RAY DIFFRACTION553301 - 310
111X-RAY DIFFRACTION5641 - 202
112X-RAY DIFFRACTION564301 - 307

+
万見について

-
お知らせ

-
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://pdbjlc1.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

+
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

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る